5,055 Matching Annotations
  1. Last 7 days
    1. Case presentation

      Case#: 64 year old (report), female

      CaseHPOsFreeText: At age 52 years, sudden difficulty with swallowing and speech, ophthalmoparesis with a vertical and horizontal eye movement disorder, dysesthesia of the hands with a quality of “pins and needles” and a glove-like distribution, as well as generalized areflexia. Diagnosed with Miller Fisher syndrome. Treatment with intravenous immunoglobulins led to remission of symptoms. Abdominal pain since childhood. At 63 years of age, she had generalized epileptic seizures with prolonged postictal confusion, persisting diarrhea, abdominal pain, renal failure, repeat episodes of lactic acidosis. Ventilated for >8 weeks due to massive metabolic acidosis and respiratory failure during seizure; tracheotomy, PEG. VitB6 supplement. Rehabilitation, and recovered after several months.

      CaseNotHPOsFreeText: Muscle strength was normal. Abdominal computer tomography (CT), magnetic resonance imaging (MRI) and gastroscopy were normal. No signs of infection in CSF. CT and MRI of the brain as well as abdominal- and thorax-CT were normal initially then fat embolies in brain, pulmonary embolism, vertebral fractures. EMG was normal. No signs of malnutrition or liver disease (which can cause hyperprolinemia).

      CasePreviousTesting: No evidence of porphyria on “laboratory tests”, or diseases of copper metabolism, lead poisoning, or adrenoleukodystrophy. Muscle biopsy showed nonspecific atrophy, but no evidence of mitochondrial disease. Serum proline 3085 μmol/l (reference 90-342 μmol/l), urine proline 46,531 μmol/g Crea (reference < 100 μmol/g Crea), CSF proline 104 mg/dl (reference < 6 mg/dl), urine Hydroxyproline 1395 μmol/g Crea (reference <100). Vitamin-B6 was decreased at 3.3 μg/l (reference > 4.9 μg/l). “targeted genetic analyses by Sanger sequencing revealed no pathogenic variant within the PRODH-gene (hyperprolinemia type I)”

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: “targeted genetic analyses by Sanger sequencing” for ALDH4A1 (no further details).

      Variant: Compound heterozygous, confirmed in trans (the patient’s son only has one of the variants) 1) NM_003748.3:c.62+1G>A, 2) NM_003748.3:c.349G>C (p.Asp117His)

      ClinVar: 1) N/A; 2) N/A

      CAID: 1) CA338769667; 2) CA338760898

      gnomAD: 1) Not in gnomAD; 2) Not in gnomAD

      VariantEvidence: No functional evidence for the missense change. Score: This patient is an adult with hyperprolinemia who is compound heterozygous for two variants in ALDH4A1, c.62+1G>A and c.349G>C (p.Asp117His). Neither variant is in gnomAD. Variants in PRODH have been ruled out.

    1. 18

      Case18: 2 mo (at biopsy), French Canadian

      Case 18 (Level 2)


      CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.655A>T (p.Asn219Tyr)

      ClinVar: 1886

      CAID: CA249731

      gnomAD: 0.0001318 (European non-Finnish)

      __

      Variant2: NM_000255.3:c.1240delG (p.Glu414LysfsTer17)

      ClinVar: n/a

      CAID: CA3846936

      gnomAD: 0.000008796 (European Non-Finnish)


      CaseAddInfo: mut0 type. Variant 2 is novel. heterozygous mutations, unknown cis or trans.

    2. 17

      Case17: 6 y (at biopsy), Black

      Case 17 (Level 2)


      CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.631_633delGAG (p.Glu211del)

      ClinVar: n/a

      CAID: CA913187321

      gnomAD: n/a


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutations. Variant 1 is novel. MUT mutations are in trans- demonstrated by RT-PCR of mRNA. Additional variant found in MCEE gene (NM_032601.3:c.428G>A, ClinVar: 336936, CAID: CA1702575, gnomAD: 0.08102 (Latino)) MCEE variant is unlikely to be associated with patient's MMA.

    3. 16

      Case16: 5 days (at biopsy), Lao/Thai/Mexican/Portugese

      Case 16 (Level 2)


      CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.581C>T (p.Pro194Leu)

      ClinVar: n/a

      CAID: CA364404418

      gnomAD: n/a


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

    4. 15

      Case15: 3 wks (at biopsy), white

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

      ClinVar: 203854

      CAID: CA312777

      gnomAD: 0.00006976 (European non-FInnish)


      Variant2: NM_000255.3:c.754-2A>G

      ClinVar: 552691

      CAID: CA364402853

      gnomAD: n/a


      CaseAddInfo: variant 2 is a novel, splice site mutation. Heterozygous mutations, unknown cis or trans.

    5. 13

      Case13: 21 y (at biopsy), English/Irish

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

      ClinVar: 203854

      CAID: CA312777

      gnomAD: 0.00006976 (European non-FInnish)


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

    6. 12

      Case12: 6y (at biopsy), no ethnicity recorded

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.556A>G (p.Met186Val)

      ClinVar: 551460

      CAID: CA3847093

      gnomAD: 0.00001760 (European Non-Finnish)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: mut- type, heterozygous mutations, unknown cis or trans

    7. 11

      Case11: 6y (at biopsy), White/Hispanic

      Case (Level 2)


      CasePreviousTesting: same as group. found 2.6 nmol/mg protein/18 h propionate incorporation, 7.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.566A>T (p.Asn189Ille)

      ClinVar: 222915

      CAID: CA3847091

      gnomAD: 0.000008804 (European Non-Finnish)


      Variant2: NM_000255.3:c.655A>T (p.Asn219Tyr)

      ClinVar: 1886

      CAID: CA249731

      gnomAD: 0.0001318 (European non-Finnish)


      CaseAddInfo: Variant 1 is novel, unknown cis or trans. mut- type.

    8. 14

      Case14: 3 mo (at biopsy), White/Australian

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

      ClinVar: 203854

      CAID: CA312777

      gnomAD: 0.00006976 (European non-FInnish)


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

    9. 10

      Case10: 6 days (at biopsy), Northern European/Filipino

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

      ClinVar: 1887

      CAID: CA249732

      gnomAD: 0.0008393 (Latino)


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    10. 9

      Case9: 46 days (at biopsy), Hispanic

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

      ClinVar: 1887

      CAID: CA249732

      gnomAD: 0.0008393 (Latino)


      Variant2: NM_000255.3:c.654A>C (p.Gln218His)

      ClinVar: 551243

      CAID: CA364404273

      gnomAD: 0.000008809 (European non-Finnish)


      CaseAddInfo: mut0 class, heterozygous mutations, unknown cis or trans.

    11. 8

      Case8: 12 days (at biopsy), White/Mexican

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

      ClinVar: 1887

      CAID: CA249732

      gnomAD: 0.0008393 (Latino)


      Variant2: NM_000255.3:c.654A>C (p.Gln218His)

      ClinVar: 551243

      CAID: CA364404273

      gnomAD: 0.000008809 (European non-Finnish)


      CaseAddInfo: mut0 class, heterozygous mutations, unknown cis or trans.

    12. 7

      Case7: 10 days (at biopsy), White

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.146_147ins279

      ClinVar: n/a

      CAID: n/a- could not register

      gnomAD: n/a


      Variant2: NM_000255.3:c.372_374dupGA (p.Lys124_Asp125insGlu)

      ClinVar: 203861

      CAID: CA312788

      gnomAD: 0.000008799


      CaseAddInfo: mut0 class. heterozygous mutations. identified to be in trans through cDNA analysis. variant 1 is novel and consists of a 279 base pair insertion.

    13. 6

      Case6 2 mo (at biopsy), White

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 3.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.129G>A (p.Trp43Ter)

      ClinVar: 222908

      CAID: CA10575886

      gnomAD: n/a


      Variant2: NM_000255.3:c.299A>G (p.Tyr100Cys)

      ClinVar: 218991

      CAID: CA347866

      gnomAD: 0.000008793 (European non-Finnish)


      CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans. variant 1 is novel.

    14. 5

      Case5: 1y 9 mo (at biopsy), Korean

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.91C>T (p.Arg31Ter)

      ClinVar: 92688

      CAID: CA249743

      gnomAD: 0.00008013 (African)


      Variant2: NM_000255.3:c.349G>T (p.Glu117Ter)

      ClinVar: 1882

      CAID: CA115264

      gnomAD: n/a


      CaseAddInfo: mut0 class. heterozygous mutations. unknown cis or trans.

    15. 4

      Case4: 2 y (at biopsy), Black

      Case (Level 2)


      CasePreviousTesting: same as group. found 2.1 nmol/mg protein/18 h propionate incorporation, 3.1 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.91C>T (p.Arg31Ter)

      ClinVar: 92688

      CAID: CA249743

      gnomAD: 0.00008013 (African)


      Variant2: NM_000255.3:c.323G>A (p.Arg108His)

      ClinVar: 100707

      CAID: CA235522

      gnomAD: 0.00006152 (African)


      CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans. Third variant in TCN2 gene (NM_000355.3:c.89T>G p.Leu30Arg, CAID: CA10184491, ClinVar: 529781, gnomAD: 0.01329 (African))

    16. 3

      Case3: 19y (at biopsy), Irish/Scottish/Polish

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.2 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.29dupT (p.Leu10PhefsTer39)

      ClinVar: 553287

      CAID: CA567155988

      gnomAD: 0.00003269 (South Asian)


      Variant2: NM_000255.3:c.1658delT (p.Val553GlyfsTer17)

      ClinVar: n/a

      CAID: CA450397348

      gnomAD: 0.000008808 (European non-Finnish)


      CaseAddInfo: mut0 class. heterozygous mutations. variant 1 is novel. unknown cis or trans.

    17. 2

      Case2: 1 mo (at biopsy), Palestinian

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2T>C (p.Met1Thr)

      ClinVar: 222903

      CAID: CA10575890

      gnomAD: n/a


      Variant2: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      CaseAddInfo: mut0 class. heterozygous mutations- unknown cis or trans. 3rd mutation in CD320 gene (NM_016579.3:c.658G>A p.Gly220Arg, ClinVar: 136684, CAID: CA289989, gnomAD: 0.3086 (African) )

    18. 1

      Case1: 13 mo (at biopsy), no recorded ethnicity

      Case (Level 2)


      CasePreviousTesting: same as group. found 2.4 nmol/mg protein/18 h propionate incorporation, 4.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1A>G (p.M1?)

      ClinVar: n/a

      CAID: CA364406084

      gnomAD: n/a


      Variant2: NM_000255.3:c.2150G>T (p.Gly717Val)

      ClinVar: 1881

      CAID: CA249729

      gnomAD: 0.0006810 (African)


      CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans

    1. Case 3

      Case# Case 3, M, Chinese, 3day onset

      CasePresentingHPOs HP:0008344, HP:0001954, HP:0005972, HP:0011968, HP:0008947

      CasePreviousTesting Tested blood aa levels with liquid chromatography-mass spectrum spectrometry, several branched chain amino acids were overly abundant. Whole exome targeted capture sequencing was applied for the mutation screening of the suspicious patients. A total of 712 genes associated with inherited metabolic diseases were selected and their coding regions were captured.

      CaseMethod1 Whole Exome

      CaseMethod2 Sanger

      CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

      Variant NM_000056.3:c.659del(p.D229fs)

      CAID CA658820635

      CaseAddInfo Mother was not tested but WES was used in the patient and father

    2. Case 1

      Case# Case 1, F, Chinese, 4day old Age of Onset

      CasePresentingHPOs HP:0011968, HP:0001276, HP:0002373, HP:0001954, HP:0008344

      CasePreviousTesting Tested blood aa levels with liquid chromatography-mass spectrum spectrometry, several branched chain amino acids were overly abundant. Whole exome targeted capture sequencing was applied for the mutation screening of the suspicious patients. A total of 712 genes associated with inherited metabolic diseases were selected and their coding regions were captured.

      CaseMethod1 Whole Exome

      CaseMethod2 Sanger

      CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

      Variant NM_000056.4(BCKDHB):c.508C>T (p.Arg170Cys), NM_000056.3:c.659del

      ClinVar 96590 (missense)

      CAID CA658820635 (c.659del)

      gnomAD 0.00001791 (European(Non-Finnish)), 0.000008123 (Overall)

      CasePMIDs missense mentioned in 25381949

    1. P39

      Case39: Female, Chinese, 3.4y (end of study)

      HPOsFreeText: 1y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case39 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1741C>T (p.Arg581Ter)

      ClinVar: 554675

      CAID: CA364395893

      gnomAD: n/a


      CaseAddInfo: one variant, not homozygous.

    2. P40

      Case40: Female, Chinese, 2.1y (end of study)

      HPOsFreeText: 8 mo onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case40 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1777G>T (p.Glu593Ter)

      ClinVar: 558328

      CAID: CA364395728

      gnomAD: n/a


      Variant2: NM_000255.3:c.2179C>T (p.Arg727Ter)

      ClinVar: 218998

      CAID: CA347913

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: variant 1 is novel. heterozygous mutations in trans

    3. P38

      Case38: Male, Chinese, 1.5y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case38 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1741C>T (p.Arg581Ter)

      ClinVar: 554675

      CAID: CA364395893

      gnomAD: n/a


      CaseAddInfo: one variant, not homozygous.

    4. P37

      Case37: Female, Chinese, 5.8y (end of study)

      HPOsFreeText: 3y onset

      NotHPOsFreeText: normal cognitive and motor development without further episodes of metabolic decompensation, not responsive to vitamin B12

      Case37 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1677-1G>A (p.=)

      ClinVar: 550012

      CAID: CA3846767

      gnomAD: 0.0003511 (East Asian)


      CaseAddInfo: one variant, not homozygous

    5. P36

      Case36: Female, Chinese, 9.3(end of study)

      NotHPOsFreeText: asymptomatic, no onset

      Case36 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      Variant2: NM_000255.3:c.1943G>A (p.Gly648Asp)

      ClinVar: n/a

      CAID: CA3846709

      gnomAD: 0.0001087 (East Asian)

      CaseAddInfo: heterozygous mutations in trans, but no symptoms. identical twin to Case35/P35.

    6. P35

      Case35: Female, Chinese, 9.3y (end of study)

      NotHPOsFreeText: asymptomatic, no onset

      Case35 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      Variant2: NM_000255.3:c.1943G>A (p.Gly648Asp)

      ClinVar: n/a

      CAID: CA3846709

      gnomAD: 0.0001087 (East Asian)

      CaseAddInfo: heterozygous mutations in trans, but no symptoms. identical twin to Case36/P36.

    7. P34

      Case34: Male, Chinese, 5.5y (end of study)

      HPOsFreeText: 2 mo onset, poor neurologic outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case34 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      Variant2: NM_000255.3:c.1880A>G (p.His627Arg)

      ClinVar: 551830

      CAID: CA3846719

      gnomAD: 0.00002639 (European non-Finnish)

      CaseAddInfo: heterozygous mutations in trans

    8. P33

      Case33: Male, Chinese, 1.8y (end of study)

      HPOsFreeText: Neonatal development

      NotHPOsFreeText: normal cognitive and motor development without further episodes of metabolic decompensation, not responsive to vitamin B12

      Case33 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1280G>A (p.

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      CaseAddInfo: one variant, not homozygous

    9. P31

      Case31: Male, Chinese, 3.7y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case31 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)

      CaseAddInfo: one variant, not homozygous.

    10. P30

      Case30: Male, Chinese, 1 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case30 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.925T>G (p.Trp309Gly)

      ClinVar: n/a

      CAID: CA364401026

      gnomAD: n/a


      Variant2: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      CaseAddInfo: heterozygous mutations in trans, died at 1 mo

    11. P32

      Case32: Male, Chinese, 1.8y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case32 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1280G>A (p.

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      Variant2: NM_000255.3:c.1677-1G>A (p.=)

      ClinVar: 550012

      CAID: CA3846767

      gnomAD: 0.0003511 (East Asian)


      CaseAddInfo: heterozygous mutations in trans

    12. P29

      Case29: Male, Chinese, 3.2 y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case29 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.755dupA (p.His252GlinfsTer6)

      ClinVar: n/a

      CAID: CA3847037

      gnomAD: 0.0001090 (East Asian)


      Variant2: NM_000255.3:c.1741C>T (p.Arg581Ter)

      ClinVar: 554675

      CAID: CA364395893

      gnomAD: n/a


      CaseAddInfo: heterozygous mutations in trans

    13. P28

      Case28: Male, Chinese, 6.8y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case28 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.754-1G>A (p.=)

      ClinVar: n/a

      CAID: CA364402849

      gnomAD: n/a


      Variant2: NM_000255.3:c.1061C>T (p.Ser354Phe)

      ClinVar: n/a

      CAID: CA364400211

      gnomAD: n/a


      CaseAddInfo: heterozygous mutations in trans.

    14. P27

      Case27: Male, Chinese, 1.8y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case27 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      CaseAddInfo: one variant, not homozygous.

    15. P26

      Case26: Female, Chinese, 6.6y (end of study)

      HPOsFreeText: responsive to vitamin B12

      NotHPOSFreeText: asymptomatic, no onset

      Case26 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      CaseAddInfo: one variant, not homozygous. asymptomatic.

    16. P25

      Case25: Male, Chinese, 3 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case25 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)

      CaseAddInfo: heterozygous mutations in trans. died at 3 mo.

    17. P24

      Case24: Male, Chinese, 6.5y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case24 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1540C>A (p.Gln514Lys)

      ClinVar: n/a

      CAID: CA364397122

      gnomAD: n/a

      CaseAddInfo: heterozygous mutations in trans. Variant 2 is novel

    18. P23

      Case23: Female, Chinese, 3y (end of study)

      HPOsFreeText: 1.8y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case23 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1295A>C (p.Glu432Ala)

      ClinVar: n/a

      CAID: CA364398703

      gnomAD: n/a

      CaseAddInfo: heterozygous mutations in trans

    19. P22

      Case22: Female, Chinese, 1.3y (end of study)

      HPOsFreeText: 11 mo onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case22 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)

      CaseAddInfo: heterozygous mutations in trans

    20. P21

      Case21: Male, Chinese, 9 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case21 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)

      CaseAddInfo: heterozygous mutations in trans, died at 9 mo

    21. P20

      Case20: Female, Chinese, 1 y (end of study)

      HPOsFreeText: neonatal onset, poor neruological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case20 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1105C>T (p.Arg369Cys)

      ClinVar: 218989

      CAID: CA347895

      gnomAD: 0.00006536 (South Asian)


      CaseAddInfo: heterozygous mutations in trans

    22. P19

      Case19: Female, Chinese, 2.4 y (end of study)

      HPOsFreeText: 1.8 y onset

      NotHPOsFreeText: normal cognitive and motor development without further episodes of metabolic decompensation, not responsive to vitamin B12

      Case19 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.655A>G (p.Asn219Asp)

      ClinVar: n/a

      CAID: CA364404270

      gnomAD: n/a


      Variant2: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      CaseAddInfo: heterozygous mutations in trans

    23. P17

      Case17: Male, Chinese, 6.5y (end of study)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12, normal cognitive and motor development without further episodes of metabolic decompensation

      Case17 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.554C>T (p.Ser185Phe)

      ClinVar: n/a

      CAID: CA364404475

      gnomAD: n/a


      Variant2: NM_000255.3:c.2062G>T (p.Glu688Ter)

      ClinVar: n/a

      CAID: CA3846672

      gnomAD: 0.00006152 (African)


      CaseAddInfo: heterozygous mutations in trans.

    24. P16

      Case16: Male, Chinese, 2.4 y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case16 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.454C>T (p.Arg152Ter)

      ClinVar: 426467

      CAID: CA3847107

      gnomAD: 0.00009813 (South Asian)


      Variant2: NM_000255.3:c.1280G>A (p.Gly427Asp)

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      CaseAddInfo: heterozygous mutations in trans.

    25. P18

      Case18: Male, Chinese, 5 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case18 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.626dupC

      ClinVar: n/a

      CAID: CA825482501

      gnomAD: n/a


      Variant2: NM_000255.3:c.1531C>T (p.Arg511Ter)

      ClinVar: 556124

      CAID: CA3846855

      gnomAD: 0.00003270 (South Asian)


      CaseAddInfo: variant 1 is novel. Heterozygous mutations in trans.

    26. P15

      Case15: Male, Chinese, 6 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case15 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.433G>A (p.Gly145Ser)

      ClinVar: n/a

      CAID: CA364404739

      gnomAD: n/a


      Variant2: NM_000255.3:c.1677-1G>A (p.=)

      ClinVar: 550012

      CAID: CA3846767

      gnomAD: 0.0003511 (East Asian)


      CaseAddInfo: heterozygous mutations in trans. Died at 6 mo.

    27. P14

      Case14: Male, Chinese, 2.4 y (onset)

      HPOsFreeText: 2.4 y onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case14 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.421G>A (p.Ala141Thr)

      ClinVar: 557678

      CAID: CA364404763

      gnomAD: n/a


      Variant2: NM_000255.3:c.810_811dupGG (p.?)

      ClinVar: n/a

      CAID: CA3847032

      gnomAD: n/a


      CaseAddInfo: lost to follow up. heterozygous mutations in trans. both novel mutations

    28. P12

      Case12: Female, Chinese, 1.5 y (end of study)

      HPOsFreeText: 11 mo onset, poor neruological outcome

      NotHPOsFreeText: not responsive to vitamin B12


      Case 12 (Level 2)

      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.323G>A (p.Arg108His)

      ClinVar: 100707

      CAID: CA235522

      gnomAD: 0.00006152 (African)


      Variant2: NM_000255.3:c.2179C>T (p.Arg727Ter)

      ClinVar: 218998

      CAID: CA347913

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: heterozygous mutations in trans

    29. P11

      Case11: Female, Chinese, 2 y (age at death)

      HPOsFreeText: 9 mo onset, responsive to vitamin B12


      Case11 (Level 2)

      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3(MMUT):c.323G>A (p.Arg108His)

      ClinVar: 100707

      CAID: CA235522

      gnomAD: 0.00006152 (African)


      Variant2: NM_000255.3:c.1514T>C (p.!le505Thr)

      ClinVar: n/a

      CAID: CA364397174

      gnomAD: n/a


      CaseAddInfo: heterozygous mutations in trans, died at 2 y

    30. P10

      Case10: Male, Chinese, 6.4 y (onset)

      HPOsFreeText: 6.4 y onset

      NotHPOsFreeText: not responsive to vitamin B12


      Case10 (Level 2)

      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3(MMUT):c.323G>A (p.Arg108His)

      ClinVar: 100707

      CAID: CA235522

      gnomAD: 0.00006152 (African)


      Variant2: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      CaseAddInfo: lost to follow up, heterozygous mutations in trans

    31. P13

      Case13: Female, Chinese, 7 mo (onset)

      HPOsFreeText: 7 mo onset

      NotHPOsFreeText: not responsive to vitamin B12


      Case13 (Level 2):

      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.419T>C (p.Leu140Pro)

      ClinVar: n/a

      CAID: CA364404765

      gnomAD: n/a


      Variant2: NM_000255.3:c.424A>G (p.Thr142Ala)

      ClinVar: n/a

      CAID: CA364404758

      gnomAD: n/a


      CaseAddInfo: Variant 1 is novel. Heterozygous mutations in trans. lost to follow up.

    32. P9

      Case1: Male, Chinese, 1.8 y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12


      Case9 (Level 2)

      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

      ClinVar: 1887

      CAID: CA249732

      gnomAD: 0.0008393 (Latino)


      Variant2: NM_000255.3(MMUT):c.323G>A (p.Arg108His)

      ClinVar: 100707

      CAID: CA235522

      gnomAD: 0.00006152 (African)


      Variant3: NM_000255.3:c.2168G>A (p.Gly723Asp)

      ClinVar: n/a

      CAID: CA3846630

      gnomAD: 0.00006533 (South Asian)


      CaseAddInfo: Variant 1 in trans to Variants 2 and 3 (cis). Variant 3 is novel

    33. P8

      Case8: Male, Chinese, 8 mo (onset)

      HPOsFreeText 8 mo onset, responsive to vitamin B12

      Case8 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.278G>A (p.Arg93His)

      ClinVar: 1880

      CAID: CA249728

      gnomAD: 0.0004777 (European-Finnish)


      Variant2: NM_000255.3:c.567T>G (p.Asn189Lys)

      ClinVar: 618734

      CAID: CA364404447

      gnomAD: n/a


      CaseAddInfo: lost to follow up, heterozygous mutations in trans

    34. P7

      Case7: Male, Chinese, 33 d (age at death)

      HPOsFreeText: Neonatal onset

      NotHPOsFreeText: Not responsive to vitamin B12

      Case7 (Level 2)


      CasePreviousTesting: Same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.103C>T (p.Gln35Ter)

      ClinVar: n/a

      CAID: CA364405751

      gnomAD: 0.00009950 (Ashkenazi Jewish)


      Variant2: NM_000255.3:c.494A>G (p.Asp165Gly)

      ClinVar: n/a

      CAID: CA138799926

      gnomAD: 0.00005443 (East Asian)


      CaseAddInfo: died at 33d, heterozygous mutations in trans

    35. P6

      Case6: Female, Chinese, 1 mo (onset)

      HPOsFreeText: not responsive to vitamin B12

      Case6 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.68C>G (p.Ser23Ter)

      ClinVar: n/a

      CAID: CA364405860

      gnomAD: n/a


      Variant2: NM_000255.3:c.323G>A (p.Arg108His)

      ClinVar: 100707

      CAID: CA235522

      gnomAD: 0.00006152 (African)


      CaseAddInfo: lost to follow up, heterozygous mutations in trans

    1. II. 1

      CaseBII-1: N/A

      CasePresentingHPOs: N/A

      HPOsFreeText: Pretreatment phenylalanine level at 890 umol/L

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband for Family B

      Variant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

      ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

      gnomAD: 0.001766, https://gnomad.broadinstitute.org/variant/12-102840493-G-A?dataset=gnomad_r3

      Variant2: NM_000277.3(PAH):c.1241A>G (p.Tyr414Cys)

      ClinVar: 593 https://www.ncbi.nlm.nih.gov/clinvar/variation/593/

      gnomAD: 0.0005264, https://gnomad.broadinstitute.org/variant/12-102840474-T-C?dataset=gnomad_r3

    2. II.2

      CaseEII-2: N/A

      CasePresentingHPOs: N/A

      HPOsFreeText: Pretreatment phenylalanine level at 320 umol/L

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      Variant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

      ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

      gnomAD: 0.001766, https://gnomad.broadinstitute.org/variant/12-102840493-G-A?dataset=gnomad_r3

      Variant2: NM_000277.3(PAH):c.533A>G (p.Glu178Gly)

      ClinVar: 92746 https://www.ncbi.nlm.nih.gov/clinvar/variation/92746/

      gnomAD: 0.0001473, https://gnomad.broadinstitute.org/variant/12-103249087-T-C

    3. I. 1

      CaseCI-1: N/A

      CasePresentingHPOs: N/A

      HPOsFreeText: Pretreatment phenylalanine level at 365 umol/L

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      Variant1: NM_000277.3(PAH):c.194T>C (p.Ile65Thr)

      ClinVar: 636 https://www.ncbi.nlm.nih.gov/clinvar/variation/636/

      gnomAD: 0.0005574, https://gnomad.broadinstitute.org/variant/12-102894893-A-G?dataset=gnomad_r3

      Variant2: NM_000277.3(PAH):c.261C>A (p.Ser87Arg)

      ClinVar: 583 https://www.ncbi.nlm.nih.gov/clinvar/variation/583/

      gnomAD: 0.00009294, https://gnomad.broadinstitute.org/variant/12-102894826-G-T?dataset=gnomad_r3

    4. 11.

      CaseDII-3: N/A

      CasePresentingHPOs: N/A

      HPOsFreeText: Pretreatment phenylalanine level at 725 umol/L

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      Variant1: NM_000277.3(PAH):c.561G>A (p.Trp187Ter)

      ClinVar: 102736 https://www.ncbi.nlm.nih.gov/clinvar/variation/102736/

      gnomAD: 0.00001760, https://gnomad.broadinstitute.org/variant/12-103249059-C-T

      Variant2: NM_000277.3(PAH):c.782G>C (p.Arg261Pro)

      ClinVar: 102832 https://www.ncbi.nlm.nih.gov/clinvar/variation/102832/

      gnomAD: Not in gnomAD

    1. 12258M19866 years726<0.5Intermediate?S97fs

      Case# Patient 12, Male, Turkish, 6yo diagnosis

      CasePresentingHPOs HP:0004923

      CasePreviousTesting screened for BH4 deficiency using dried blood and urine spots, Final di-agnosis was made by measurements of neurotransmitter and pterinmetabolites in cerebrospinal fluid (CSF) and urine, in addition toDHPR enzyme activity, which was assessed in whole red bloodcells

      CaseMethod1 PCR

      CaseMethod2 DGGE

      Variant NM_000320.2:c.371delC(p.S97fs)

      CAID CA658795310

      VariantEvidence frameshift

    2. 17182F19842 months9080SevereExitusR221X

      Case# Patient 17, Female, Turkish, 2mo diagnosis

      CasePresentingHPOs HP:0004923

      CasePreviousTesting screened for BH4 deficiency using dried blood and urine spots, Final di-agnosis was made by measurements of neurotransmitter and pterinmetabolites in cerebrospinal fluid (CSF) and urine, in addition toDHPR enzyme activity, which was assessed in whole red bloodcells

      CaseMethod1 PCR

      CaseMethod2 DGGE

      Variant NM_000320.2:c.741A>T(p.R221Ter)

      CAID CA658795309

      VariantEvidence null

    1. 11

      Patient11: Group 2

      CasePresentingHPOs: same as group 2

      CasePreviousTesting: same as group 2

      CaseGenotypingMethod: same as group 2

      Variant1: NM_002225.3(IVD):c.941C>T (p.Ala314Val) listed in paper as c.932C>T (p.Ala282Val)

      ClinVar: 100060, https://www.ncbi.nlm.nih.gov/clinvar/variation/100060/

      gnomAD: 0.0006507, http://gnomad.broadinstitute.org/variant/15-40707653-C-T

      Variant2: NM_001354598.2:c.868G>A

      CAID: CA391720951, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391720951

      gnomAD: n/a

    2. 10

      Patient10: Group 2

      CasePresentingHPOs: same as group 2

      CasePreviousTesting: same as group 2

      CaseGenotypingMethod: same as group 2

      Variant1: NM_002225.3(IVD):c.941C>T (p.Ala314Val) listed in paper as c.932C>T (p.Ala282Val)

      ClinVar: 100060, https://www.ncbi.nlm.nih.gov/clinvar/variation/100060/

      gnomAD: 0.0006507, http://gnomad.broadinstitute.org/variant/15-40707653-C-T

      Variant2: NM_002225.4:c.436A>G

      CAID: CA391716744, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716744

      **In ClinVar as: NM_002225.3(IVD):c.445A>G (p.Lys149Glu), https://www.ncbi.nlm.nih.gov/clinvar/variation/553403/

      gnomAD: n/a

    1. Family 8

      CaseFZ8: Male, United States, 3 yrs report

      CasePresentingHPOs: HP:0001511, HP:0008897, HP:0001999, HP:0000973, HP:0100678, HP:0000963, HP:0010648, HP:0001388, HP:0001374, HP:0001181, HP:0000938, HP:0000270, HP:0025356, HP:0001252, HP:0000518, HP:0000325, HP:0011220, HP:0000337, HP:0000411, HP:0000369, HP:0100790, HP:0005116, HP:0000717, HP:0008872, HP:0000486, HP:0500163, HP:0003572, HP:0500139 (Intrauterine growth retardation, Postnatal growth retardation, Abnormal facial shape, Cutis laxa, Premature skin wrinkling, Thin skin, Dermal translucency, Joint laxity, Congenital hip dislocation, Adducted thumb, Osteopenia, Delayed cranial suture closure, Psychomotor retardation, Muscular hypotonia, Cataract, Triangular face, Prominent forehead, Broad forehead, Protruding ear, Low-set ears, Hernias, Arterial tortuosity, Autism, Feeding difficulties in infancy, Strabismus, Hypoornithinemia, Low plasma citrulline, Hypoprolinemia)

      HPOsFreeText: Typical facial gestalt

      CaseNotHPOs: HP:0002645, HP:0012443, HP:0001762, HP:0002650, HP:0000252, HP:0001348 (Wormian bones, Abnormality of brain morphology, Talipes equinovarus, Scoliosis, Microcephaly, Brisk reflexes)

      NotHPOsFreeText: N/A

      CaseAddInfo: Variant is confirmed de novo in this case with one other confirmed and one non-confirmed case with the same variant and similar presentation, No family history

      CasePreviousTesting: N/A

      CaseGenotypingMethod: ALDH18A1 and PYRC1 were investigated by Sanger sequencing, with the latter revealing no abnormalities and the former showing a heterozygous change at the Arg138 residue.Investigation revealed no further variants in the coding regions. Familial sequencing revealed the inheritance was de novo with no variants in the parents.

      Variant: NM_002860.4(ALDH18A1):c.413G>A (p.Arg138Gln)

      ClinVar: 217260 https://www.ncbi.nlm.nih.gov/clinvar/variation/217260/

      gnomAD: Not in gnomAD

    1. Patient K.A. (BIODEF 264)

      Case: K.A./ BIODEF 264, male, Caucasian, 1 day

      CasePresentingHPOs:  HP:0008297, HP:0040206, HP:0040210, HP:0001252

      HPOText: Plasma Phe level of 290umol/L at 3 days old, 853 umol/L at 6 days old, and 1997 umol/L at 13 days old. Urinary pterins indicated high neopterin/biopterin ratio and increased levels of primapterin. At 1 month old, neopterin and biopterin levels in normal range. At one month old showed mild hypotonia (extermities and trunk), but at 2.5 years Phe diet stopped and patient developed normally.

      CasePreviousTesting: n/a

      CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

      Variant: NM_000281.3(PCBD1):c.292C>T (p.Gln98Ter)

      ClinVar ID: 16799

      No-stars, 1 submission from OMIM.

      Homozygous, non-LOF.

      gnomAD: MAF (Euro-NF)= 2.2291E-4 (29/126606) hets only. No homozygotes recorded

      http://gnomad.broadinstitute.org/variant/10-72643730-G-A

      AddCaseInfo: The only individual in the family diagnosed with HyperPhe.

      VariantEvidence: The mutant Q97X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mQ97X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some activity in vitro. Interestingly, when more Q97X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was 2-3 times higher than wildtype (text only, no figures to compare).

      Patient part of the BIODEF database: PMID:8830181

    2. Patient I.B. (BIODEF 273)

      Case: I.B./ BIODEF 273, male, Ashkenazi Jewish, 3 days

      CasePresentingHPOs: HP:0040210, HP:0008297,

      HPOText: Plasma Phe levels were 240 umol/L at 3 days old, and 1845 umol/L at 14 days old. A low-Phe diet caused a rapid decline of Phe level to normal within 36 hours. An oral BH4–loading test (10 mg/kg body weight) resulted in a decrease of plasma Phe from 540 μmol/liter to 234 μmol/liter and then to 196 μmol/liter within 4 and 8 h, respectively. At 1 month, pterin and neurotransmitter in the CSF were normal. Starting a 2 month of age the patient was administered a low Phe diet and BH4 for 4 months. After the 4 months, the BH4 was discontinued, and Phe levels are between 120-300 umol/L at 5 years. Patient is developing normally.

      CaseNOTHPOs: n/a

      CasePreviousTesting: n/a

      CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

      Variant: NM_000281.3(PCBD1):c.259G>T (p.Glu87Ter) 

      ClinVar ID: 16795

      No star, one submission for OMIM

      Homozygous

      gnomAD: MAF (Ashkenazi Jewish)= 1.183E-3 (12/10146) in heterozygous only. No homozygous reported.

      http://gnomad.broadinstitute.org/variant/10-72643763-C-A

      AddCaseInfo: The proband's older sister (J.B., 18 . months older) has the same genotype (homozygous for the T79I mutation), but was never noted as having HyperPhe, and was never treated. She has developed "normally." This family is recorded as Family B in the paper.

      VariantEvidence: The mutant E86X/E87X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mutant E86X/E87X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some enzyme activity in vitro. Interestingly, when more E86X/E87X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was similar to wildtype levels (text only, no figures to compare).

      Patient part of the BIODEF database: PMID:8830181

    3. Patient J.S. (BIODEF 211)

      Case: J.S./ BIODEF 211, female, Hispanic, 3 days

      CasePresentingHPOs: HP:0008297, HP:0001252, HP:0001270

      HPOText: Phe levels were 9 umol/L on day 1, 756 ummol/L on day 28. Primapterinuria was diagnosed on day 8. Following oral BH4 administration (2 mg/kg/d), neopterin normalized, and biopterin as well as primapterin increased about eight-fold; the same results were observed when dihydrobiopterin and sepiapterin were administered. At 8.5 years old, on a normal diet, the patient is developing normally with no HyperPhe.

      CasePreviousTesting: n/a

      CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

      Variant: NM_000281.3(PCBD1):c.236C>T (p.Thr79Ile)

      ClinVar ID: 16797

      No stars, 1 submission for OMIM.

      Homozygous

      gnomAD: n/a

      AddCaseInfo: Family history (Family S) of HyperPhe, as the patients older brother, T.S./ BIODEF212, who is 1.5 years older, showed the same biochemical pattern and is now considered normal and normally developing.

      At 8.5 years old, on a normal diet, the patient J.S. is developing normally with no HyperPhe.

      VariantEvidence: The T78I/T79I variant was retained completely within the insoluble fraction of the E.Coli lysate in which the recombinant proteins were produced. When the soluble fraction was examined for PCBD1 activity, no activity was observed. The authors note that the absence of activity could be due to the absence of the protein in the soluble fraction alone, instead of being indicative of the mutation causing a loss of enzyme activity. Only if the mutant recombinant protein could be retained in the soluble fraction can the true enzyme activity be assessed.

      Patient part of the BIODEF database: PMID:8830181

    4. Patient B.E. (BIODEF 272)

      Case: B.E./ BIODEF 272, male, 3 weeks

      CasePresentingHPOs: HP:0008297, HP:0001252, HP:0001270

      HPOText: Neonatal (3 days old) plasma screen showed Phe levels at 183 umol/L, which is below the normal cutoff. Repeat screen was only performed at 3 weeks old in which the Phe level was shown to be 1600 umol/L. Peak Phe level was at 3.5 weeks and was 2589 umol/L. Child had considerable Phe tolerance ( ~100mg/kg). Initial neopterin-to-biopterin ratio of 15. A BH4-loading test (6 mg/kg) at age 6 wk showed only a slight response (Phe at 0 h, 731 μmol/liter; at 3 h, 612 μmol/liter; and at 6 h, 502 μmol/liter). A week later, at a BH4 dose of 22 mg/kg, there was a definite response (Phe at 0 h, 773 μmol/liter; at 3 h, 517 μmol/liter; and at 6 h, 155 μmol/liter). CSF neurotransmitter concentrations were normal, suggesting a peripheral deficiency. At 4 months of age, the BH4 was discontinued, no low Phe diet, and the Phe levels have remained normal. at 3.5 years, patient developing normally.

      CaseNOTHPOs:

      CasePreviousTesting: n/a

      CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

      Variant: NM_000281.3(PCBD1):c.292C>T (p.Gln98Ter)

      ClinVar ID: 16799

      No star, one submission for OMIM

      Homozygous

      gnomAD: MAF (Euro-NF)= 2.2291E-4 (29/126606) hets only. No homozygotes recorded

      AddCaseInfo: Family E in the article, and the proband had an older sibling that also carried the homozygous mutation in PCBD1, she was not noted as having increased Phe plasma levels, nor was ever treated with BH4 or low-Phe diet.

      VariantEvidence: The mutant Q97X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mQ97X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some activity in vitro. Interestingly, when more Q97X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was 2-3 times higher than wildtype (text only, no figures to compare).

      Patient part of the BIODEF database: PMID:8830181

    1. Biallelic

      Case#: Patient 10, male, 5.9 years (report)

      CaseHPOs: HP:0003235 (hypermethioninemia)

      CaseHPOsFreeText: Identified by newborn screening

      CaseNotHPOsTest: Normal neurologic and/or muscular status, IQ 111

      CasePreviousTesting: Plasma methionine 484-742; transamination products in plasma 5.01-6.21 uM (normal 0.2-0.54) and in urine 45.2-75.6 mmol/mol creatinine (normal 1.2-4.6), urine dimethylsuphide 10 nM (normal – trace-2 nM).

      Variant: p.Arg199Cys (homozygous)

      ClinVar: N/A

      CAID: CA5576749

      gnomAD: The highest population minor allele frequency in gnomAD is 0.0001735 (Latino); no homozygotes in any population.

      VariantEvidence: When the variant was expressed in bacteria, the amount of MAT1A protein was reduced on Western blot, and MAT1A activity was 11% of normal.

      CasePMIDs: 7573050

      Points: 1 point. This individual is homozygous for a missense change, p.Arg199Cys, in MAT1A. When the variant was expressed in bacteria, the amount of MAT1A protein was reduced on Western blot, and MAT1A activity was 11% of normal. The highest population minor allele frequency in gnomAD is 0.0001735 (Latino); no homozygotes in any population.

    2. Biallelic

      Case#: Patient 8, female, 14 years (report)

      CaseHPOs: HP:0003235, HP:0001249, HP:0001332 (Hypermethioninemia, Intellectual disability, dystonia)

      CaseHPOsFreeText: demyelination

      CasePreviousTesting: Plasma methionine 1114–1629; transamination products in plasma 41.2 uM (normal 0.2-0.54) and in urine 992 mmol/mol creatinine (normal 1.2-4.6), urine dimethylsuphide 535 nM (normal – trace-2 nM).

      Variant: c.1043_1044delTG (homozygous)

      ClinVar: NA

      CAID: CA594460387

      gnomAD: The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population

      VariantEvidence: When the variant was expressed in bacteria, the amount and size of the protein was reduced on Western blot, and there was no detectable MAT1A activity.

      CasePMIDs: 7573050 Points: 1 point. This individual is homozygous for a frameshift variant in MAT1A. When the variant was expressed in bacteria, there was no detectable MAT. The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population. The score is reduced because other causes of hypermethioninemia have not been ruled out.

    1. c.1A > T

      Case# PB1, Saudi Arabia

      CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

      CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

      CaseMethod1 PCR

      CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

      Variant NM_000056.3:c.1A>T

      CAID CA364657845

      gnomAD 0.00003656 (European (Non-Finnish)), 0.00001346 (Overall)

      VariantEvidence none

      CaseAddInfo consanguineous family

    1. Clinical data

      Case#: Guo 2015 Proband, M, 18 months (onset), Chinese

      CasePresentingHPOs: HP:0002329, HP:0011968, HP:0002317, HP:0012088, HP:0001946

      Onset of symptoms upon episode of fever. Slightly reduced muscle tension. Second episode 2 months later and plasma amino acid analysis was performed: 431.67 umol/L leucine (normal 4.2-367), 167.13 umol/L isoleucine (normal 26.9-146), 47.81 umol/L valine (normal 117.6-495.7), 44.88 umol/L alloisoleucine (normal 0-7.7).

      CaseNotHPOs: HP:0002373, HP:0002013, HP:0002361

      CaseGenotyping Method: BCKDHA, BCKDHB, DBT, and DLD were screened for mutations using second generation sequencing. Direct sequencing was performed on the parents to confirm variants.

      Variant: 1. NM_000056.3:c.767A>G (p.Y256C); 2. NM_000056.3:c.768C>G (p.Y256X)

      CAID: 1. CA364659935; 2. CA142287564

      gnomAD: 1. 4.069e-6 overall

    1. 2DBT

      Case#: Patient 2, Lebanon, Arab

      CasePresentingHPOs: Intermediate form of MSUD

      CasePreviousTesting: Previously diagnosed with MSUD by GC/MS/MS.

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Genomic DNA extracted, sequencing of BCKDHA, BCKDHB and DBT.

      Variant: NM_001918.3:c.224G>A (homozygous)

      CAID: CA341345382

      gnomAD: Not in gnomAD

      VariantEvidence: Mutation is present in lipoyl-binding domain, likely preventing binding of the lipoyl co-factor. Possibly results in a defect in the lipoyl-binding function (Alamut software analysis).

      CaseAddInfo: Same variant reported in patient 1 from the same geographical location, but unrelated according to the authors.

    1. 54

      Case54 Male, 7.3yo report, Ethnicity: Turkish

      CasePresentingHPOs HP:0003571, HP:0008872, HP:0002013, HP:0008947, HP:0002789, HP:0002045

      (propionicacidemia, feeding difficulties in infancy, vomiting, infantile hypotonia, tachypnea, hypothermia)

      HPOsFreeText feeding difficulties, vomiting, hypotonia, tachypnea, hypothermia(3do). 55 IQ on Culture Free Test

      CaseNotHPOs n/a

      CasePreviousTesting Diagnosis by selective metabolic screen. Patient fibroblasts had 1.5% PCC activity of control

      Variant NM_000532.4(PCCB):c.990dupT (p.Glu331Terfs), homozygous

      ClinVar 167423

      gnomAD MAF= 0.001001(African), no homozygotes

      CaseAddInfo parental consanguinity

      CasePMIDs n/a

    2. 35

      Case35 Male, 7.1yo report, Ethnicity: Syrian

      CasePresentingHPOs HP:0003571, HP:0002789

      (propionicacidemia, tachypnea)

      HPOsFreeText tachypnea(6do). 55 IQ on Culture Free Test

      CaseNotHPOs n/a

      CasePreviousTesting Diagnosis by NBS. Patient fibroblasts had 1.5% PCC activity of control.

      Variant NM_000532.4:c.1313C>T (p.Ala438Val), homozygous

      ClinVar n/a

      CAID CA354649295

      gnomAD not in gnomAD

      CaseAddInfo no parental consanguinity

      CasePMIDs n/a

    3. 34

      Case34 female, 5.5yo report, Ethnicity: German

      CasePresentingHPOs HP:0003571, HP:0012523, HP:0001531, HP:0002791, HP:0001944

      (propionicacidemia, oral aversion, failure to thrive in infancy, bradypnea, dehydration)

      HPOsFreeText feeding refusal, failure to thrive, bradypnea, dehydration(2do). 55 IQ on Culture Free Test

      CaseNotHPOs n/a

      CasePreviousTesting Diagnosed on newborn screen. PCC activity in patient fibroblasts was 0.9% of control

      Variant NM_000532.4:c.483dup (p.Gly162TrpfsTer?), homozygous

      ClinVar n/a

      CAID to register

      gnomAD not in gnomAD

      CaseAddInfo no parental consanguinity

      CasePMIDs n/a

    1. Table 1:

      Case6: Female, 16 days at initiation of follow up, European ancestry

      HPOsFreeText: NBS C4-acylcarnitine 2.0 umol/L, Plasma C4-acylcarnitine 1.36 umol/L, in vitro probe isoC4-acylcarnitine 0.160 umol/g protein, in vitro probe C4-acylcarnitine 0.150 umol/g protein, urine c4 acylcarnitine 19.13 mmol/mol creatinine, urine C4/C3 ratio 101

      CaseNotHPOs: normal urine isobutyryglycine

      CaseAddInfo: no data for clinical condition or SCAD gene variants

      Case6 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2(ACAD8):c.958G>A (p.Ala320Thr)

      ClinVar: 372297

      CAID: CA6373180

      gnomAD: 0.001725 (European Finnish)


      Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

      ClinVar: 5356

      CAID: CA117435

      gnomAD: 0.0001551 (European non-Finnish)


      CaseAddInfo: compound heterozygote, specified allele 1 and 2 but not maternal and paternal. no potential splice site alteration

    2. younger brother

      Case7a: Male, 7 days at initiation of follow up, Hispanic ancestry

      HPOsFreeText: NBS C4-acylcarnitine 2.2 umol/L, plasma C4-acylcarnitine 2.09 umol/L, in vitro probe isoC4-acylcarnitine 0.070 umol/g protein, urine C4-acylcarnitine 3.58 mmol/mol creatinine, Urine C4/C3 ratio 130.

      CaseNotHPOs: normal in vitro probe C4-acylcarnitine, normal urine isobutyrylglycine,

      CaseAddInfo: younger brother of patient 7b, part of Family2, unremarkable clinical condition

      Case7a (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2:c.687T>G (p.Phe229Leu)

      ClinVar: n/a

      CAID: CA6373030

      gnomAD: 0.00008673 (Latino)


      Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

      ClinVar: 5356

      CAID: CA117435

      gnomAD: 0.0001551 (European non-Finnish)


      CaseAddInfo: no potential splice site alteration, no data for SCAD gene variants

    3. One patient

      Case1: Female, 9 days at follow up, North African ancestry

      CasePresentingHPOs: HP:0002013, HP:0001944,HP:0031123, HP:0000388 (emesis, dehydration, recurrent gastroenteritis, otitis media)

      HPOsFreeText: NBS C4-acylcarnitine 2.9 umol/L, plasma C4 acylcarnitine 1.35 umol/L, isoC4-acylcarnitine 0.090 umol/g protein,

      CaseNotHPOs:

      NotHPOsFreeText: normal urine isobutyrylglycine

      CaseAddInfo: repeatedly hospitalized during first 2 years of life.

      CasePMIDs:

      Case (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant: NM_014384.2(ACAD8):c.988C>T (p.Arg330Trp)

      ClinVar: 5357

      CAID: CA117438

      gnomAD: 0.00006155 (African)


      CaseAddInfo: homozygous mutations

    1. 4

      Case4 Female, 9yo report, USA, Lumbee

      CasePresentingHPOs HP:0003150, HP:0011471, HP:0002540, HP:0001344, HP:0100309, HP:0012751, HP:0200147, HP:0100952

      (Glutaricaciduria, Gastronomy tube feeding in infancy, Non-ambulatory, Nonverbal, Subdural haematoma, Abnormal basal ganglia MRI signal intensity, Neuronal loss in basal ganglia, Enlarged sylvian fissure)

      HPOsFreeText Urine glutaric acid was highly elevated and 3-hydroxyglutaric acid was elevated. Patient presented with acute metabolic decompensation at 6mo. After decompensation, brain MRI found subdural hematomas, atrophied temporal lobes with widened Sylvian fissures, and elevated signal intensity in basal ganglia. Follow-up report studies noted volume loss in basal ganglia. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting n/a

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.

      Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous

      ClinVar 167133

      gnomAD MAF=0.0002017(African), no homozygotes

      CaseAddInfo nonconsanguineous

      CasePMIDs n/a

    2. 3

      Case3 Male, 5yo report, USA, Lumbee

      CasePresentingHPOs HP:0003150

      (Glutaricaciduria)

      HPOsFreeText Patient had elevated glutaric acid and small 3-hydroxyglutaric acid in urine. Patient feeds by mouth. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.

      CaseNotHPOs HP:0002540, HP:0001344, HP:0011471

      (Non-ambulatory, Nonverbal)

      NotHPOsFreeText Patient did not present with acute metabolic decompensation.

      CasePreviousTesting Patient's NBS detected glutarylcarnitine of 1.07μM(cutoff at >0.38). GCD enzyme activity was 0%.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.

      Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous

      ClinVar 167133

      gnomAD MAF=0.0002017(African), no homozygotes

      CaseAddInfo nonconsanguineous

      CasePMIDs n/a

    1. 75) w

      Case1875(M.C.) Female, 22yo died, Irish

      CasePresentingHPOs HP:0001263, HP:0001249, HP:0001250, HP:0002650, HP:0002625, HP:0005625, HP:0002857, HP:0000545, HP:0000276, HP:0000275, HP:0000218, HP:0000678, HP:0002878, HP:0001695, HP:0002240

      (Developmental delay, Intellectual disability, Seizures, Scoliosis, Deep vein thrombosis, Osteoporosis of vertebrae, Genu valgum, Myopia, Long face, Narrow face, High palate, Crowded teeth, Respiratory failure, Cardiac arrest, Enlarged liver)

      HPOsFreeText Diagnosed with homocystinuria after exam for developmental delay at 13mo. Patient had severe intellectual disability and seizures. At 14yo she had surgery for scoliosis, postsurgery she had a popliteal vein thrombosis. In addition to osteoporosis of the spine, she had genu valgum and myopia. The patient also had a long and narrow face, high-arched palate and crowded teeth. Respiratory failure and cardiac arrest at 22yo likely due to overuse of antiasthmatic medication.

      (PMID:20329304): She was delivered normally at term, weighed 3kg, made uncomplicated neonatal progress, no history of convulsions,reached early milestones at expected times but did not sit up until 13mo. On report she was well fed and well developed, but with persistent shadow in right upper load on roentgenogram, enlarged liver of normal consistence, spleen was not palpable, negative neurological exam, mental age was 9mo. Aortogram was negative for vascular abnormalities in upper left chest. Skull and long bones were normal but osteoporosis of the spine was detected by roentgenogram.

      CaseNotHPOs HP:0001083

      (Lens dislocation)

      NotHPOsFreeText no malar flush, lens displacement, or skeletal deformity on exam at 13mo.

      CasePreviousTesting Plasma homocysteine was 45μM pretreatment. Pyroxidine treatment reduced those levels to trace amounts. In patient fibroblasts, no CBS protein was detect on Western blot and CBS assay detected no activity. (PMID: 20329304): "Full hemogram, routine urine analysis, liver function tests, serum ion and iron-binding capacity, plasma magnesium, serum calcium, inorganic phosphate, fasting blood sugars, blood urea nitrogen, and bone marrow examination were all normal". Strong positive on cyanide nitroprusside, heavy homocysteine spot on chromatogram of urinary amino acids.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod Created a bacteria expression system in E.coli by substituting one of three fragments of (PCR amplified)patient cDNA into WT CBS sequence already subcloned in expression plasmids. Bacteria were screened based on which ones did not have CBS activity. Those that did not have activity were thought to have LOF variants in CBS. Plasmids containing the inactivating fragments, one cut with NcoI/XmaI and another cut with Bpu1102/BstX, were sequenced.

      Variant 1. NM_000071.2:c.715G>A (p.Glu239Lys),

      1. NM_000071.2:c.233C>G (p.Pro78Arg);3. NM_000071.2:c.306G>C (p.Lys102Asn) - 2&3 in cis, compound heterozygous

      ClinVar 1. n/a, 2. 188988;3. 188989

      CAID 1. CA410600501

      gnomAD 1. not in gnomAD, 2. MAF=0.0001631(Other), no homozygotes, 3. MAF=0.0001630(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs 20329304

    1. AHN3.4

      CaseAHN3.4: Australia, White

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variants segregate with the disease

      CasePMIDs: 15286788

      CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography

      CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.

      Variant1: NM_001003841.3:c.719G>A (p.Arg240Gln)

      CAID: CA3182844, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182844

      gnomAD: 0.0001307, https://gnomad.broadinstitute.org/variant/5-1213633-G-A

      Variant2: NM_001003841.3(SLC6A19):c.1701+1G>A

      ClinVar: 623442, https://www.ncbi.nlm.nih.gov/clinvar/variation/623442/

      gnomAD: 0.00005286, https://gnomad.broadinstitute.org/variant/5-1221429-G-A

    2. AHN5.1

      CaseAHN5.1: Australia, White

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variant 1 is in-trans with Variants 2 and 3, which are in cis; Variant segregates with the disease

      CasePMIDs: 17555458

      CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography;

      CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.

      Variant1: NM_001003841.3:c.196G>A (p.Gly66Arg)

      CAID: CA359061114 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA359061114

      gnomAD: Not in gnomAD

      Variant2: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

      ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

      gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A

      Variant3: NM_001003841.3(SLC6A19):c.718C>T (p.Arg240Ter)

      ClinVar: 2020 https://www.ncbi.nlm.nih.gov/clinvar/variation/2020/

      gnomAD: 0.0001960, https://gnomad.broadinstitute.org/variant/5-1213632-C-T

    3. AHN9.2

      CaseAHN9.2: Australia, White

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variants segregate with the disease

      CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography;

      CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.

      Variant1: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

      ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

      gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A

      Variant2: NM_001003841.3:c.1550A>G (p.Asp517Gly)

      CAID: CA3183226, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3183226

      gnomAD: 0.00004675, https://gnomad.broadinstitute.org/variant/5-1221277-A-G

    1. Proband

      CaseF3P: 4 yrs report, India

      CasePresentingHPOs: HP:0001010, HP:0000750, HP:0001249, HP:0006801, HP:0004923 (Hypopigmentation of the skin, Delayed speech and language development, Intellectual disability, Brisk deep tendon reflexes, Hyperphenylalaninemia)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Family is consanguinous, Parents were confirmed heterozygous, Variant may not undergo NMD however would be missing essential domains (but PAH level supports some residual function)

      CasePreviousTesting: Blood phenylalanine before treatment was 439 μmol/l, Blood tyrosine before treatment was 121 μmol/l, PKU diagnosis was based on ferric chloride test on patient urine samples and detection of elevated Phenylalanine levels in blood samples by using HPLC, in addition to analysis of clinical features.

      CaseGenotypingMethod: Genomic DNA was isolated from blood samples of proband and family members. PCR amplification and sequencing was used to screen for mutations. Each mutation was confirmed by bi-directional DNA sequencing.

      Variant: NM_000277.3:c.976del (p.Trp326Glyfs*15)

      CAID: CA16020912 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA16020912

      gnomAD: Not in gnomAD

    1. AM7162

      CaseAM7162: Female, 6 yrs report

      CasePresentingHPOs: HP:0001992, HP:0002179, HP:0010864, HP:0008936, HP:0002509, HP:0000750, HP:0011968, HP:0008872, HP:0100247, HP:0002373, HP:0001347, HP:0011449 (Organic aciduria, Opisthotonus, Severe Intellectual disability, Muscular hypotonia of the trunk, Limb hypertonia, Delayed speech and language development, Feeding difficulties, Feeding difficulties in infancy, Recurrent singultus, Febrile seizure, Hyperreflexia, Knee clonus)

      HPOsFreeText: Birth weight 2.86 kg, Cranial circumference is 49 cm (3rd percentile), weight 18.6 kg (25th percentile) and height 115 cm (50th percentile) at 6 yrs of age

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are first cousin consanguineous; Proband is confirmed homozygous for this variant via a QFM‐PCR assay for the dosage of ACY1 exons 12 and 13; Variant leads to skipping of Exon 13 and a resulting frameshift with a premature termination

      CasePreviousTesting: Urinary organic acid analysis confirmed by enzyme assay showed elevated levels of N ‐acetylated derivatives of glutamic acid, leucine, valine and isoleucine; Several genetic investigations, such as karyotyping, ring 15 chromosome analysis and mutational analysis of MECP5 and STXBP1 genes, were performed and were found to be normal; MRI showed dilatation of the left temporal horn at the age of 13 months;

      CaseGenotypingMethod: Genomic DNA was isolated and the ACY1 gene was PCR-amplified and sequenced. PCR analysis of retrotranscribed RNA was performed to analyze the effect of this variant on splicing.

      Variant: NM_000666.3(ACY1):c.1001_1001+5del

      ClinVar: 162019, https://www.ncbi.nlm.nih.gov/clinvar/variation/162019/

      gnomAD: 0.00001758, https://gnomad.broadinstitute.org/variant/3-52022618-ATGTGAG-A

    1. one male

      CaseWA: Male, 2 yrs onset, Germany

      CasePresentingHPOs: HP:0002013, HP:0012470, HP:0004372, HP:0002069, HP:0010819, HP:0007359, HP:0010845, HP:0002133, HP:0007979, HP:0000572, HP:0000577, HP:0000543, HP:0001263, HP:0001310, HP:0002075, HP:0002317, HP:0002188 (Vomiting, Setting-sun eye phenomenon, Lowered consciousness, Bilateral tonic-clonic seizure, Atonic seizure, Focal-onset seizure, EEG with generalised slow activity, Status epilepticus, Gaze-evoked horizontal nystagmus, Visual loss, Exotropia, Optic disc pallor, Global developmental delay, Dysmetria, Dysdiadochokinesis, Unsteady gait, Delayed CNS myelination)

      HPOsFreeText: Tonic flexion of the right limbs, The right hemisphere showed continuous spike and slow-spike waves with a temporo-occipital maximum

      CaseNotHPOs: HP:0010841 (Multifocal epileptiform discharges)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are nonconsanguineous, Proband is confirmed homozygous via parental testing

      CasePreviousTesting: EEG showed severe cerebral dysfunction of the right hemisphere (continuous subdelta and delta activity); Antiepileptic treatment with phenobarbital was initiated after the first seizure but was replaced by levetiracetam after the second seizure

      CaseGenotypingMethod: Exome sequencing was performed and potential variants prioritized. Identified variants were selected for Sanger sequencing in both the proband and parents.

      Variant: NM_004171.4:c.1421+1G>C

      CAID: CA380121375, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA380121375

      gnomAD: Not in gnomAD

    1. Patient 2

      Case2: Newborn, Hmong (China)

      CasePresentingHPOs:

      HPOFreeText: Born after normal pregnancy, postnatal course normal except for moderately elevated C5-acylcarnitine found during NBS. Treatment with L-carnitine supplementation. Treatment was discontinued without consequence.

      CaseNotHPOs:

      CasePreviousTesting: Plasma C5-acylcarnitine 3.0, 3.2 umol/L (ref <0.6); urine 2-MBG 2.9, 15.5 ug/mg creatinine (ref 0.3-7.5); urine IVG 0.1, 0.6 ug/mg creatinine (ref 0.3-14.3).

      CaseGenotypingMethod: PCR and sequencing of entire gene.

      Variant: NM_001609.3:c.1165A>G (p.Met389Val) (homozygous)

      CAID: CA5730948

      gnomAD: East Asian 0.0005513

      VariantEvidence: PCR of cDNA using primers in exon 9 and exon 11 showed that exon 10 was missing. Analysis of intron exon junctions flanking exon 10 did not reveal any changes.

      CaseAddInfo: Diagnosis confirmed by Western blot of fibroblasts which showed no SBCAD protein.

      CasePMIDs:

    1. Biallelic

      Case#: Patient 1, female, 25 years (report), German

      CaseHPOs: HP:0003235 (hypermethioninemia)

      CaseHPOsFreeText: Identified by newborn screening.

      CaseNotHPOsFreeText: Hepatic, vascular or neurological symptoms have never been noted, and cranial MRI was normal at the age of 20 years

      CasePreviousTesting: Over a period of 25 years, methionine concentrations ranged from 850 to 1100 µmol/L (normal 20–40), and fasting total plasma homocysteine was 30–45 µmol/L (normal 5–15).

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

      Variant: c.65C>T (p.Ser22Leu) (homozygous)

      ClinVar: N/A

      CAID: CA377364910

      gnomAD: The highest population minor allele frequency in gnomAD is 0.00002891 (Latino)

      VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to <50% of wild type (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

      CaseAddInfo: Parents are reported to be unrelated

      Points: 0.5

    1. Theproband

      CaseC: Male, Childhood onset, Asian, China

      CasePresentingHPOs: HP:0004923 (Hyperphenylalaninemia)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are confirmed heterozyogus and proband is homozygous for this mutation

      CasePreviousTesting: "Classical Severe PKU" presence confirmed by Guthrie test and clinical criteria described in PMID:7006308, Plasma phenylalanine level in excess of 20 mg/dl, Homozygous for RFLP haplotype 4

      CaseGenotypingMethod: PCR amplification of PAH exon three plus the flanking intronic regions was performed. The genomic DNA was cloned and sequenced to confirm the presence of the mutation. Haplotype analysis confirmed linkage disequillibrium with RFLP haplotype 4.

      Variant: NM_000277.3(PAH):c.331C>T (p.Arg111Ter)

      ClinVar: 581 https://www.ncbi.nlm.nih.gov/clinvar/variation/581/

      gnomAD: 0.0001230, https://gnomad.broadinstitute.org/variant/12-103288534-G-A

    1. t

      CaseSE4: Male, Australia

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseGenotypingMethod: Five loci were investigated for evidence of linkage to Hartnup due to their established role in amino acid transport including SLC3A2, SLC7A8, SLC1A5, SLC6A18, and SLC6A19. These 5 regions were studied with microsattelite markers and produced linkage only between D5S392 and D5S417, the region with SLC6A18 and 19. SLC6A18 did not increase neutral amino acid uptake in X. laevis oocytes so SLC6A19 was investigated and directly sequenced in the families each of which displayed a causal variant.

      CasePreviousTesting: SLC1A5 had no causative variants detected.

      CaseAddInfo: Asymptomatic except for hyperaminoaciduria

      Variant: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

      ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

      gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A?dataset=gnomad_r2_1

    2. a

      CaseSE7: Female, Australia

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseGenotypingMethod: Five loci were investigated for evidence of linkage to Hartnup due to their established role in amino acid transport including SLC3A2, SLC7A8, SLC1A5, SLC6A18, and SLC6A19. These 5 regions were studied with microsattelite markers and produced linkage only between D5S392 and D5S417, the region with SLC6A18 and 19. SLC6A18 did not increase neutral amino acid uptake in X. laevis oocytes so SLC6A19 was investigated and directly sequenced in the families each of which displayed a causal variant.

      CasePreviousTesting: SLC1A5 had no causative variants detected.

      CaseAddInfo: Asymptomatic except for hyperaminoaciduria

      Variant1: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

      ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

      gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A?dataset=gnomad_r2_1

      Variant2: NM_001003841.3(SLC6A19):c.718C>T (p.Arg240Ter)

      ClinVar: 2020 https://www.ncbi.nlm.nih.gov/clinvar/variation/2020/

      gnomAD: 0.0001960, https://gnomad.broadinstitute.org/variant/5-1213632-C-T

    1. 2927 (F)

      Case2927: Female, 2 years diagnosis, Czech

      CasePresentingHPOs: HP:0001270, HP:0001263, HP:0003153, HP:0012443, HP:0000486, HP:0012795, HP:0000639, HP:0000545, HP:0000646, HP:0002280, HP:0030890, HP:0000488, HP:0001744 (Motor delay, Global developmental delay, Cystathioninuria, Abnormality of brain morphology, Strabismus, Abnormality of the optic disc, Nystagmus, Myopia, Amblyopia, Enlarged cisterna magna, White matter hyperintensity, Retinopathy, Splenomegaly)

      HPOsFreeText: Normal total homocysteine (7.1 μM/l; reference 5.1–13.9), Elevated cystathionine (6 μM/l; reference 0.04–0.34), Normal total cysteine (306 μmol/l; reference 203–369), Birth weight was 2400 g, Responsive to B6 treatment

      CaseNotHPOs: HP:0002240, HP:0001977 (Hepatomegaly, Abnormal thrombosis)

      NotHPOsFreeText: N/A

      CaseAddInfo: Patient is homozygous for this mutation

      CasePreviousTesting: Cystathionine (Cysta), total cysteine (tCys), and total homocysteine (tHcy) panels

      CaseGenotypingMethod: PCR amplification of CTH coding regions and exon-intron boundaries was performed. These fragments were sequenced and aligned with a reference to find mutations. Those found were confirmed by restriction digest of 100 controls.

      Variant: NM_001902.5:c.200C>T (p.Thr67Ile)

      ClinVar: 2939 https://www.ncbi.nlm.nih.gov/clinvar/variation/2939/

      gnomAD: Ashkenazi Jewish 9.934e-3, Overall 6.308e-3 https://gnomad.broadinstitute.org/variant/1-70881670-C-T

    1. AC013 II-1

      CaseAC013_II-1: Female, 7 yrs report, Turkey

      CasePresentingHPOs: HP:0001992, HP:0001249, HP:0004322, HP:0001513, HP:0030838 (Organic aciduria, Intellectual disability, Short stature, Obesity, Hip pain)

      HPOsFreeText: BMI 93rd percentile

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are consanguineous, Proband is asserted homozygous for this variant

      CasePreviousTesting: Identified by the assessment of urinary organic acids by gas chromatography–mass spectrometry; Accumulation of N-acetylated amino acids was much less pronounced than in previously reported patients; Metabolic studies were initiated after the patient complained of pain in her left hip

      CaseGenotypingMethod: Genomic DNA was extracted either from peripheral blood or EBV-transformed lymphocytes. PCR-amplification and bidirectional sequencing of all exons and exon-intron boundaries of ACY1 was performed.

      Variant: NM_000666.3(ACY1):c.1133G>A (p.Arg378Gln)

      ClinVar: 809490, https://www.ncbi.nlm.nih.gov/clinvar/variation/809490/

      gnomAD: 0.003104, https://gnomad.broadinstitute.org/variant/3-52022997-G-A

    1. 6

      Patient6: Male, 8yo

      CasePresentingHPOs: HP:0002572 (episodic vomiting)

      HPOsFreeText: chronic intermittent IVA, 3 monthly attacks of cyclic vomiting, treated with IVA special formula, elevated isovalerylglycine, C5-carnitine = 9.06 µmol/l

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: symptom onset at 6mo, diagnosis at 72mo via clinical presentation, consanguineous family

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_002225.3(IVD):c.465+2T>C

      ClinVar: 94055, https://www.ncbi.nlm.nih.gov/clinvar/variation/94055/

      gnomAD: 0.00001991, https://gnomad.broadinstitute.org/variant/15-40702998-T-C

      Variant2: NC_000015.9:g.40699940T>C (NM_002225.4(IVD):c.234+14C=)

      CAID: CA147572, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NC_000015.9%3Ag.40699940T%3EC

      ClinVar: 94053, https://www.ncbi.nlm.nih.gov/clinvar/variation/94053/

      gnomAD: 0.6830, https://gnomad.broadinstitute.org/variant/15-40699940-T-C

    1. 7

      CasePU7: Female, 8 months report, White

      CasePresentingHPOs: HP:0012120, HP:0003193, HP:0004322, HP:0000964 (Methylmalonic aciduria, Allergic rhinitis, Short stature, Eczema)

      HPOsFreeText: Malonic aciduria

      CaseNotHPOs: HP:0003353 (Propionyl-CoA carboxylase deficiency)

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband cannot be confirmed in-trans due to lack of parental testing

      CasePreviousTesting: 6.3 propionate incorporation (nmol/mg protein/18 h); Plasma homocysteine and plasma amino acid levels were within the reference range; MMA levels responded partially to cobalamin treatment

      CaseGenotypingMethod: Genomic DNA was extracted from fibroblasts. Next-generation sequencing was performed with 24 genes being sequenced including all coding exons and 20 bp of their flanking intronic regions.

      CasePMIDs: PMID:30740739 as Case 5

      Variant1: NM_001243279.3:c.1239+2T>G

      CAID: CA397142431, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397142431

      gnomAD: Not in gnomAD

      Variant2: NM_001243279.3(ACSF3):c.1672C>T (p.Arg558Trp)

      ClinVar: 31134, https://www.ncbi.nlm.nih.gov/clinvar/variation/31134/

      gnomAD: 0.004790, https://gnomad.broadinstitute.org/variant/16-89220556-C-T

    1. 39, 40

      Case39 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 16(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 77(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.764C>T (p.Ser255Leu), compound heterozygous

      ClinVar 1. 2083, 2. 374435

      gnomAD 1. MAF= 0.0004013(African), no homozygotes, 2. MAF= 0.00005437(East Asian), no homozygotes

      CaseAddInfo Sibling (Case 40) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 10mmol/mol creatinine and 3-OH-glutarate was 31mmol/mol creatinine.

      CasePMIDs see notes on previous studies

    2. 30

      Case30 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 25(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 571(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 1. Patient tested negative in glutarylcarnitine blood spot test, even under carnitine supplementation.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

      ClinVar 1. 2088, 2. 2085

      gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    3. 22

      Case22 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 1028(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 291(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing.

      Variant NM_000159.3:c.541G>A(p.Glu181Lys), homozygous

      ClinVar n/a

      CAID CA404318015

      gnomAD not in gnomAD

      CaseAddInfo n/a

      CasePMIDs see note on previous studies

    4. 36

      Case36 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 24(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 221(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 22. Patient tested negative in glutarylcarnitine blood spot test, even under carnitine supplementation.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. Likewise, the R227P variant creates a NlaIV site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.680G>C (p.Arg227Pro), compound heterozygous

      ClinVar 1. 2088, 2. 2089

      gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0003566(European(non-Finnish)), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    5. 12

      Case12 sex unknown, Spain

      CasePresentingHPOs HP:0002540, HP:0001344, HP:0001332

      (Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 8188(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 3573(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. Likewise, the R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

      ClinVar 1. 2083, 2. 2085

      gnomAD 1. MAF=0.0004013(African), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    6. 19

      Case19 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 8955(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 2262(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R372K variant destroys an MnlI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant 1. NM_000159.3(GCDH):c.1115G>A (p.Arg372Lys), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

      ClinVar 1. 557606, 2. 370106

      gnomAD 1. not in gnomAD, 2. MAF= 0.00005646(Latino), no homozygotes

      CaseAddInfo n/a

      CasePMIDs see note on previous studies

    7. 8

      Case8 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 1098(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 148(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 6.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.268G>A (p.Glu90Lys), compound heterozygous

      ClinVar 1. 2083, 2. 459949

      gnomAD 1. MAF=0.0004013(African), no homozygotes, 2. MAF= 0.00008011(African), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    1. c G

      Case17 4yo diagnosis, Anglo-Celtic

      CasePresentingHPOs HP:0001083

      (Lens dislocation)

      HPOsFreeText Diagnosis was based on dislocated lenses. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient was not responsive to the treatment, plasma homocysteine levels went unchanged. This patient was given additional oral betaine(3g twice per day) with a low protein diet.

      CaseNotHPOs HP:0001249

      (Intellectual disability)

      NotHPOsFreeText no other sequelae

      CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      Variant NM_000071.2(CBS):c.919G>A (p.Gly307Ser), homozygous

      ClinVar 117

      gnomAD MAF= 0.00041539(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    2. 29

      Case29 Male, 1yo diagnosis (Family 25)

      CasePresentingHPOs HP:0001256, HP:0001263

      (Mild intellectual disability, Developmental delay)

      HPOsFreeText Diagnosed was on the basis of developmental delay. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet.

      CaseNotHPOs n/a

      NotHPOsFreeText no other sequelae

      CasePreviousTesting n/a

      Variant 1. NM_000071.2(CBS):c.536_553del18 (p.Asp179_Leu184del), 2. NM_000071.2(CBS):c.325T>C (p.Cys109Arg), comp het

      ClinVar 1. 198388, 2. 212878

      gnomAD 1. MAF=0.00002683(European(non-Finnish), no homozygotes, 2. MAF= 0.0001631(Other), no homozygotes

      CaseAddInfo son of patient 30

      CasePMIDs n/a

    3. lo-

      Case25 9yo diagnosis, Australia, Anglo-Celtic

      CasePresentingHPOs HP:0001083, HP:0002342, HP:0000939, HP:0001263, HP:0001369

      (Lens dislocation, Moderate intellectual disability, Osteoporosis, Developmental delay, Arthritis)

      HPOsFreeText Patient had severe osteoporosis, juvenile arthritis and was diagnosed on the basis of dislocated lenses and developmental delay. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided. (PMID:9156316): Total homocysteine was 252μmol/l before and 34μmol/l after treatment of betaine, folic acid, and low-dose aspirin.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS. (PMID: 9156316): Restriction analysis confirmed the presence of two variants. The variant c.430G>A destroys a TaqI site. Thus, TaqI digestion yielded uncleaved 155bp fragments in both the proband and his father, while the WT was cleaved into 107 and 48bp fragments. The c.1316G>A variant likewise destroys a HapII site. The proband and his father had uncleaved 120bp fragments while the WT had 87 and 33bp fragments on HapII digestion. As both variants were detected in the proband, father, and two paternal aunts, c.1316G>A and c.430G>A were proposed to be in cis.

      Variant 1. NM_000071.2:c.892dup (p.Gln298ProfsTer?), 2. NM_000071.2(CBS):c.430G>A (p.Glu144Lys); 3. NM_000071.2(CBS):c.1316G>A (p.Arg439Gln), comp het, 2&3 in cis

      ClinVar 1. n/a, 2. 122; 3. 189088

      CAID 1. register

      gnomAD 1. MAF=0.00001777(European(Non-finnish)), no homozygotes 2. MAF=0.00009799(South Asian), no homozygotes, 3. MAF=0.00005341(African), no homozygotes

      CaseAddInfo n/a

      CasePMIDs 9156316

    4. Celt

      Case15 3yo diagnosis, Anglo-Celtic

      CasePresentingHPOs HP:0001083, HP:0001256

      (Lens dislocation, Mild intellectual disability)

      HPOsFreeText Diagnosis was based on dislocated lens and intellectual disability. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient was not responsive to the treatment, plasma homocysteine levels went unchanged. This patient was given additional oral betaine(3g twice per day) with a low protein diet.

      CaseNotHPOs n/a

      NotHPOsFreeText no other sequelae

      CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      Variant NM_000071.2(CBS):c.919G>A (p.Gly307Ser), homozygous

      ClinVar 117

      gnomAD MAF= 0.00041539(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    1. 4

      CaseGM01781: Female, 18 years report, Caucasian, Europe

      CasePresentingHPOs: HP:0003153 (Cystathioninuria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband is a compound heterozygote for these variants, Variants were confirmed in trans by parental testing

      CasePreviousTesting: N/A

      CaseGenotypingMethod: Primers were developed and the CTH exons 1-12 and exon-intron boundaries were PCR amplified and sequenced. All sequence variations were verified by restriction enzyme analysis and/or repeat sequencing.

      Variant1: NM_001902.5:c.200C>T (p.Thr67Ile)

      ClinVar: 2939 https://www.ncbi.nlm.nih.gov/clinvar/variation/2939/

      gnomAD: Ashkenazi Jewish 9.934e-3, Overall 6.308e-3 https://gnomad.broadinstitute.org/variant/1-70881670-C-T

      Variant2: NM_001902.5:c.718C>G (p.Gln240Glu)

      ClinVar: 2940 https://www.ncbi.nlm.nih.gov/clinvar/variation/2940/

      gnomAD: European (Non-Finnish) 1.759e-5, Overall 7.957e-6 https://gnomad.broadinstitute.org/variant/1-70896071-C-G

    1. A 2-year-old boy

      Case: Male, 5 days onset, Iran

      CasePresentingHPOs: HP:0002572, HP:0004923 (Episodic vomiting, Hyperphenylalaninemia)

      HPOsFreeText: Brown eyes

      CaseNotHPOs: HP:0001249, HP:0032807 (Intellectual disability, Neonatal seizure)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are consanguineous first cousins

      CasePreviousTesting: Screened for HPAs by Guthrie test and on special diet

      CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood. PAH gene was screened but no mutations were found. BH4-metabolizing genes were screened via STR markers, with PCBD1 having a homozygous pattern. Direct sequencing revealed a homozygous termination codon extension.

      Variant: NM_000281.4(PCBD1):c.313T>C (p.Ter105Gln)

      ClinVar: 428616, https://www.ncbi.nlm.nih.gov/clinvar/variation/428616/

      gnomAD: 0.00003301, https://gnomad.broadinstitute.org/variant/10-72643709-A-G

    1. Homozygous c.295 C>T in exon 3 (p.Gln99X, precursor protein)

      Case1: Newborn, Indian (consanguineous)

      CasePresentingHPOs:

      HPOFreeText: Identified by NBS with elevated C5-carnitine levels. Asymptomatic up to 3 year follow up. Levels of C5-carnitine decreased with time.

      CaseNotHPOs:

      CasePreviousTesting: Followup C5 carnitine 0.88 nM/ml (ref <0.8). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts.

      CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

      Variant: NM_001609.3(ACADSB):c.295C>T (p.Gln99Ter) (homozygous)

      ClinVar: 281177

      gnomAD: 0.00006537 South Asian

      VariantEvidence: LOF

      CaseAddInfo:

      CasePMIDs:

    1. Case#: Patient 2; English/Dutch/German/French

      CaseHPOs: Clinical details in Weleber et al, 1982, “Gyrate atrophy of the choroid and retina… Birth defects: Original Article Series 18 (6) 219-230. Article has been requested.

      CaseHPOsFreeText: Not responsive to Vitamin B6.

      CaseNotHPOs:

      CasePreviousTesting: OAT activity was nondetectable in the patient’s fibroblasts. Northern analysis detected no OAT mRNA. Western blot analysis of OAT protein in the patient's fibroblasts demonstrated an essentially negligible amount of OAT.

      CaseMethod1: PCR

      CaseMethod2: Sequence analysis

      CaseGenotypingMethod: Truncated 5.0-kbp EcoRI OAT gene fragment in addition to the normal 5.8-kbp fragment on Southern blot analysis (Inana et al., 1988), suggesting heterozygosity for a deletion. Cloning and sequencing of the truncated fragment revealed a deletion of 1,072 base pairs. DGGE and sequence analysis of genomic DNA was carried out to identify the variant on the other allele.

      Variant: Variant 1: A 1,072-bp deletion starting in intron 5, 172 bp upstream of exon 6, and ending in intron 6, 772 bp downstream of exon 6 Variant 2: NM_000274.3(OAT):c.627T>A (p.Tyr209Ter)

      ClinVar: Variant 1: 174; Variant 2: 175

      gnomAD: Variant 1: Not listed (but large deletion may not be picked up) Variant 2: Maximum population minor allele frequency = 0.00004645 (European non-Finnish); no homozygotes in any population.

    1. 4

      Case4: Male, 1y 2m, Chinese

      HPOsFreeText: (at 21 days) 0.77 C4 umol/L, 0.07 C4/C2, 0.86 C4/C3

      NotHPOsFreeText: normal urine isobutyrylglycine

      Case4 (Level 2):


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2:c.286G>A (p.Gly96Ser)

      ClinVar: n/a

      CAID: CA6372895

      gnomAD: 0.001453 (East Asian)

      Variant2: NM_014384.2:c.444G>T (p.Pro148=)

      ClinVar: n/a

      CAID: CA6372946

      gnomAD: 0.0002772 (Other)


      CaseAddInfo: trans heterozygous, inherited one allele from each parent

    2. 1

      Case1: Female, 1y 7m, Chinese

      HPOsFreeText: (at 13 days) C4 1.31 umol/L, C4/C2 0.21, C4/C3 1.96

      NotHPOsFreeText: normal urine isobutyrylglycine

      Case1 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2:c.235C>G (p.Arg79Gly)

      ClinVar: n/a

      CAID: CA6372884

      gnomAD: 0.0002718 (East Asian)


      Variant2: NM_014384.2:c.1000C>T (p.Arg334Cys)

      ClinVar: n/a

      CAID: CA6373194

      gnomAD: 0.0003007 (East Asian)


      CaseAddInfo: trans heterozygous, inherited one allele from each parent

    1. F-15

      CaseF-15 female, 1yo onset, Ethnicity: North Indian, Hindu

      CasePresentingHPOs HP:0006846, HP:0001254, HP:0011968, HP:0002098, HP:0002013, HP:0001942, HP:0001943, HP:0003571

      (Acute encephalopathy, Lethargy, Poor feeding, Respiratory distress, Vomiting, Metabolic acidosis, Hypoglycemia, Propionicacidemia)

      HPOsFreeText Ketones present, acycarnitines 6.2(normal <3.6nmol/mL), died after acute crisis(1yo)

      CaseNotHPOs n/a

      CasePreviousTesting Also screened for variants in PCCA

      Variant NM_000532.4(PCCB):c.493C>T (p.Arg165Trp)

      ClinVar 217894

      gnomAD MAF= 0.00001456(European(non-Finnish), no homozygotes

      CaseAddInfo nonconsanguineous, no abnormality in family history noted

      CasePMIDs n/a

    1. Patient 5

      Case5: Male, 16 yrs report

      CasePresentingHPOs: HP:0012072, HP:0010864, HP:0000734 (Aciduria, Severe intellectual disability, Disinhibition)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo:

      CasePreviousTesting: Patient fibroblasts were analyzed for mutations in SLC25A21 and activities of KATII with no abnormalities; Metabolic work-up at 17 years of age revealed strongly elevated AAA (549 mmol/mol creatinine; ref <14) and KAA

      CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced.

      Variant1: NM_018706.6:c.2185G>A (p.Arg455Gln)

      CAID: CA5407838 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA5407838

      gnomAD: 0.0002538, https://gnomad.broadinstitute.org/variant/10-12139688-G-A

      Variant2: NM_018706.6:c.2329T>C (p.Ser777Pro)

      CAID: CA376014875 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA376014875

      gnomAD: 0.000008948, https://gnomad.broadinstitute.org/variant/10-12159681-T-C

    1. Patient 2

      Case2: male, 9.6 y (evaluation), Italian, Family 1

      CasePresentingHPOs:

      HPOsFreeText: birth weight 3850 g, 5y slightly elevated serum transaminases SGOT 60 U/L, SGPT 52 U/L. elevated alkaline phosphatase 1042 U/L). elevated triglycerides (342 mg/dl). fasting plasma methionine elevated to 426 umol/L. elevated tHcy 13 umol/L, elevated urinary methionine 34 umol/mmol. increased pyruvate excretion.

      CaseNotHPOs:

      NotHPOsFreeText: normal neurological examination and normal somatic growth. normal serum amylase and lipase. hepatic dysfunction.

      CaseAddInfo: proband, first child

      Case (Level 2)


      Variant1: NM_018960.5(GNMT):c.149T>C (p.Leu50Pro)

      ClinVar: 4169

      CAID: CA248600

      gnomAD: 0.0002319 (East Asian)


      Variant2: NM_018960.5(GNMT):c.529C>A (p.His177Asn)

      ClinVar: 4170

      CAID: CA248601

      gnomAD: 0.0006993 (European non-Finnish)


      CaseAddInfo: compound heterozygote, Leu50Pro maternal mutation, His177Asn paternal mutation. The amino acid shifts are one # different than those predicted in the paper (Leu49Pro and His176Asn).

    1. Amale1-year-oldC

      Case: Citron-1/ BIODEF 270, male, 4 days

      CasePresentingHPOs: HP:0008297

      HyperPhe was noted, with a plasma Phe level of 700uM. Normal neopterin and biopterin levels were observed in the urine, but the presence of primapterin was found.

      CaseNOTHPOs:

      CasePreviousTesting: n/a

      CaseGenotypingMethod: PCR of exons 2-4 of PCBD1 followed by direct sequencing of the products.

      Variant 1: NM_000281.3(PCBD1):c.259G>T (p.Glu87Ter)

      ClinVar ID 1: 16795

      Variant 2: NM_000281.3(PCBD1):c.244T>C (p.Cys82Arg)

      ClinVar ID 2: 16796

      Compound heterozygous

      gnomAD 1: MAF (Ash-Jews)= 1.183E-3, all hets no homozygous.

      gnomAD 2: MAF (Euro-NF)= 2.690E-5 all hets, no homozygous noted. http://gnomad.broadinstitute.org/variant/10-72643778-A-G

      AddCaseInfo: Parents were tested and found to have normal Phe levels. The father carriers the termination variant, E87X, the mother harbors the C82R, and both parents are heterozygous for their respective PCBD1 variants.

      VariantEvidence:  For the Glu87Ter variant, Thony et al., PMID: 9585615 showed that the mutant E86X/E87X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mutant E86X/E87X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some enzyme activity in vitro. Interestingly, when more E86X/E87X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was similar to wildtype levels (text only, no figures to compare).

      For the C82R/C81R variant was analyzed by Ayling et al., 2000 (PMID:10924272) and was found to still be retained in the soluble fraction in bacteria expressing the recombinant protein. Furthermore, enzyme assays show that the soluble C82RPCBD1 variant retained activity, albeit at 40% of the wildtype.

    1. HIBCHD patient

      Case1: Female, Anglo-Celtic, Birth onset

      CasePresentingHPOs: HP:0001511, HP:0008872, HP:0025404, HP:0000737, HP:0010845, HP:0001263, HP:0001290, HP:0002059, HP:0012448, HP:0002079, HP:0002474, HP:0002421 (Intrauterine growth retardation, Feeding difficulties in infancy, Abnormal visual fixation, Irritability, EEG with genaralized slow activity, Developmental delay, Hypotonia, Cerebral atrophy, Delayed myelination, Thinning of the corpus callosum, Communication delay, Poor head control)

      HPOsFreeText: Birth weight was 2160 g, Inability to follow with eyes at four months, EEG showed poorly modulated background, MRI showed markedly increased signals in the brain stem, upper pons, basal ganglia and thalami, Inability to sit unsupported

      CaseNotHPOs: HP:0001250, HP:0001946 (Seizures, Ketosis)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents were not consanguineous, parental testing confirms in trans

      CasePreviousTesting: Routine metabolic investigations at 4 months (plasma and CSF amino acids, urine amino and organic acids, transferrin isoforms, very long chain fatty acids) were uninformative, Increased excretion of SCPC, Increased levels of urine metabolites derived from methacrylate such as S-(2-carboxypropyl)cysteine (18,27 μmol/mmol of creatinine; reference <5.3), N-acetyl-S-(2-carboxypropyl)cysteine (30,42 μmol/mmol of creatinine; reference <4.2), S-(2-carboxypropyl)cysteine carnitine ester (5.8,5.3 μmol/mmol of creatinine; reference <1.0), and S-(2-carboxypropyl)cysteamine (13,16 μmol/mmol of creatinine; reference <10), Increased erythro-2,3-dihydroxy-2-methylbutyrate compared to controls, The coding region of the E1α gene was sequenced and was found normal

      CaseGenotypingMethod: The HIBCH gene was sequenced after the metabolite testing. Other details were not described.

      Variant1: NM_014362.4(HIBCH):c.1033G>A (p.Gly345Ser)

      ClinVar: 208532 https://www.ncbi.nlm.nih.gov/clinvar/variation/208532/

      gnomAD: European (Non-Finnish) 8.805e-6, Overall 3.982e-6 https://gnomad.broadinstitute.org/variant/2-191073618-C-T

      Variant2: NM_014362.4(HIBCH):c.129dup (p.Gly44Argfs*20)

      ClinVar: 208531 https://www.ncbi.nlm.nih.gov/clinvar/variation/208531/

      gnomAD: South Asian 9.834e-5, Overall 1.597e-5 https://gnomad.broadinstitute.org/variant/2-191161628-C-CT

    1. r

      CaseST-7: Male, 1 day onset, Italy

      CasePresentingHPOs: HP:0006579, HP:0001508, HP:0003215, HP:0000825, HP:0003256, HP:0006254, HP:0008947, HP:0006580, HP:0011968, HP:0002572, HP:0001251 (Prolonged neonatal jaundice, Failure to thrive, Dicarboxylic aciduria, Hyperinsulinemic hypoglycemia, Coagulopathy, Elevated alpha-fetoprotein, Infantile muscular hypotonia, Portal fibrosis, Feeding difficulties, Episodic vomiting, Ataxia)

      HPOsFreeText: Small gallbladder stone

      CaseNotHPOs: HP:0001250 (Seizure)

      NotHPOsFreeText: N/A

      CaseAddInfo: Family is consanguineous, Proband is homozygous for the variant

      CasePreviousTesting: See Group

      CaseGenotypingMethod: See Group

      Variant: NM_001123.3:c.199C>T (p.Gln67Ter)

      CAID: CA5563907, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA5563907

      gnomAD: 0.000008818, https://gnomad.broadinstitute.org/variant/10-76074480-C-T

    1. HCU-101-3

      Case# HCU-101-3, 10yo report, Iran, Sistani

      CasePresentingHPOs HP:0001249, HP:0001083, HP:0002970, HP:0001634, HP:0003235, HP:0000924

      (Intellectual disability, Ectopia lentis, Genu varum, Mitral valve prolapse, Increased methionine in blood, Skeletal abnormality)

      HPOsFreeText skeletal abnormality/elongated long bones, elevated, elevated plasma homocysteine, elevated urinary cysteine, elevated plasma methionine

      CaseNotHPOs HP:0001010, HP:0000501

      (Hypopigmentation, Glaucoma)

      NotHPOsFreeText n/a

      CasePreviousTesting Plasma homocysteine 330μm/l(upper normal limit 15μm/l), plasma methionine 142μm/l(normal range 6-40μm/l)

      CaseMethod1 Sanger

      CaseMethod2 n/a

      CaseGenotypingMethod Sanger sequenced exon 3 of the CBS gene

      Variant NM_000071.2(CBS):c.346G>A (p.Gly116Arg), homozygous

      ClinVar 188787

      gnomAD MAF=0.00002892(Latino), no homozygotes

      CaseAddInfo from the province of Sistan and Baluchestan. no known consanguinity although the patient is homozygous for a founder variant

      CasePMIDs n/a

    1. Patient 1

      CaseIV-2: Female, 4 months onset, Lebanese

      CasePresentingHPOs: HP:0002463, HP:0002376, HP:0001332, HP:0002510, HP:0002522, HP:0000648, HP:0011471, HP:0011968, HP:0001508, HP:0002453, HP:0007374, HP:0002518, HP:0007042, HP:0011931, HP:0012751, HP:0200147, HP:0000252, HP:0001141, HP:0000486, HP:0002300, HP:0002421, HP:0002540, HP:0008936, HP:0002509, HP:0040288, HP:0002650, HP:0002828, HP:0002827, HP:0010465, (Language impairment, Developmental regression, Dystonia, Spastic quadriplegia, Areflexia of lower limbs, Optic atrophy, Gastrostomy tube feeding in infancy, Poor feeding, Failure to thrive, Abnormality of the globus pallidus, Atrophy/Degeneration involving the caudate nucleus, Abnormality of the periventricular white matter, Focal white matter lesion, Abnormality of the cerebellar peduncle, Abnormal basal ganglia MRI signal intensity, Neuronal loss in basal ganglia, Microcephaly, Severe visual impairment, Strabismus, Mutism, Poor head control, Inability to walk, Truncal hypotonia, Limb hypertonia, Nasogastric tube feeding, Scoliosis, Multiple joint contractures, Hip dislocation, Precocious puberty in females,

      HPOsFreeText: Normal early developmental milestones, Not able to bear weight, Unable to fix or follow, Intermittent roving eye movement,

      CaseNotHPOs: HP:0000240, HP:0001999, HP:0025336, (Abnormality of head circumference, Dysmorphic facies, Delayed ability to sit,

      NotHPOsFreeText:

      CaseAddInfo: Parents are consanguinous (first cousins),

      CasePreviousTesting: Elevated hydroxy-C4-carnitine at 0.88 μM for patient 1 (control < 0.3 μM).

      CaseGenotypingMethod: Whole exome sequencing was performed on the proband's sibling, with all SNVs and variants detected called, investigated, and filtered for pathogenicity. Mitochondrial DNA mutation tests were negative, as well as a southern blot for deletions in the muscle. Sanger sequencing of SURF1, SCO1, SCO2, COX10, NDUFV1, NDUFS7, and PANK2 revealed no pathogenic mutation. The WES identified a homozygous variant in HIBCH that was orthogonally validated. PCR-based Sanger sequencing was performed on the proband and the parents to confirm the presence of the mutations and recessive inheritance.

      Variant: NM_014362.3:c.196C>T (p.Arg66Trp)

      ClinVar: 190268 https://www.ncbi.nlm.nih.gov/clinvar/variation/190268/

      gnomAD: Latino 2.892e-5, Overall 1.193e-5 https://gnomad.broadinstitute.org/variant/2-191161562-G-A

    1. 2.1.3. Patient 3

      Case#: Patient 3, M, 6 days (onset), Tunisia

      CasePresentingHPOs: HP:0100022, HP:0011968, HP:0000737, HP:0001250, HP:0001257, HP:0001254, HP:0001993, HP:0012088

      CasePreviousTesting: Clinical diagnosis of classic MSUD due to elevated levels of plasma BCAAs and presence of L-alloisoleucine.

      CaseMethod1: PCR

      CaseMethod2: Direct sequencing

      CaseGenotypingMethod: Entire coding regions and flanking intronic regions of BCKDHA, BCKDHB and DBT amplified from genomic DNA and sequenced.

      Variant: NM_001918.3:c.1333_1336delAATG (homozygous)

      CAID: CA658820833

      gnomAD: Not in gnomAD

      VariantEvidence: NMD unlikely. The truncated protein, however, is likely unable to self-assemble (several copies of E2 form the core of the BCKD complex).

      CaseAddInfo: Consanguineous parents.

    1. OA-20

      Case#: OA-20, F, 10 months (report), Indian

      CasePresentingHPOs: Classic form of MSUD.

      CasePreviousTesting: Initially diagnosed with MSUD based on clinical features and biochemical tests (urine screening by DNPH and thin layer chromatography for amino acids). Confirmed diagnosis by blood amino acid quantification using HPLC.

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Genomic DNA extracted from peripheral blood leukocytes. PCR of exonic and flanking intronic regions of BCKDHA, BCKDHB, and DBT.

      Variant: 1. NM_001918.3:c.827T>C (p.Phe276Cys); 2. NM_001918.3:c.190G>A (p.Val64Ile).

      ClinVar: 1. 11943

      CAID: CA341345584

      gnomAD: 1. European (Non-Finnish) 0.0002210, Overall 0.0001154; 2. Not in gnomAD

      VariantEvidence: p.Phe276Cys results in an enzyme activity of the DBT protein similar to wild type (PMID: 2914958, 1847055).

      CaseAddInfo: Unsure if the variants are in trans.

    1. We evaluated 16 patients with IVA, including 3 pairs of siblings

      Patient10: Female, 11yo, sibling to patient 11

      CasePresentingHPOs:

      HPOsFreeText: intermittent isovaleric acidemia, C5 (DBS) = 15.7 μmol l−1, IVA incorp (%) = 7, IVG in urine mmol permol creatinine = 4376, pH = 7.35, Protein intake (g kg−1 per day) = 0.64, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 85

      CaseNotHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

      (poor feeding, vomiting, dehydration, lethargy, coma)

      NotHPOsFreeText: sweaty feet odor

      CaseAddInfo: diagnosed via family evaluation at 2 days old

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_002225.3(IVD):c.884T>C (p.Leu295Pro)

      ClinVar: 555464, https://www.ncbi.nlm.nih.gov/clinvar/variation/555464/

      gnomAD: n/a

      Variant2: NM_002225.3:c.1211A>G

      CAID: CA391724518, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391724518

      gnomAD: n/a

    2. We evaluated 16 patients with IVA, including 3 pairs of siblings

      Patient6: Female, 4yo

      CasePresentingHPOs:

      HPOsFreeText: Asymptomatic, C5 (DBS) = 3.1 μmol l−1, IVG in urine mmol permol creatinine = 230, Ammonium (μmol l−1) = 56, pH = 7.37, Protein intake (g kg−1 per day) = 1.5, PDI/IQ in follow-up = 104

      CaseNotHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

      (poor feeding, vomiting, dehydration, lethargy, coma)

      NotHPOsFreeText: sweaty feet odor

      CaseAddInfo: diagnosed with NBS at 10 days old

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_002225.3:c.158G>A listed in ClinVar as: NM_002225.4(IVD):c.149G>A (p.Arg50His)

      CAID: CA7480513, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA7480513

      ClinVar: 370843, https://www.ncbi.nlm.nih.gov/clinvar/variation/370843/

      gnomAD: 0.00002784, http://gnomad.broadinstitute.org/variant/15-40699841-G-A

      Variant2: NM_002225.3(IVD):c.941C>T (p.Ala314Val)

      ClinVar: 100060, https://www.ncbi.nlm.nih.gov/clinvar/variation/100060/

      gnomAD: 0.0006507, http://gnomad.broadinstitute.org/variant/15-40707653-C-T

    1. Case 1

      Case1: male, German, 4 days (onset)

      CasePresentingHPOs:

      HPOFreeText: Neonatal screening suggestive of MBD deficiency. Treatment since 9 months with 90 mg L-carnitine per kg body weight. Normal at 6 years old.

      CaseNotHPOs:

      CasePreviousTesting: Day 4: elevated C5 acylcarnitine (0.57 umol/l, ref <0.31) confirmed by 3 of 4 subsequent tests of DBS. Urinary organic acids showed normal N-isovalerylglycine but increased N-methylbutyrylglycine.

      CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced.

      Variant: NM_001609.3(ACADSB):c.38G>A (p.Arg13Lys) (homozygous)

      ClinVar: 299068

      gnomAD: European (Finnish): 0.4494; 1546 homozygotes

      VariantEvidence: High frequency, listed as benign in ClinVar.

      CaseAddInfo:

      CasePMIDs:

    1. 13

      Case#: Patient 13, 3 days (onset), China

      CasePresentingHPOs: HP:0012758, HP:0008344

      HPOsFreeText: Thiamine-responsive form of MSUD.

      CasePreviousTesting: Diagnosed based on elevated blood levels of leucine, valine and the ratio of leucine to phenylalanine (tandem mass spec), as well as abnormal urine BCKAs (gas phase chromatography-mass spec). . CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Genomic DNA from peripheral blood leukocytes from patients and parents extracted. PCR amplification of exons and intron/exon boundaries for BCKDHA, BCKDHB, DBT.

      Variant: 1. NM_001918.3(DBT):c.51+5G>C

      ClinVar: 1. 94004

      CAID: 2. CA658820834

      gnomAD: 1. East Asian 6.165e-4, overall 3.229e-5 ; 2. Not in gnomAD

      VariantEvidence: Predicted LOF

      CaseAddInfo: Parents tested.

    1. EG1291

      CaseEG1291: Female, 5 days onset

      CasePresentingHPOs: HP:0200134, HP:0012469, HP:0032794, HP:0032667, HP:0002187, HP:0032792, HP:0002069, HP:0007359, HP:0010841, HP:0002188, HP:0006913, HP:0002079, HP:0001290 (Epileptic encephalopathy, Infantile spasms, Myoclonic seizure, Myoclonic status epilepticus, Profound intellectual disability, Tonic seizure, Bilateral tonic-clonic seizure, Focal-onset seizure, Multifocal epileptiform discharges, Delayed CNS myelination, Frontal cortical atrophy, Hypoplasia of the corpus callosum, Generalized hypotonia)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0002521 (Hypsarrhythmia)

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband confirmed de novo heterozygous by parental sequencing; Father had two seizures as an adult, no further seizures while on LTG

      CasePreviousTesting: Currently on levitiracetam and valproate; previously on pyridoxine, prednisolone, vigabatrin, zonisamide and ketogenic diet

      CaseGenotypingMethod: About 10% of the original 290 genes where a single de novo variant had been identified was chosen for targeted sequencing in a new cohort. Most of these individuals had been tested for mutations of known and novel candidate genes as well as pathogenic copy-number variants. These genes were sequenced in the parents and proband to look for de novo variants.

      Variant: NM_004171.4(SLC1A2):c.244G>C (p.Gly82Arg)

      ClinVar: 254265, https://www.ncbi.nlm.nih.gov/clinvar/variation/254265/

      gnomAD: Not in gnomAD

    1. Table 2

      Case8: Female, South America

      CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001627 (Cardiac abnormality)

      NotHPOsFreeText: N/A

      CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period

      CasePreviousTesting: N/A

      CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

      Variant1: NM_198271.4:c.723_733del (p.Asp242Glufs*4)

      CAID: CA2488932 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.723_733del

      gnomAD: Latino 2.896e-4, Overall 4.416e-5 https://gnomad.broadinstitute.org/variant/3-69168772-AAGCTCCCATCC-A

      Variant2: NM_198271.4:c.976G>C (p.Gly326Arg)

      CAID: CA353473660 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.976G%3EC

      gnomAD: Not in gnomAD

    2. Table 2

      Case9: Female, Italy

      CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798, HP:0001561, HP:0001558, HP:0000602, HP:0001622, HP:0001371 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies, Polyhydramnios, Decreased fetal movements, Ophthalmoplegia, Preterm delivery, Contractures)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001627 (Cardiac abnormality)

      NotHPOsFreeText: N/A

      CaseAddInfo: Severe congenital myopathy, Deceased in 4 months

      CasePreviousTesting: N/A

      CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

      Variant: NM_198271.4:c.860delT (p.Phe287Serfs*3)

      CAID: CA913203455 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203455

      gnomAD: Not in gnomAD

    1. (OS-152II-1)

      CaseOS-152_II-1: Female, 1 yr report, United Kingdom

      CasePresentingHPOs: HP:0001992, HP:0002013, HP:0002013, HP:0040293, HP:0010628, HP:0007359 (Organic aciduria, Vomiting, Bilateral tonic-clonic seizure, Right hemiplegia, Facial palsy, Focal-onset seizure)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001263 (Global developmental delay)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous, Proband is confirmed compound heterozygous for these variants via parental testing, R353C variant inherited from father but R393H supposedly de novo or mosaic

      CasePreviousTesting: Routine urine screening for organic acidurias by gas chromatography–mass spectrometry showed markedly increased urinary excretion of several N-acetylated amino acids; Normal cranial imaging

      CaseGenotypingMethod: PCR-amplification and bidirectional sequencing of all exons and exon-intron boundaries was performed on genomic DNA.

      Variant1: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

      ClinVar: 18110 https://www.ncbi.nlm.nih.gov/clinvar/variation/18110/

      gnomAD: 0.004135 (4 homozygotes), https://gnomad.broadinstitute.org/variant/3-52022837-C-T

      Variant2: NM_000666.3(ACY1):c.1178G>A (p.Arg393His)

      ClinVar: 18114 https://www.ncbi.nlm.nih.gov/clinvar/variation/18114/

      gnomAD: 0.006571 (3 homozygotes), https://gnomad.broadinstitute.org/variant/3-52023042-G-A

    1. English family described in 1956

      FamilyHA: White, Great Britian

      FamilyPresentingHPOs: HP:0000988, HP:0002344, HP:0002359, HP:0002355, HP:0007210, HP:0000712, HP:0002066, HP:0000639, HP:0001347, HP:0008353 (Skin rash, Progressive neurologic deterioration, Frequent falls, Difficulty walking, Lower limb amyotrophy, Emotional lability, Gait ataxia, Nystagmus, Hyperreflexia, Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      FamilyNotHPOs: N/A

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Homozygosity mapping and fine mapping in ten members of two consanguineous families (the siblings in whom Hartnup disorder was originally discovered; family A) and in siblings from the US revealed linkage of Hartnup disorder to 5p15 only in family A, with a maximum combined multipoint lod score of 2.31 at 11.24 cM. This confirmed a previous study showing linkage to the same region. Both SLC6A18 and SLC6A19 were investigated for possible pathogenicity, with SLC6A19's pattern of expression supporting it as a primary candidate. Intronic primers were used to bidirectionally sequence each exon and flanking intronic regions, locating a homozygous splice site mutation that perfectly segregated with the phenotype.

      FamilyPreviousTesting: Consistent testing showed the consistent phenotypes were the hyperaminoaciduria among all family members; Linkage analysis for SLC3A2, SLC7A8, SLC1A5, SLC6A18, and SLC6A20 were all negative for amy correlation

      FamilyAddInfo:

      FamilyProband: Case EHAA

      FamilyPMIDs: 13358233

      Variant: NM_001003841.3(SLC6A19):c.1173+2T>G

      ClinVar: 449553 https://www.ncbi.nlm.nih.gov/clinvar/variation/449553/

      gnomAD: 0.00008019, https://gnomad.broadinstitute.org/variant/5-1217062-T-C?dataset=gnomad_r2_1

      Affected: 4

      Unaffected: 5

      pLOD: 2.31 at 11.24 cM

      AddSegregationInfo: Family is consanguineous (first cousins), Candidate gene sequencing, Pedigree in Figure 1aA

    1. 5

      Case5 Female, 6yo diagnosis, Korean

      CasePresentingHPOs HP:0001083, HP:0003235

      (Ectopia lentis, Increased blood methionine)

      HPOsFreeText pretreatment homocysteine was normal, increased post-treatment total homocysteine, patient treated with low-methionine diet, vitamin B6, folate, vitamin B12, and betaine after diagnosis

      CaseNotHPOs HP:0001249

      (Intellectual disability)

      NotHPOsFreeText Marfan syndrome, vascular occlusion

      CasePreviousTesting pretreatment/posttreatment methionine: 697/648 μM(nv 7-47), pretreatment homocysteine: 3 μM(nv 0-5), posttreatment total homocysteine 121 μM(nv 5-15)

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified all 16 coding exons of CBS gene, then direct sequenced

      Variant 1. NM_001178008.1:c.464C>T(p.Ala155Val), 2. NM_000071.2(CBS):c.1039G>A (p.Gly347Ser), compound heterozygous

      ClinVar 1. n/a, 2. 188801

      CAID 1. CA410601498

      gnomAD 1. not in gnomAD, 2. MAF=0.00006497(European(non-Finnish)), no homozygotes

      CaseAddInfo A155V inherited from father, G347S from mother

      CasePMIDs n/a

    1. 9

      CaseHE9: 6 month onset

      CasePresentingHPOs: HP:0001250, HP:0001943, HP:0001942, HP:0012120 (Seizure, Hypoglycemia, Metabolic acidosis, Methylmalonic aciduria)

      HPOsFreeText: Elevated proionyl-carnitine and methyl-citrate in urine

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband is homozygous for this variant,

      CasePreviousTesting: Fibroblast cell lines taken from 150 patients with mild but clear MMAuria were studied; Urinary MMA at 143–184 mmol/mol creat. (ref 0.3-1.1); Low propionate incorporation in fibroblasts both +/- OHCbl of 3.0 nmol/16 h/mg (ref 3.5–24.4 −OHCbl, 4.3–28.9 +OHCbl); Not responsive to Vitamin B12 treatment

      CaseGenotypingMethod: Genomic DNA and RNA extraction was performed and the MCEE gene was sequenced to identify any likely pathogenic variants.

      Variant: NM_032601.3:c.158T>G (p.Ile53Arg)

      CAID: CA347189175, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA347189175

      gnomAD: Not in gnomAD

    1. 16392

      Case# 16392, Spanish, 4yo report

      Variant NM_000709.3(BCKDHA):c.659C>T (p.Ala220Val), NM_000709.3(BCKDHA):c.853G>C (p.Ala285Pro)

      ClinVar 93367(c.659), 93375(c.853)

      gnomAD c.659=0.00005805(East Asian), 0.000008156(Overall), c.853=0.00007896(European (Non-Finnish)), 0.00003970(Overall)

      VariantEvidence 4% of normal BCKD activity in patient fibroblasts

      CaseAddInfo in trans

    1. GA8

      Case#: GA8, England, 15 years (onset), gender unknown.

      CaseHPOs: HP:0000662, HP:0012026 (night blindness, (hyperornithinemia)

      CaseHPOsFreeText: Presented with visual disturbances. Vitamin B6 responsive.

      CaseNotHPOs: Neonatal encephalopathy

      CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 728 umol/L (normal <100)

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Sequence analysis of the OAT gene from fibroblast or lymphocyte cDNA and genomic DNA. Variant: NM_000274.3(OAT):c.952G>A (p.Glu318Lys)

      ClinVar: 56138

      gnomAD: The maximum population minor allele frequency in gnomAD is 0.00002328 (European non-Finnish); no homozygotes in any population. VariantEvidence: When the variant was expressed in yeast, OAT enzymatic activity was <10% normal. This variant did not significantly affect protein levels but displayed a marked reduction of the hexamer (the active form) and an accumulation of the monomeric form.

    1. Patient 1

      Patient1: Male, 14 yo, Thai

      CasePresentingHPOs: HP:0011968, HP:0001254, HP:0001250, HP:0001876, HP:0002919, HP:0001942, HP:0001987, HP:0002187, HP:0002300, HP:0002540, HP:0006846, HP:0002901, HP:0001510 (poor feeding, lethargy, seizures, pancytopenia, ketonuria, metabolic acidosis, hyperammonemia, profound mental retardation, inability to speak, inability to walk, acute encephalopathy, hypocalcemia, growth delay)

      HPOsFreeText: acute neonatal IVA, hemoglobin = 10g/dL, WBC = 3370/mm^3, platelets = 27,000/mm^3, bicarbonate = 10mmol/L, anion gap = 36mmol/L, low serum calcium, ammonia = 420µmol/L, treated with total blood exchange, treated with low-protein diet and leucine-free formula (150–250mg/kg per day of l‐glycine, and 100mg/kg per day of l‐carnitine), urine isovalerylglycine = 515

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: non-consanguineous family, symptom onset at 7 days old, diagnosed at 2wks old

      CasePMIDs:

      CasePreviousTesting: urine organic acid analysis with GC/MS (PMID: 27082169)

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Genomic DNA extracted from peripheral blood, IVD coding exons and flanking introns amplified with PCR (primer in table 1), PCR products purified and sequenced with Big Dye Primer Cycle Sequencing Kit and ABI 210 Genetic Analyzer

      Variant1: c.457–3_2CA>GG / no ClinVar or CAID

      Variant2: NM_002225.3:c.1025A>G (p.Tyr342Cys) listed in paper as (p.Tyr371Cys)

      CAID: CA7480839, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_002225.3%3Ac.1025A%3EG

      gnomAD: 0.000003977, https://gnomad.broadinstitute.org/variant/15-40708332-A-G

    1. Family 1

      Case#: Patient 1, male, died on DOL 4, from the Faroe islands

      CaseHPOs: HP:0003811 (neonatal death)

      CaseHPOsFreeText: At 16 hours old, began grunting, was jittery, and had tachypnea. At 48 hours, had increased jitteriness, hypertonia, hypothermia, and alkalosis. Coma and death at 4 days. In urine, undetectable citrulline, argininosuccinate, and orotic acid. Plasma amino acids showed extremely elevated glutamine and alanine suggestive of hyperammonemia. No ammonia levels were available.

      CaseNotHPOs: HP:0003218 (Orotic aciduria)

      CasePreviousTesting: Analysis of urea cycle enzymes on post mortem liver tissue: CPSI activity was 30.7 U (normal >12), basal NAGS activity was 10 U (normal >34), arginine stimulated NAGS activity was 20 U (normal >144).

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Tissue or DNA from the deceased infant of family 1 was unavailable; blood genomic DNA from both parents to search for a mutation in the NAGS gene. All seven exons including intron/exon boundaries of the NAGS gene were amplified and sequenced.

      Variant: NM_153006.2(NAGS):c.971G>A (p.Trp324Ter) (homozygous) (based on parental results; both parents are heterozygous)

      ClinVar: 2428

      gnomAD: Absent

      VariantEvidence: NA

    1. Case#: Pedigree 6 proband, Finland

      CaseHPOs: HP:0012026 (hyperornithinemia)

      CaseHPOsText: Patient noted to be "of historical interest" because he was the first patient in whom hyperornithinemia was recognized in gyrate atrophy (PMID 4122112). At age 8, choroidal degeneration ultimately diagnosed as gyrate atrophy, abnormal ERG; plasma ornithine concentration 10 times normal.

      CaseGenotypingMethod: Variant identified by sequencing of genomic clones of OAT; sequencing of the remainder of the coding region and exon/intron boundaries was normal.

      Variant: NM_000274.3(OAT):c.539G>C (p.Arg180Thr) (homozygous)

      ClinVarID: 153

      gnomAD: Maximum population minor allele frequency = 0.0007166 (Finnish); no homozygotes

      VariantEvidence: When expressed in CHO-K1 cells, the variant results in no detectable OAT activity. Another Finnish patient (out of a group of 16) was also found to be homozygous for this variant.

    1. CaseLE19: Male, 16 yrs report

      CasePresentingHPOs: HP:0000964, HP:0002650, HP:0000501, HP:0000518, HP:0000750, HP:0010862, HP:0002572 (Eczema, Scoliosis, Glaucoma, Cataract, Delayed speech and language development, Delayed fine motor development, Episodic vomiting)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variants not confirmed in-trans due to lack of parental testing

      CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2; Congenital unilateral persistent hyperplastic primary vitreous (PHPV), causing glaucoma and cataract

      CaseGenotypingMethod: See Group

      Variant1: NM_001243279.3(ACSF3):c.1075G>A (p.Glu359Lys)

      ClinVar: 31136, https://www.ncbi.nlm.nih.gov/clinvar/variation/31136/

      gnomAD: 0.001054, https://gnomad.broadinstitute.org/variant/16-89180844-G-A

      Variant2: NM_001243279.3:c.1239+2T>G

      CAID: CA397142431, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397142431

      gnomAD: Not in gnomAD

    1. CaseWG2797: N/A

      CasePresentingHPOs: HP:0012120 (Methylmalonic aciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband is asymptomatic and has an affected sibling with similar aciduria

      CasePreviousTesting: Propionate Incorporation w/o hydroxycobalamin at 3.9 nmols/mg protein/18hr; Propionate Incorporation with hydroxycobalamin at 4.0 nmols/mg protein/18hr; Adenosylcobalamin synthesis percentage at 12.4%; Elevated methylmalonic values of 1400 µmol/mmol creatinine (reference 0.8-5.2 µmol/mmol creatinine)

      CaseGenotypingMethod: Genomic DNA was extracted from patient fibroblasts, sequenced, and the three MCEE/thirteen MUT exons were analyzed and amplified. Any reported mutations were resequenced from fresh PCR product.

      Variant: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)

      ClinVar: 2343, https://www.ncbi.nlm.nih.gov/clinvar/variation/2343/

      gnomAD: 0.0004884, https://gnomad.broadinstitute.org/variant/2-71351575-G-A

    1. Proband II.3

      CaseII-3: Female, Turkey

      CasePresentingHPOs: HP:0001561, HP:0001789, HP:0000494, HP:0000463, HP:0005280, HP:0011829, HP:0000319, HP:0002705, HP:0002033, HP:0006829, (Polyhydramnios, Hydrops fetalis, Downslanted palpebral fissures, Anteverted nares, Depressed nasal bridge, Thin philtrum, Smooth philtrum, High narrow palate, Poor suck, Severe muscular hypotonia,

      HPOsFreeText: Birth weight was 1890 g and length was 42 cm, Absent Moro reflex, Required ventilator support from birth

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Born with fractures of the left humerus and pes equinovarus

      CasePreviousTesting: N/A

      CaseGenotypingMethod: Whole blood smaples were obtained from the parents and the probands and DNA was extracted. WES was performed on II-2, with the results being sequenced and filtered for pathogenicity. Once the LMOD3 variant was detected, PCR amplification and Sanger sequencing was used to amplify exon 1 and confirm the results.

      Variant: NM_198271.4:c.138dup (p.Ser47Glnfs*13)

      ClinVar: 162215 https://www.ncbi.nlm.nih.gov/clinvar/variation/162215/

      gnomAD: European (Non-Finnish) 8.879e-6, Overall 8.049e-6 https://gnomad.broadinstitute.org/variant/3-69171399-T-TG

    1. patients 2

      Case2: 8 days onset

      CasePresentingHPOs:

      HPOFreeText: Identified by after metabolic studies performed for evaluation of clinical disease.

      CaseNotHPOs:

      CasePreviousTesting: DBS C5 carnitine 0.97 umol/L (ref <0.46); plasma alloisoleucine 1.5 umol/L (ref <2.1); urine C5 carnitine 35.8, 80.6 umol/mmol creatine (ref <3.0); urine 2-EHA 116, 132 U (ref <5); urine 2-MBG 20.2, 36.7 (ref <2.3); urine 2-methylbutyric acid conjugates as R-isomer 45%, 43% (ref 43-56%).

      CaseGenotypingMethod: PCR amplification and sequencing of genomic DNA (entire coding region) from patient and available family members.

      Variant: NM_001609.3:c.908G>C (p.Gly303Ala) (homozygous)

      CAID: CA378620840

      gnomAD: European (non-Finnish) 0.00002323

      VariantEvidence:

      CaseAddInfo:

      CasePMIDs:

    2. 3

      Case3: 11 months onset

      CasePresentingHPOs:

      HPOFreeText: Identified by after metabolic studies performed for evaluation of clinical disease.

      CaseNotHPOs:

      CasePreviousTesting: DBS C5 carnitine 1.75 umol/L (ref <0.46); urine C5 carnitine 2.7 umol/mmol creatine (ref <3.0); urine 2-EHA 32, 8, 15 U (ref <5); urine 2-MBG 14.5 umol/mmol creatine (ref <2.3); urine 2-methylbutyric acid conjugates as R-isomer 46%, (ref 43-56%).

      CaseGenotypingMethod: PCR amplification and sequencing of genomic DNA (entire coding region) from patient and available family members.

      Variant: NM_001609.3:c.443C>T (p.Thr148Ile) (homozygous)

      ClinVar: 9202

      gnomAD: South Asian 0.002678

      VariantEvidence: Decreases ACADSB enzymatic activity to 2.8% of wild type in vitro (PMID: 20547083).

      CaseAddInfo:

      CasePMIDs:

    3. 4

      Case4: 6 years onset

      CasePresentingHPOs:

      HPOFreeText: Identified by after metabolic studies performed for evaluation of clinical disease.

      CaseNotHPOs:

      CasePreviousTesting: DBS C5 carnitine 0.5, 0.55 umol/L (ref <0.46); urine 2-EHA 152, 19, 43 U (ref <5).

      CaseGenotypingMethod: PCR amplification and sequencing of genomic DNA (entire coding region) from patient and available family members.

      Variant: NM_001609.3:c.1102T>C (p.Ser368Pro) (homozygous)

      CAID: CA5730911

      gnomAD: Ashkenazi Jewish 0.002200; Overall 0.0002488

      VariantEvidence:

      CaseAddInfo:

      CasePMIDs:

    1. 1752

      Case1752 Caucasian

      CasePresentingHPOs HP:0003571 (Propionicacidemia)

      CaseNotHPOs n/a

      CasePreviousTesting none reported

      Variant 1. NM_000532.4(PCCB):c.1218_1231delGGGCATCATCCGGCinsTAGAGCACAGGA (p.Gly407Argfs), 2. NM_000532.4:c.1222del (p.Ile408SerfsTer?)

      ClinVar 1.38875, 2. n/a

      CAID 2. unregistered

      gnomAD 1. not in gnomAD

      CaseAddInfo parents NOT tested, phase unknown

      CasePMIDs n/a

    1. Case 16

      Case16 Female, Finland

      CasePresentingHPOs HP:0003826, HP:0000202, HP:0000347, HP:0001162, HP:0001829, HP:0010066, HP:0000157, HP:0002101, HP:0000238, HP:0007370, HP:0010664, HP:0007260

      (Stillbirth, Oral cleft, Micrognathia, Postaxial hand polydactyly, Foot polydactly, Duplicated hallux, Tongue abnormality, Defective lung lobation, Hydrocephalus, Callosal agenesis, Fused thalami, Type II lissencephaly)

      HPOsFreeText Crown-heel body length 47cm, body weight 2520g, abnormal larynx/trachea, uterus duplex, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus

      CaseNotHPOs HP:0001627

      (Congenital heart defect)

      NotHPOsFreeText Hydranencephaly/anencephaly, true alobar or semilobar holoprosencephaly

      CasePreviousTesting n/a

      Variant NM_145014.2(HYLS1):c.632A>G (p.Asp211Gly), homozygous

      ClinVar 1143

      gnomAD MAF= 0.009594(European(Finnish)), no homozygotes

      CaseAddInfo stillbirth, 34+0wk gestational age

      CasePMIDs n/a

    1. 5

      Case5: Female, 50 yrs report

      CasePresentingHPOs: HP:0002355, HP:0100753, HP:0003089, HP:0003798, HP:0031237, HP:0031318 (Difficulty walking, Schizophrenia, Hamstring contracture, Nemaline bodies, Internally nucleated skeletal muscle fibers, Myofiber disarray)

      HPOsFreeText: Jaw contractures, Pectoral contractures, Ankle dorsiflexor contractures, Quad contractures, Increased oxidative staining

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Daughter of Case 4, Sibling of Case 6

      CasePreviousTesting: N/A

      CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

      Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

      ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

      gnomAD: Not in gnomAD

    1. Faisalabad histiocytosis

      Case: Family 1 Moynihan Proband VII:7, female, Pakistani

      CasePresentingHPOs: HP:0000407, HP:0004322, HP:0000135, HP:0100540, HP:0012385, HP:0002716, HP:0034920, HP:0034677, HP:0034391, HP:0030075, HP:0002862

      CasePresentingHPOsFreeText: Eyelid swellings due to histiocytic deposits, diverse cytoplasmic inclusions in phagocytes and reticulum cells of bone marrow, Lymph node and eyelid show reactive features with small reactive lymphoid follicles and histiocytes within dilated sinuses resembling RDD. invasive ductal carcinoma grade 3 ER negative breast aged 43 years and carcinoma bladder (grade 3 papillary TCC) age 46 years

      CaseNOTHPOs:

      CaseNOTHPOSFreeText:

      CasePreviousTesting: direct sequencing of PRF1 and UNC5B

      CaseGenotypingMethod: autozygosity mapping, genotyping (genome-wide linkage scan was performed using Affymetrix 250k SNP arrays), direct sequencing, PCR

      Variant: c.300+1G>A homozygous

      ClinVarID: or CAID: 130339/CA155238

      gnomAD: This splice site variant in intron 2 is present in gnomAD v4.0.0 at a MAF=0.0002197 (20/91048 alleles) in the South Asian population with 0 homozygotes.

      AddCaseInfo: brother is affected as well

      PreviouslyPublished: PMID: 9545394

      VariantEvidence: n/a

    1. P4

      CaseP4 male, 45yo report, Tunisia

      CasePresentingHPOs HP:0012207, HP:0012865, HP:0012868, HP:0003251

      (reduced sperm motility, sperm head anomaly, sperm tail anomaly, male infertility)

      HPOsFreeText Patient's sperm volume: 2.2mL(lower reference limit: 1.5), sperm concentration: 56million/mL(reference: 15), total motility after 1hr: 0%(reference: 40), vitality: 79%(reference:53%), normal spermatozoa: 0%(reference: 4), abnormal acrosome: 78%, abnormal head morphology: 58%, abnormal base: 14%, absent flagella: 50%, short flagella: 32%, coiled flagella: 34%, flagella of irregular caliber: 50%, multiple anomalies index: 3.4%.

      CaseNotHPOs n/a

      CasePreviousTesting Previously screened all patients for DNAH1, CFAP43, and CFAP44 variants. Somatic karyotypes were normal.

      Variant NM_144668.5:c.3007_3337del

      ClinVar 586974

      gnomAD not in gnomaD

      CaseAddInfo consanguinity

      CasePMIDs 29449551

    2. P3

      CaseP3 male, 51yo report, Tunisia

      CasePresentingHPOs HP:0012207, HP:0012865, HP:0012868, HP:0003251

      (reduced sperm motility, sperm head anomaly, sperm tail anomaly, male infertility)

      HPOsFreeText Patient's sperm volume: 1.7mL(lower reference limit: 1.5), sperm concentration: 56million/mL(reference: 15), total motility after 1hr: 5%(reference: 40), vitality: 73%(reference:53%), normal spermatozoa: 0%(reference: 4), abnormal acrosome: 56%, abnormal head morphology: 20%, abnormal base: 32%, absent flagella: 22%, short flagella: 59%, coiled flagella: 27%, flagella of irregular caliber: 37%, multiple anomalies index: 2.7%.

      CaseNotHPOs n/a

      CasePreviousTesting Previously screened all patients for DNAH1, CFAP43, and CFAP44 variants. Somatic karyotypes were normal.

      Variant NM_144668.5:c.3007_3337del

      ClinVar 586974

      gnomAD not in gnomAD

      CaseAddInfo consanguinity

      CasePMIDs 29449551

    3. P2

      CaseP2 male, 54yo report, Tunisia

      CasePresentingHPOs HP:0012207, HP:0012865, HP:0012868, HP:0003251

      (reduced sperm motility, sperm head anomaly, sperm tail anomaly, male infertility)

      HPOsFreeText Patient's sperm volume: 1.8mL(lower reference limit: 1.5), sperm concentration: 6million/mL(reference: 15), total motility after 1hr: 1%(reference: 40), vitality: 80%(reference:53%), normal spermatozoa: 0%(reference: 4), abnormal acrosome: 56%, abnormal head morphology: 10%, abnormal base: 2%, absent flagella: 6%, short flagella: 32%, coiled flagella: 17%, flagella of irregular caliber: 68%, multiple anomalies index: 2.3%.

      CaseNotHPOs n/a

      CasePreviousTesting Previously screened all patients for DNAH1, CFAP43, and CFAP44 variants. Somatic karyotypes were normal.

      Variant NM_144668.5:c.3007_3337del

      ClinVar 586974

      gnomAD n/a

      CaseAddInfo consanguinity

      CasePMIDs 29449551

    1. II-9

      Case#: II-9, male, Asian, 38 yr, proband

      DiseaseAssertion: HCM, LQT1

      FamilyInfo: HCM passed on in family (figure 1)

      CasePresentingHPOs: HP:0001279, HP:0001712, HP:0001639 (Syncope, Left ventricular hypertrophy, Hypertrophic cardiomyopathy)

      CaseHPOFreeText: physical examination; 12-lead ECG (SR, HR 57 bpm, P 80 ms, PR 164 ms, QRS 102 ms, QTc 423 ms); 2D echocardiographic study with S5-1 probe (MLVWT 14 mm, EF 62%, LVMI 94.27 g/m^2);

      CaseNotHPOs: HP:0030148 (Heart murmurs)

      CaseNotHPOFreeText: No inverted T wave: Normal QTc 440 ms

      CasePreviousTesting: Additional Sanger sequencing for KCNQ1, MKLY2, TMEM70

      CaseGenotypingMethod: Illumina-SolexaHiSeq 2000 sequencing from peripheral blood leococytes; bi-directional Sanger sequencing;

      Variant: absent

      ClinVar: absent

      CAID: CA389036862 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA389036862

      gnomAD: absent

      MultipleGeneVariants:

      (1) KCNQ1 Variant:

      Variant: NM_181798.1(KCNQ1):c.187C>T (p.Arg63Trp)

      ClinVar: 53070 https://www.ncbi.nlm.nih.gov/clinvar/variation/53070/

      CAID: n/a

      gnomAD: absent

      (2) MKLY2 Variant:

      Variant: absent

      ClinVar: absent

      CAID: CA408526793 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA408526793

      gnomAD: African 0.00006453 https://gnomad.broadinstitute.org/variant/20-30412153-A-G

      (3) TMEM70 Variant:

      Variant: NM_017866.6(TMEM70):c.440T>C (p.Ile147Thr)

      ClinVar: 571761 https://www.ncbi.nlm.nih.gov/clinvar/variation/571761/

      CAID: n/a

      gnomAD: East Asian 0.0004893 https://gnomad.broadinstitute.org/variant/8-74893513-T-C

    1. We here add our observation of a similar bi-allelic OPA1 case with Behr syndrome. This proband is a 20-year-old Italian boy, born from unrelated parents (Fig. 1A, IV-4 in the pedigree), who presented a congenital nystagmus at birth and bilateral optic atrophy was recognized in the first year of life. He acquired autonomous walking at 14 months of age, but clumsy gait and frequent falls were reported. Motor difficulties and visual acuity worsened during childhood whereas cognitive development was normal. Brain MRI performed at the age of 4 and 7 years were normal. At 6 years of age, neurological examination showed ataxic-spastic gait with positive Romberg sign. Fundus exam confirmed bilateral optic atrophy (Fig. 1B). Tendon reflexes were brisk at the lower limbs and there was bilateral Babinski sign. The patient also had bilateral talipes equinovarus. Nerve conduction studies showed delayed sensory-motor velocities with reduced amplitudes of motor potentials and loss or severe reduction of sensory action potentials. Somatosensory evoked potentials could not be recorded and motor evoked potentials showed absent potentials at lower limbs and delayed latency at upper limbs. Brainstem evoked potentials were delayed bilaterally. Repeated urine organic acid gas chromatography/mass spectrometry analysis revealed mild elevation of 3-methylglutaconic acid (8–20 μmol/mmol creatinine). At muscle biopsy histology was normal and spectrophotometric assessment of the OXPHOS enzymatic activities was normal in muscle homogenate. Sural nerve biopsy demonstrated a marked reduction of the large-diameter myelinated axons (Fig. 1E–G). Teased fibre analysis disclosed regions of demyelination confined to the paranodal region, clustered in some axons, suggesting secondary demyelination. Ultrastructural examination confirmed the reduction of myelinated axons (not shown). A clinical revaluation at 15 years of age demonstrated elevated serum lactic acid after standardized exercise (3.9 mM, normal range 0.6–2.4mM) and optical coherence tomography revealed a generalized reduction of the retinal fibre layer thickness (Fig. 1D). At neurological examination, the patient was wheelchair bound due to severe sensory ataxia and spastic paraparesis and signs of cerebellar dysfunction, such as dysmetria, dysdiadochokinesia and positive Holmes rebound phenomenon, were evident. His vision was light perception with severe nistagmus in any direction of gaze. This clinical picture remained stable in the subsequent years. Figure 1. Open in a new tab (A) Reconstruction of the paternal and maternal genealogies of the proband with Behr syndrome (IV-4). The maternal side is remarkable for segregating isolated optic neuropathy in a dominant fashion associated with the heterozygous c.1705+1G>T splicing mutation. (B–D) Ophthalmological investigations. The fundus picture of the proband (IV-4) reveals severe optic atrophy with bilateral pale optic disc (B). The fundus picture of the mother (III-4) shows only a mild optic atrophy with temporal pallor of the optic discs bilaterally (C). Optical coherence tomography examination of retinal nerve fibre layer (RNFL) thickness in the proband shows a diffuse reduction of thickness compatible with the severe optic atrophy (D). (E–G) Semithin cross-section of the sural nerve biopsy. A marked depletion of large myelinated axons affects the sural nerve (E and F). At higher magnification some axons appear to have a thin myelin sheath related to the axonal diameter (G). (H–L) Brain MRI and 1HMR spectroscopy studies. On the left (H) the sagittal FSPGR (Fast SPoiled GRadient echo) T1 shows a mild cerebellar atrophy in the proband (IV-4), and on the right (I) a mild pathological accumulation of lactate (rectangle) was detected in the CSF of lateral ventriculi. On the axial FLAIR T2 sequence no signal changes were detected in the proband (IV-4) (J), whereas few focal hyperintensities, related to not specific areas of gliosis, in the cerebral white matter of the proband’s father (III-3) (K) and mother (III-4) (L) were present. TEMP = temporal; SUP = superior; NAS = nasal; INF = inferior; MRI = magnetic resonance imaging; HMR = proton magnetic resonance; CSF = cerebrospinal fluid; FLAIR = Fluid attenuated inversion recovery.The 43-year-old proband’s mother (Fig. 1A, III-4 in the pedigree) had isolated optic atrophy, most evident on the temporal side (Fig. 1C), which segregated as a dominant trait in her family (Fig. 1A). The remaining neurological examination was normal. Nerve conduction velocities and somatosensory evoked potentials were normal. The other affected individuals in this family all suffered a non-syndromic optic atrophy, which started in childhood and progressively worsened, but remained as an isolated symptom. The proband’s father and the elder sister (Fig. 1A, III-3 and IV-3, respectively) are healthy. In particular, neither signs of optic neuropathy nor abnormal nerve conduction velocities were recorded upon neuro-ophthalmological exam. Both parents and the proband have been investigated by brain MRI and proton magnetic resonance spectroscopy (1H-MRS) in a 1.5 T scanner. There were no MRI structural or metabolic abnormalities in the father (III-3) and the mother (III-4) of the proband, except for a few focal hyperintensities in the cerebral white matter (Fig. 1K–L), whereas in the proband mild cerebellar atrophy (Fig. 1H,J) and pathological accumulation of lactate in the CSF of lateral ventriculi (Fig. 1I) were evident. Direct sequencing of the entire coding regions of the OPA1 gene and the flanking intronic boundaries disclosed two heterozygous mutations. The first c.1705+1G>T mutation occurs in intron 17 and involves the highly conserved donor splice site consensus sequence. Analysis of cDNA revealed aberrant transcript splicing with the activation of a cryptic splice donor site in exon 17, which predicts a prematurely truncated gene product (data not shown). This haploinsufficiency mutation was also identified in the affected mother and in nine maternal relatives, three of which (III-10, III-14 and III-18) are clinically unaffected (Fig. 1A). The second mutation identified in the proband is missense, c.1146A>G (p.I382M), which lies in exon 12, being also present in the clinically unaffected father and sister. Interestingly this is the same missense mutation already reported in other bi-allelic cases (Schaaf et al., 2011; Bonifert et al., 2014). This mutation was found only in one other patient in Italy, out of 132 OPA1 complete sequences. This patient is currently under investigation, being another case of Behr syndrome with optic atrophy complicated by ataxia, but with only the heterozygous c.1146A>G (p.I382M) mutation at the moment (Leonardo Caporali and Valerio Carelli, unpublished data). In the Tübingen cohort of patients with bilateral optic atrophy (in most cases isolated optic atrophy) no further case with the c.1146A>G mutation was found among ∼500 patients that underwent sequencing of all coding exons of the OPA1 gene. This mutation has also been found at low frequency (about 1/1000) in large public data sets (1000 Genome Project, NHLBI GO Exome Sequencing Project). Sequence analysis of the OPA3 gene excluded the presence of pathogenic mutations. Fibroblasts were grown from skin biopsies obtained from the proband and both parents, after approval of the Internal Review Board and signed informed consent. In fibroblasts we first assessed mitochondrial network morphology, after loading mitochondria with Mitotracker Red and examination by fluorescence microscopy as previously reported (Zanna et al., 2008). The mitochondrial network of fibroblasts grown in standard Dulbecco’s modified Eagle’s medium-glucose medium bearing the heterozygous c.1705+1G>T (III:4) and c.1146A>G (III:3) mutations, respectively was similar to controls (Fig. 2A–C), whereas the fibroblasts from the proband were scored into three categories, those with a typical normal filamentous network (Fig. 2D), those with a hyperfragmented pattern (Fig. 2E) and those with filamentous mitochondria containing balloon-like structures (Fig. 2F), each class being present at approximately the same percentage. To investigate whether these OPA1 mutations could affect the bioenergetic efficiency, we measured the rate of mitochondrial ATP synthesis in digitonin-permeabilized fibroblasts. Compared to controls, mitochondrial ATP synthesis driven by complex I substrates (pyruvate and malate) was increased in the proband’s father fibroblasts (III:3) bearing the c.1146A>G mutation, and incrementally reduced in the mother’s fibroblasts bearing the c.1705+1G>T (III:4) mutation and in the proband’s fibroblasts (IV:4) carrying both mutations. The latter was significantly lower compared to his father’s fibroblasts. A similar but less severe situation was observed for the ATP synthesis driven by the complex II substrate (succinate) (Fig. 2G). Overall, these results indicate that the biallelic mutation in the proband led to abnormal network dynamics and impaired ATP synthesis through complex I. Both parent’s mutations were not severe enough to impair mitochondrial network dynamics under the experimental conditions used, but the mother’s mutation impaired partially complex I-dependent ATP synthesis. Figure 2. Open in a new tab (A–F) Mitochondrial network morphology. Control (A) and patient (B–F) fibroblasts were grown in Dulbecco’s modified Eagle’s medium-glucose and loaded with Mitotracker Red as described in Zanna et al. (2008). Representative out of eight similar images are shown for each individual. (G) ATP synthesis. Fibroblasts were treated with 50 µg/ml digitonin, the rate of ATP synthesis was measured as described in Zanna et al. (2008) and was normalized for citrate synthase (CS) activity. Data (mean ± SEM) were obtained from five controls and the three OPA1 mutated fibroblasts. The experiment was performed at least in triplicate. Asterisk denotes values significantly different (P < 0.05) by Kruskal-Wallis one-way ANOVA on Ranks. GPD = Glyceraldehyde 3-phosphate dehydrogenase.

      Case#: Carelli proband, 20yo, Italian, male, onset in first year of life

      DiseaseAssertion: Behr syndrome

      FamilyInfo: Parents are unrelated. c.1705+1G>T was also identified in the affected mother and in nine maternal relatives, three of which (III-10, III-14 and III-18) are clinically unaffected (pedigree in Fig. 1A). The 43-year-old proband’s mother (Fig. 1A, III-4 in the pedigree) had isolated optic atrophy, most evident on the temporal side (Fig. 1C), which segregated as a dominant trait in her family (Fig. 1A). The other affected individuals in this family all suffered a non-syndromic optic atrophy, which started in childhood and progressively worsened, but remained as an isolated symptom. c.1146A>G (p.I382M) is present in the clinically unaffected father and sister. There were no MRI structural or metabolic abnormalities in the father (III-3) and the mother (III-4) of the proband, except for a few focal hyperintensities in the cerebral white matter (Fig. 1K–L). Neither signs of optic neuropathy nor abnormal nerve conduction velocities were recorded upon neuro-ophthalmological exam of the proband’s father and the elder sister (III-3 and IV-3).

      CasePresentingHPOs: HP:0006934, HP:0000648, HP:0002066, HP:0002359, HP:0007663, HP:0002064, HP:0002403, HP:0001776, HP:0002395, HP:0003487, HP:0007078, HP:0012898, HP:0012897, HP:0003535, HP:0003387, HP:0001272, HP:0000543, HP:0010871, HP:0002313, HP:0001310, HP:0002075, HP:0000639

      CaseHPOFreeText: Bilateral optic atrophy. Motor difficulties and visual acuity worsened during childhood. Nerve conduction studies showed delayed sensory-motor velocities with reduced amplitudes of motor potentials. Somatosensory evoked potentials could not be recorded and motor evoked potentials showed absent potentials at lower limbs and delayed latency at upper limbs. Brainstem evoked potentials were delayed bilaterally. Repeated urine organic acid gas chromatography/mass spectrometry analysis revealed mild elevation of 3-methylglutaconic acid (8–20 μmol/mmol creatinine). Sural nerve biopsy demonstrated a marked reduction of the large-diameter myelinated axons (Fig. 1E–G). Teased fibre analysis disclosed regions of demyelination confined to the paranodal region, clustered in some axons, suggesting secondary demyelination. Ultrastructural examination confirmed the reduction of myelinated axons (not shown). Elevated serum lactic acid after standardized exercise. mild cerebellar atrophy and pathological accumulation of lactate in the CSF of lateral ventriculi. OCT examination of retinal nerve fibre layer (RNFL) thickness shows a diffuse reduction of thickness compatible with the severe optic atrophy. Positive Holmes rebound phenomenon. Vision was light perception with severe nystagmus in any direction of gaze. Compared to controls, mitochondrial ATP synthesis driven by complex I substrates (pyruvate and malate) was incrementally reduced in the mother’s fibroblasts bearing the c.1705+1G>T (III:4) mutation and in the proband’s fibroblasts (IV:4) carrying both mutations.

      CaseNotHPOs:

      CaseNotHPOFreeText: cognitive delay

      GenotypingMethod: Direct sequencing of the entire coding regions of the OPA1 gene and the flanking intronic boundaries. Sequence analysis of the OPA3 gene excluded the presence of pathogenic mutations.

      PreviouslyPublished:

      Variant: c.1705+1G>T; c.1146A>G (p.I382M)

      CAID: CA10576007

      SupplementalData:

    1. VII-3 Son

      CaseVII-3: Male, 4 years report, Turkey

      CasePresentingHPOs: HP:0004912, HP:0002540, HP:0002970 (Hypophosphatemic rickets, Inability to walk, Genu varum)

      HPOsFreeText: -3.44 standard deviation score

      CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

      NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

      CaseAddInfo: Variant is asserted de novo and confirmed by parental testing, Proband is hemizygous for this mutation, Mutation is at splice donor site at Intron 2

      CasePreviousTesting: Calcium levels (9.0 mg/dL), Decreased serum phosphate levels (3.1 mg/dL; reference 3.8-6.5), Elevated serum ALP (393 IU/L; reference 90-325), 25OHD3 levels (4.9 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (154.7 ng/L), TPR levels (58.7), Decreased TmP/GFR levels (1.82; reference 2.9-6.1)

      CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

      Variant: NM_000444.5(PHEX):c.187+1G>T

      CinVar: 438537 https://www.ncbi.nlm.nih.gov/clinvar/variation/438537/

      gnomAD: Not in gnomAD

    1. Case Description

      Case#: Ma_Proband

      Demographics: east Asian? referenced in passing in discussion section

      CasePresentingHPOs: HP:0003182, HP:0008812, HP:0002655, HP:0003621, HP:0000943, HP:0001498, HP:0003049, HP:0002857, HP:0004689,

      CaseNotHPOs: HP:0008445, HP:0002751, HP:0000768, HP:0008445

      CasePreviousTesting: Previous diagnosis Developmental dysplasia of the hip (DDH)

      CaseMethod1: quantify urinary excretion of glycosaminoglycans using dimethylmethylene blue

      CaseMethod2:

      CaseGenotypingMethod: Whole exome sequencing

      Variant HGVS: 1) NM_000512.5:c.1156C>T 2) NM_000512.5:c.1288C>G

      ClinVar: 1) 700 2) N/A

      CAID: 1) CA221040 2) CA397096290

      gnomAD v2: 1) 16-88891261-G-A 2) N/A

      VariantEvidence:

      CaseAddInfo: Onset of symptoms age 8, compound het

      CasePMIDs:

    1. Case#: Consequence 23 Table 1 in Data Supplement (1 cases)

      DiseaseAssertion: HCM

      FamilyInfo: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

      CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

      Variant: NM_000257.4(MYH7):c.2788G>A (p.Glu930Lys)

      ClinVar: 42933 https://www.ncbi.nlm.nih.gov/clinvar/variation/42933/

      CAID: n/a

      gnomAD: absent

    2. Case#: Consequence 20 Table 1 in Data Supplement (3 cases)

      DiseaseAssertion: HCM

      FamilyInfo: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

      CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

      Variant: NM_000257.4(MYH7):c.4066G>A (p.Glu1356Lys)

      ClinVar: 164294 https://www.ncbi.nlm.nih.gov/clinvar/variation/164294/

      CAID: n/a

      gnomAD: absent

    3. Case#: Consequence 9 Table 1 in Data Supplement (1 cases)

      DiseaseAssertion: HCM

      FamilyInfo: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

      CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

      Variant: NM_000257.4(MYH7):c.427C>T (p.Arg143Trp)

      ClinVar: 164401 https://www.ncbi.nlm.nih.gov/clinvar/variation/164401/

      CAID: n/a

      gnomAD: 0.0001087 East Asian https://gnomad.broadinstitute.org/variant/14-23901923-G-A

    4. Case#: Consequence 5 Table 1 in Data Supplement (1 cases)

      DiseaseAssertion: HCM

      FamilyInfo: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

      CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

      Variant: NM_000257.4(MYH7):c.2198G>T (p.Gly733Val)

      ClinVar: 181177 https://www.ncbi.nlm.nih.gov/clinvar/variation/181177/

      CAID: n/a

      gnomAD: absent

    1. A 5-year-old south Asian female was incidentally found to have hepatomegaly on a trip to India, where she became acutely ill with fever, vomiting, and abdominal pain. Blood work done at that time demonstrated mildly elevated liver function tests (AST 48 U/L, ALT 80 U/L), and an abdominal ultrasound revealed hepatomegaly without biliary or splenic abnormalities. She was prescribed an antibiotic and her symptoms gradually resolved.A month after her return to the United States, her pediatrician noted persistent hepatomegaly and the new development of fever. She was referred to the emergency department because of suspicion of a tropical infectious disease. A repeat ultrasound demonstrated persistent hepatomegaly. Her transaminases (AST 133 U/L, ALT 112 U/L) remained elevated. The infectious workup was negative for cytomegalovirus, hepatitis A, Lyme disease, and malaria. She did have a positive Epstein-Barr virus IgM. Repeat blood work was obtained at follow-up infectious disease clinic visit where she was again found to have hepatomegaly (7 cm below the costal margin) and mildly abnormal transaminases. A computed tomography of the abdomen and pelvis (Figure 1) was performed that demonstrated hepatomegaly but had otherwise normal findings. Her fever resolved within 2 weeks. She was otherwise well and was not on any medications. There was no family history of liver disease. Her immunizations were up to date. Because of persistent hepatomegaly, she was referred to the liver clinic.Open in a separate windowFigure 1Computed tomography of abdomen and pelvis. The liver is enlarged, measuring up to 17 cm in width and craniocaudal dimension. The contour is smooth. The hepatic parenchyma is homogenous without a focal mass. There is no intrahepatic biliary dilatation. The portal and hepatic venous systems are patent and nondilated.In the liver clinic, she was noted to have an enlarged, firm liver, palpable 8 cm below the costal margin with no associated splenomegaly. Test results for autoimmune hepatitis, WD, and alpha-1-antitrypsin deficiency were negative. Nonfasting lipid levels were abnormal; repeat testing showed a fasting total cholesterol of 305 mg/dL and a triglyceride level of 142 mg/dL.On the basis of a clinical suspicion of a diagnosis of CESD, a liver biopsy was performed. It revealed diffuse, microvesicular steatosis in the hepatic parenchyma (Figure 2(a)). Portal tracts were expanded by foamy macrophages containing finely vacuolated material, which was periodic acid-Schiff positive and resistant to diastase digestion. Trichrome stain for collagen showed mild portal fibrosis with early delicate bridging fibrosis. Ultrastructurally, the cytoplasm had a moth-eaten appearance with the presence of lipid droplets and cholesterol crystals (Figure 2(b)). There was no evidence of hepatocellular necrosis, cholestasis, or bile duct proliferation.Open in a separate windowFigure 2(a) Liver biopsy, periodic acid-Schiff stain with diastase (magnification, ×40). Lipid demonstrated within the hepatocellular cytoplasm (arrows). (b) Electron micrograph (direct magnification, ×2500). The hepatocellular cytoplasm in places has a moth-eaten appearance with lipid droplets (arrows). Additionally, some foci show cholesterol crystals (∗) free in the hepatocellular cytoplasm.Liver tissue was sent to Dr. D. Wenger's Lysosomal Diseases Testing Laboratory at Thomas Jefferson University. She was found to have a low acid lipase activity of 7.2 (no units provided by Dr. D. Wenger's laboratory) in the liver. Follow-up testing through a commercial laboratory demonstrated low level of lysosomal acid lipase activity (0.008 nmol/punch/h) in blood. Lysosomal acid lipase gene sequence analysis was performed, which demonstrated that she was heterozygous for the following two mutations: c.57_60delTGAG and c.894G>A. Both parents underwent mutation analysis. The mother was confirmed to have the c.894G>A mutation while the father carried the c.57_60delTGAG mutation. The c.57_60delTGAG is a new mutation not previously described in the literature in patients with CESD.Go to:

      Case: Lin Patient-female, south Asian, 5 years old at diagnosis

      CasePresentingHPOs: HP:0001945, HP:0002013, HP:0002027, HP:0002240

      CasePresentingHPOsFreeText: Mildly elevated liver function tests (AST 48 U/L, ALT 80 U/L) upon initial visit, transaminases (AST 133 U/L, ALT 112 U/L) remained elevated after a month. Non-fasting lipid levels were abnormal; repeat testing showed a fasting total cholesterol of 305 mg/dL and a triglyceride level of 142 mg/dL. Diffuse, microvesicular steatosis in the hepatic parenchyma. Portal tracts were expanded by foamy macrophages containing finely vacuolated material, which was periodic acid-Schiff positive and resistant to diastase digestion. Trichrome stain for collagen showed mild portal fibrosis with early delicate bridging fibrosis. Ultrastructurally, the cytoplasm had a moth-eaten appearance with the presence of lipid droplets and cholesterol crystals. Low acid lipase activity of 7.2 (no units provided) in the liver, with follow up low level of lysosomal acid lipase activity (0.008 nmol/punch/h) in blood.

      CaseNOTHPOs: HP:0032316, HP:0001744, HP:0001404, HP:0001396, HP:0001408

      CaseNOTHPOSFreeText:

      CasePreviousTesting: Abdominal ultrasound. Infection workup was negative for cytomegalovirus, hepatitis A, Lyme disease, and malaria. She did have a positive Epstein-Barr virus IgM. CT of the abdomen and pelvis revealed an enlarged liver measuring up to 17cm in width and craniocaudal dimension. Test results for autoimmune hepatitis, WD, and alpha-1-antitrypsin deficiency were negative. Liver biopsy.

      CaseGenotypingMethod: LAL gene sequence analysis was performed.

      Variant: c.57_60delTGAG and c.894G>A

      ClinVarID: or CAID: CA2573331826 and 203361

      gnomAD: This proband has a four-nucleotide deletion, c.57_60delTGAG, in exon 2 of the LIPA gene. This variant is predicted to result in a premature translation stop downstream of the deletion (p.Glu20GlyfsTer6). The variant is not present in gnomAD. This proband is scored default points.

      This proband has a synonymous variant, Gln298= on exon 8/10 in a cononical splice site, which causes an abnormal splicing that results in the in-frame skipping of exon 8. The variant is reported in 167/128942 European (non-Finnish) alleles at a frequency of 0.001295, with no homozygotes in gnomAD v2.1.1. This is the most frequent variant in CESD patients (present in 40-60% of patients reported in the literature), but it is not confirmed if this is due to a hotspot or a common ancestor. This proband is scored default points.

      AddCaseInfo: Confirmed in trans

      PreviouslyPublished: no

      VariantEvidence: Predicted evidence only for deletion variant.

      Expression analysis in patient fibroblasts found lysosomal acidic lipase (LAL) activity to be reduced to 6-12% of wild type (PMID: 22227072).

    1. WES analysis of the proband (V:3, Figure 1) resulted in the identification of a biallelic variant (c.697G>A, p.Asp233Asn) in GALNS

      Case#: V:3

      Demographics: Pakistani

      CasePresentingHPOs: HP:0004322, HP:0000768, HP:0000470, HP:0002857, HP:0002650, HP:0002007, HP:0000431, HP:0010674, HP:0002515, HP:0009803, HP:0006119, HP:0001216, HP:0002986, HP:0003027, HP:0008802, HP:0030299, HP:0000926, HP:0004568

      CaseNotHPOs:

      CasePreviousTesting:

      CaseMethod1:

      CaseMethod2:

      CaseGenotypingMethod: Proband whole exome seq

      Variant: NM_000512.5:c.697G>A

      ClinVar: 1048200

      CAID: CA8235027

      gnomAD: 16-88902194-C-T

      VariantEvidence: previous pub as pathogenic, and in silico data suggesting damage to catalytic domain

      CaseAddInfo: Family was tested via single gene sanger seq., consanguineous parents both carriers, two affected siblings and three unaffected siblings

      CasePMIDs:

    1. 9

      Case: Individual 9, male, AOR= 3 years 10 months

      CasePresentingHPOs:  HP:0004322, HP:0004325, HP:0000252, HP:0001263, HP:0001611, HP:0001256, HP:0001290, HP:0002360, HP:0000736, HP:0030213, HP:0001090, HP:0002553, HP:0000527, HP:0000494, HP:0000316, HP:0000426, HP:0000455, HP:0000322, HP:0000219, HP:0000307, HP:0000179, HP:0000400, HP:0011271, HP:0200055, HP:0009836, HP:0001212, HP:0001852, HP:0000565, HP:0000915

      CasePresentingHPOText: Began walking at 13 months, first words at 23 months. Intelligence testing should an IQ of 75-88 but noted as uneven profile.

      CaseNOTHPOs: HP:0001250, HP:0002376, HP:0000202

      CasePreviousTesting: Affymetrix Cytoscan Array screening was normal

      CaseGenotypingMethod: Individual WES (Illumina HiSeq 2500), filtering against known and candidate genes from SysID (by Konchinke et al., 2016 PMID: 26748517). Sanger sequencing for confirmation and to test the parents and show absence of the variant. The sample identity was also confirmed.

      Variant: hg19:chr2: g.4806682 1_4806682 2del, c.319_320 del, p.(Leu107Alafs45) OR* NM_001190274.1:c.319_320del

      CA ID: CA658820927

      de novo

      gnomAD: n/a

      AddCaseInfo:

      VariantEvidence: The Leu107Alafs*45 mutation causes a frameshift mutation and premature stop codon. The mutation start in exon 2 and thus removes the F-BOX, all three CASH domains and the zinc-finger UBR region, thus it should act as a loss of function variation. No functional assays or variant evidence was provided.

    1. A second mutation

      Case7: Female, 8 yrs onset

      CasePresentingHPOs: HP:0006785, HP:0003236, HP:0040083, HP:0003701, HP:0003323, HP:0008981, HP:0003458, HP:0030951 (Limb-girdle muscular dystrophy, Elevated serum creatine kinase, Toe walking, Proximal muscle weakness, Progressive muscle weakness, Calf muscle hypertrophy, EMG: myopathic abnormalities, Skeletal muscle fibrosis)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0100543 (Cognitive impairment)

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband is homozygous for this deletion, Mother is confirmed heterozygous

      CasePreviousTesting: Peak CPK at 17,000 IU/l, Partially absent α- and β-sarcoglycan staining, Normal dystrophin content, Totally absent γ-sarcoglycan staining

      CaseGenotypingMethod: Total mRNA was isolated from muscle biopsies and cDNA was synthesized from it via reverse transcriptase. PCR and SSCP analysis was performed and excised, amplified, and sequenced. After finding the mutations, DNA from peripheral blood leukocytes or muscle biposies was isolated, PCR amplified, and sequenced to confirm the results.

      Variant: SGCG, 2-BP DEL, 793TG

      ClinVar: 2007 https://www.ncbi.nlm.nih.gov/clinvar/variation/2007/

      Also Reported As

      Variant: NM_000231.2(SGCG):c.794_795GT[3] (p.Cys267fs)

      ClinVar: 552513 https://www.ncbi.nlm.nih.gov/clinvar/variation/552513/

      gnomAD: 0.00009923, https://gnomad.broadinstitute.org/variant/13-23898596-CTG-C

    1. 5FemaleT1.40.6[c.1037 T > G] + [c.1091C > T][p.L346R] + [p.T364 M]8, 8K [44]/K [45]0.81Positive

      Case#: Newborn 5, female, 1.4 months, Taiwan

      DiseaseAssertion: MPS1

      FamilyInfo: proband is a twin with newborn 6, who has the same genotype

      CasePresentingHPOs:

      CaseHPOFreeText: IDUA enzyme activity in leukocytes= 0.81 (Ref. 4.87 ~ 54.70 μmol/g protein/h, with cut-off values of < 3.0), positive GAG tests (GAG tests including GAG quantification (DMB/Cre ratio), 2-dimensional electrophoresis, and quantitative analyses of GAG-derived disaccharides (DS and HS) by tandem mass spectrometry assay). DS=99.61 (ug/mL), HS=13.31 (ug/mL)-average DS and HS values of the normal population were 0.17 (±0.23) and 0.11 (±0.21), respectively

      CaseNotHPOs:

      CaseNotHPOFreeText:

      PreviouslyPublished: n/a

      Variant: c.1037 T > G (p.L346R)  +  c.1091C > T (p.T364M)

      ClinVar: 11925

      CAID: CA256126

      SupplementalData: n/a

    1. In this study we analyzed 30 Italian MPS-I patients with different phenotypes (20 severe, 6 intermediate, 4 mild) in an attempt to recognize the mutational spectrum in our population and to identify major DNA alterations specific to our country.

      unable to annotate on PDF.

      Case#: Case #20, Lombardia region of Italy

      DiseaseAssertion: MPS1, intermediate

      FamilyInfo: n/a

      CasePresentingHPOs:

      CaseHPOFreeText: Diagnosis of was based on the clinical features, excessive urinary glycosaminoglycan excretion, and reduced IDUA activity in fibroblasts and/or leukocytes. Intermediate phenotype is described as an onset of symptoms between 1 and 6 years, variable survival, and mental retardation being absent or mild but never before 3 years of age

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting: n/a

      GenotypingMethod: direct sequencing

      PreviouslyPublished: n/a

      Variant: R628X homozygous

      ClinVar: 550421

      CAID: CA2802462

      gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

      SupplementalData: n/a

    1. Q380RR628PA8, A20, L14Mild, survival beyond age 35, no mental retardation

      Case#: Patient #17, Brazilian

      DiseaseAssertion: MPS1, mild

      FamilyInfo:

      CasePresentingHPOs:

      CaseHPOFreeText: survival beyond age 35

      CaseNotHPOs:

      CaseNotHPOFreeText: mental retardation

      GenotypingMethod:

      PreviouslyPublished:

      Variant: Q380R; R628P (also A8, A20, L14)

      ClinVar: 1064675

      CAID:

      SupplementalData:

    1. The aspartate-to-asparagine substitution in exon 5 of the α-tropomyosin gene (Asp175Asn, numbered according to Reference 15), which was previously identified in the proband, results from a guanine-to-adenine transition at nucleotide residue 579 (G579A)

      Case#: Proband_DBIII-2, 53 y.o., M

      CasePresentingHPOs: HP:0001712

      CaseHPOFreeText: Max LVWT 18 mm; LA size 40 mm; episode of sustained VT

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting: None

      CaseMethod1: PCR amplification of TPM1 exon 5 followed by cycle sequencing

      CaseMethod2: STR polymorphisms to construct haplotypes

      CaseGenotypingMethod: PCR amplification of TPM1 exon 5 followed by cycle sequencing

      Variant: The nucleotide position 579 refers to that described in the initial cloning of the gene in 1988 (PMID: 3336363), but aligns to NM_001018005.2(TPM1):c.523G>A (p.Asp175Asn).

      ClinVar: ClinVar:12456

      CAID: CA018106

      gnomAD: Grpmax FAF = 7.900e-7, SNV: 15-63060899-G-A, gnomADv4_D175N

      CasePMIDs:

    1. c.829A>T (p.T277S)

      Case# Baskin TS, Male, 16

      CasePresentingHPOs HP:0006956, HP:0100749, HP:0001962, HP:0004756

      CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).

      CaseMethod1 PCR

      CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.

      Variant NM_024334.2(TMEM43):c.829A>T (p.Thr277Ser)

      ClinVar 165456

      gnomAD 0.006432 link

    1. SERPING1ID2704Ac.551-2A > Gnewdis AcExon 4 skipping (band B), use of cr: c.604 (band A)p.Gly184_Pro228delp.Ala185 Leufs*54 (NMD?)Normal exon inclusion (band A) *, exon 4 skipping (band B), exon 4 + 5 skipping (band C)p.Gly184_Pro228delp.Gly184_Ser296del

      Patient: ID270

      Variant: c.551-2A > G

      CAID: CA380696603

      Functional effect: Normal exon inclusion (band A) *, exon 4 skipping (band B), exon 4 + 5 skipping (band C). Observed in blood.

    1. two affected Italian siblings

      Case: Bolino Proband 3, reported at 14yo, symptom onset at 4yo

      CasePresentingHPOs: HP:0009053, HP:0008959, HP:0007181, HP:0009049, HP:0001284, HP:0010871, HP:0001337, HP:0001761, HP:0001765, HP:0012447, HP:0003383 (distal lower limb muscle weakness, distal upper limb muscle weakness, interosseous muscle atrophy, peroneal muscle atrophy, absent tendon reflexes, sensory ataxia, tremor, pes cavus, hammertoe, abnormal myelination, onion bulb formation)

      HPOsFreeText: interosseous muscle weakness, normal psychomotor development, sensory ataxia noted with tremor, normal autonomic function and superficial sensations, unremarkable general examination, routine laboratory tests normal, CSF exam normal, CMAPS absent from peroneal and median nerves, SNAPs absent from sural nerves. Light microscopy showed irregularities and outfoldings of myelin sheath

      CountryOrigin: Italy

      FamilyInfo: non-consanguineous parents

      PreviouslyPublished: 10673338, 8195799

      GenotypingMethod: PCR of genomic DNA, establishment of MTMR2 genomic structure, cDNA sequence aligned with partial genomic sequence from PAC clone CMB9-9116, available family members analyzed and segregation of variant with disease confirmed in pedigree

      Variant: NM_016156.5(MTMR2):c.1444C>T (p.Gln482Ter), homozygous

      ClinVar: 6234, https://www.ncbi.nlm.nih.gov/clinvar/variation/6234/

      gnomAD: 0.000003988, https://gnomad.broadinstitute.org/variant/11-95574816-G-A

    1. The patient in family 2 who also had the Hurler phenotype was heteroallelic for the novel missense mutation I270S and the previously reported nonsense mutation R628X.

      Article is a PDF, so annotating here.

      Case#: Family 2, Proband 3, Tunisia (Mednine), female, death at 5yo

      DiseaseAssertion: MPS1, Hurler

      FamilyInfo: Offspring of consanguineous marriage between first cousins. Variants were said to be found in parents as well. Mother had I270S and father had R628X

      CasePresentingHPOs:

      CaseHPOFreeText: Leukocyte IDUA activity= <0.1% of normal

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting: n/a

      GenotypingMethod: PCR sequencing with possible confirmation by restriction enzyme digestion on a second PCR product.

      PreviouslyPublished: n/a

      Variant: c.1882C>T p.(R628X) and c.809T>G p.(I270S) compound heterozygous. Confirmed in trans. Also has the following polymorphisms: R105Q, N181N, T410T, V454I, IVS8+2573insC.

      ClinVar: 550421

      CAID: CA2802462; CA355962322

      gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

      SupplementalData: n/a

    1. c.1705+1G>T p.(V556Qfs*40) Intron 17 CS061312

      Case#: n/s

      DiseaseAssertion: bilateral optic atrophy

      FamilyInfo:

      CasePresentingHPOs:

      CaseHPOFreeText:

      CaseNotHPOs:

      CaseNotHPOFreeText:

      GenotypingMethod: Genetic testing of the OPA1 gene was initially performed by a combined analysis using either single-strand conformation polymorphism or denaturing high performance liquid chromatography followed by Sanger sequencing to validate aberrant bands or melting profiles. The presence of copy number variations was assessed using multiplex ligation-dependent probe amplification. Since 2012, genetic testing was based on next-generation sequencing platforms.

      PreviouslyPublished: likely since S. Schimpf is an author, patients were sent to the same German institution (Institute for Ophthalmic Research in Tübingen-same institution S.Schimpf is associated with), some patients came from Italian referring centers (proband from Carelli et al was said to be Italian), this is a retrospective study and the paper states "many variants have already been described and published by us"

      Variant: c.1705+1G>T p.(V556Qfs*40)

      CAID: CA10576007

      SupplementalData:

    1. Subject 1

      Case# Subject 1, M, 5mo died, British

      CasePresentingHPOs HP:0001319, HP:0003324, HP:0008872, HP:0001531, HP:0002020, HP:0000407, HP:0002910, HP:0002151, HP:0002490, HP:0003198, HP:0003200, HP:0003688, HP:0002098, HP:0003348 (Neonatal hypotonia, Generalized muscle weakness, Feeding difficulties in infancy, Failure to thrive in infancy, Gastroesophageal reflux, Sensorineural hearing impairment, Elevated transaminases, Increased serum lactate, Increased CSF lactate level, Myopathy, Ragged red muscle fibers, Cytochrome C oxidase-negative muscle fibers, Respiratory distress, Elevated blood alanine)

      HPOFreeText: Hypotonic and weak soon after birth, had difficulty feeding, slow weight gain and gastro-esophageal reflux, confirmed sensorineural deafness after neonatal screen. Lateral skull X-ray showed fused sutures, supporting possible craniosynostosis. Died of 5.5 months of respiratory distress after rhinovirus bronchiolitis.

      CaseNotHPOs HP:0045045 (Elevated acylcarnitine)

      CasePreviousTesting Alanine transaminase (439 U/L; normal range 4–45 U/L), blood lactate (5 to 10 mmol/L; normal range 0.7–2.1 mmol/L). Screened panel of known mitochondrial disease genes. Analysis of mtDNA and mtDNA copy number were normal in patient muscle cells, thus excluding mtDNA rearrangements and point mutations.

      CaseMethod1 WES

      CaseMethod2 Sanger

      CaseGenotypingMethod WES confirmed with Sanger in patient and parents to confirm in trans

      Variant (1) NM_017819.3(TRMT10C):c.542G>T (p.Arg181Leu), (2) NM_017819.3(TRMT10C):c.814A>G (p.Thr272Ala)

      ClinVar (1) 224316, (2) 224317

      gnomAD (1) 0.0003508(Latino), 0.0001121(Total) - no homozygotes listed (2) n/a

      VariantEvidence n/a

      CaseAddInfo non-consanguineous, healthy older sister, c.542G>T variant in ExAC (10/120,324 alleles) and ESP6500 (1/11,824 alleles), c.814A>G was not in ExAC, ESP6500 or COSMIC

      CaseAddPMIDs n/a

    1. In 30 families, either one or both of the mutations were not identified, which accounted for 25.9% of the total alleles. Therefore, all 14 exons of the alpha-L-iduronidase gene were screened in these patients and 23 different sequence changes were found, 17 of which were previously unknown. The novel sequence changes include 4 deletions (153delC, 628del5, 740delC, 747delG), 5 nonsense mutations (Q60X, Y167X, Q400X, R619X, R628X), 6 missense mutations (C205Y, G208V, H240R, A319V, P496R, S633L), a splice site mutation (IVS12+5g>a), and a rare polymorphism (A591T)

      article is a PDF, so annotating here.

      Case#: Beesley Families 3 and 4, Middle Eastern

      DiseaseAssertion: MPS1, Hurler

      FamilyInfo: said to be from different families, but from the same region

      CasePresentingHPOs:

      CaseHPOFreeText: reduced/absent enzyme activity. IDUA enzyme activity in leukocytes= range from 0 to 2.47 nmol/h/mg protein (reference range: 28–92 nmol/h/mg protein) for the 85 patients in study, but no individual activity provided. No individual phenotype information given.

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting: n/a

      GenotypingMethod: intron/exon boundaries of the IDUA gene were analysed by PCR, SSCP and DNA sequencing

      PreviouslyPublished: n/a

      Variant: p.R628X homozygous

      ClinVar: 550421

      CAID: CA2802462

      gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

      SupplementalData: n/a

    1. family 2, a deletion variant, c.371delA, was found in theaffected male IV-2 (Fig. 1B, E), causing a frameshift leading to atruncated putative protein p. Lys124Serfs*10

      Case#: Ciammola_Family 1_Proband IV-2

      Demographics: Male, 49y at report

      CasePresentingHPOs: HP:0002378, HP:0002067, HP:0002172, HP:0002322, HP:0000729, HP:0100543, HP:0000338, HP:0002063, HP:0002067, HP:0002174,

      Onset of bradykinesia and postural instability at 44yo. Rest tremor developed in the right hand and then spread bilaterally. Gait was slow. Fronto-subcortical involvement pattern was seen on neurological assessment.

      CaseNotHPOs:

      CasePreviousTesting:

      CaseMethod1:

      CaseMethod2:

      CaseGenotypingMethod:

      Variant: NM_171998.4:c.370del (Lys124SerfsTer10)

      ClinVar:

      CAID: CA658795322

      gnomAD: NR

      VariantEvidence: The proband was hemizygous for the frameshift variant, Lys124SerfsTer10, but showed mosaicism. Segregation analysis in the family revealed that the variant was de novo and proband cDNA analysis showed normal and mutant transcripts in a 1:1 ratio, and this was also confirmed in oral mucosa cells and urine. Immunoblotting of HeLa cells transfected with variant RAB39B revealed complete loss of function.

      CaseAddInfo:

      CasePMIDs:

    2. family 1, a frameshift variant, c.137dupT, was found in theaffected siblings II-1 and II-3 (Fig. 1A, C), resulting in a putativepremature stop codon after 91 aminoacids from the start codon(p.Ser47Leufs*44).

      Case#: Ciammola_Family 1_Proband II-3

      Demographics: Male, 67y

      CasePresentingHPOs: HP:0002378, HP:0002174, HP:0030186, HP:0002135, HP:0002322, HP:0001288, HP:0002067, HP:0001276,

      Developmental milestones were unremarkable, but experienced severe learning disabilities at primary school. Proband developed a postural tremor in both hands at 11yo. At 44y, he was diagnosed with essential tremor in both hands and CT scan revealed left basal ganglia calcification. He developed progressive rest tremor in right hand and progressive gait difficulty from 62yo. Bradykinesia at finger tapping, slow gait, decreased arm swing, especially on the right side, and good response to L-dopa therapy were noted. Mild-moderate front-subcortical involvement pattern

      CaseNotHPOs:

      CasePreviousTesting: No pathogenic variants were detected in GBA, LRRK2 exons 29-30-31-35-41, PRKN, PINK1, DJ-1, ATP13A2, FBXO7, PLA2G6, DNAJC6 and SYNJ1 analyzed by Sanger sequencing. No deletion/duplications in PRKN analyzed by quantitative PCR were detected.

      CaseMethod1: Sanger

      CaseMethod2:

      CaseGenotypingMethod: RAB39B gene was sequenced.

      Variant: NM_171998.4:c.137dup

      ClinVar:

      CAID: CA658795323

      gnomAD: NR

      VariantEvidence: The proband was hemizygous for the frameshift variant, Ser47LeufsTer44. Immunoblotting in HeLa cells transfected variant RAB39B revealed absence of RAB39B protein, indicating complete loss of function due to the variant.

      CaseAddInfo:

      CasePMIDs:

    1. KMP 8

      Case#: KMP 8, male, 62 yrs, East Slovakia

      DiseaseAssertion: HCM

      FamilyInfo: n/a

      CasePresentingHPOs: n/a

      CaseHPOFreeText: symptomatic; LVOTO yes; LVEF 60%; ECG; echocardiography;

      CaseNotHPOs: n/a

      CaseNotHPOFreeText: no ICD

      CasePreviousTesting: Additional Sanger sequencing of exons 12, 24, 25 of MYBPC3, exon 12 NEBL, exons 12, 20, 21 of SCN5A, exon 7 of TNNI3, and exon 9 of TNNT2 gene

      CaseGenotypingMethod: Sanger sequencing;

      Variant: NM_000257.4(MYH7):c.2845G>A (p.Glu949Lys)

      ClinVar: 14093 https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/

      CAID: n/a

      gnomAD: absent

    1. 2Kuwait1.5M00.54p.Arg628* (c.1882C>T)p.Arg628*b,2 (c.1882C>T)

      Case#: Patient 2, Kuwait, 1.5yo at report, male

      DiseaseAssertion: MPS1

      FamilyInfo: n/a

      CasePresentingHPOs:

      CaseHPOFreeText: IDUA activity on DBS= 0 nmol/21 h*punch

      CaseNotHPOs:

      CaseNotHPOFreeText:

      CasePreviousTesting: n/a

      GenotypingMethod: exon-specific PCR amplification of individual exons together with short flanking intronic sequences, followed by conventional Sanger sequencing

      PreviouslyPublished:

      Variant: p.Arg628* (c.1882C>T) homozygous

      ClinVar: 550421

      CAID: CA2802462

      gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

      SupplementalData: n/a

    1. proband

      FamilyName: Kar 2018 Family 1

      FamilyPresentingHPOs: HP:0001249, HP:0000508, HP:0010442

      FamilyNotHPOs:

      CountryOrigin: India

      Ethnicity:

      Race: Asian

      FamilyPreviousTesting: Authors stated that homozygosity mapping did not identify any significant CNVs. Loss of heterozygosity (greater than 1kb) were observed over all affected siblings in shromosome 2, 7, 10, and 14. The Chromosome 2q had a 11Mb region with 141 genes, of which none were associateed with ID, ptosis, and polydactyly together.

      FamilyMethod1:

      FamilyMethod2:

      FamilyGenotypingMethod: Homozygosity mapping, using SNP array analysis ( Illumina Human-CytoSNO-12v2.1. DNA) on the entire family (including parents), and exome sequencing in all the siblings. All mutations were confirmed by Sanger sequencing in the proband, parents, siblings (affected and unaffected) and a control was used. WES identified mutations in the UGT1A7 gene (c.654A>C) within the shared chromosome 2 region, as well as ARMC( (c.879G>A). They also found mutations in the gene ZFPM1 (c.1331_1339delinsCCC), but this was not within any shared region of homozygosity between the siblings. Neither UGT1A7 or ZFPM1 is associated with a disease/ phenotype per OMIM.

      Affected: 3

      Unaffected: 1

      Segregations:

      PublishedLOD: n/a

      eLOD: 1.32

      AddSegregationInfo: Family is consanguineous.

      ProbandLabel: Kar 2018 Family- II:1, male

      Variant: NM_025139.5(ARMC9):c.879G>A (p.Thr293=)

      ClinVar: 522606

      gnomAD: MAF (Ash-JEw)= 0.0001022, no homozygotes

      FamilyAddInfo:

      FamilyPMIDs:

      CasePresenting HPOs: HP:000148, HP:0000494, HP:0000316, HP:0000311, HP:0000218, HP:0030084, HP:0001182, HP:0006369, HP:0002761, HP:0005880, HP:0006253, HP:0004322, HP:0007068, HP:0002419

      VariantEvidence: The ARMC9 c.879G>A synonymous mutation is the last base in exon 9 (of 21 total exons) and is predicted to alter splicing. ARMC9 was transcribed into the pCAS2 minigene system and expressed in COS7 cells. RT-PCR of the transfected cells showed skipping of exon 9 in the mutant (Mt) cells compared to ARMC9 wildtype (Wt) cells that retained exon 9 (Figure 2). Sanger sequencing of the ARMC9-pCAS_Mt vector showed a 99 base pair deletion of exon 9 (Supplementary Figure 1), which is a loss of 33 amino acids encoded by exon 9. Exon 9 of ARMC9 encodes part of the ARM Domain 1 which is highly conserved among several speciies. Structural modeling indicates that the loss of the 33 amino acids (aa261-293) would critically disrupt the structure of ARMC9 ( Figure 3).

    1. a novel truncating TUBA4A variant, p.H393Pfs*19 (chr2:220115243_220115244insG, c.1177_1178insC), in a familial ALS proband who also harboured the SOD1 p.E133V variant (chr21:33040827A>T, c.401A>T).

      Case#: Li 2018 fALS H393Pfs*19, Chinese

      MonDO: MONDO:0005144 for fALS

      CasePresentingHPOs: HP:0007354

      CaseGenotypingMethod: Sanger sequencing. TUBA4A sequencing was performed using Sanger. No further details provided.

      Variant: NM_006000.3(TUBA4A):c.1177dup (p.His393ProfsTer19)

      CAID: CA2018007640

      CaseAddInfo: This variant failed to cosegregate with affected family members. This proband also carried the SOD1 p.E133V variant (chr21:33040827A>T, c.401A>T).

    1. g

      CaseP550: Male, 8 yrs onset,

      CasePresentingHPOs: HP:0002078, HP:0000639, HP:0007340, HP:0007210, HP:0002495, HP:0001760 (Truncal ataxia, Nystagmus, Lower limb muscle weakness, Lower limb amyotrophy, Impaired vibratory sensation, Abnormal foot morphology)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0000648, HP:0001639, HP:0002015, HP:0001260 (Optic atrophy, Hypertrophic cardiomyopathy, Dysphagia, Dysarthria)

      NotHPOsFreeText: Not wheelchair-bound

      CaseAddInfo: N/A

      CasePreviousTesting: 30.9% fratraxin protein levels

      CaseGenotypingMethod: See Group

      Variant1: FXN, (GAA)n REPEAT EXPANSION, IVS1

      ClinVar: 561195, https://www.ncbi.nlm.nih.gov/clinvar/variation/561195/

      gnomAD: Not in gnomAD

      Variant2: NM_000144.5(FXN):c.157del (p.Arg53fs)

      CAID: 3985, https://www.ncbi.nlm.nih.gov/clinvar/variation/3985/

      gnomAD: 0.000 MAF

    1. Patient NIJ

      MonDO: MONDO:0032706

      Case: Patient NIJ. 46 year old Dutch/Egyptian female onset of gait difficulties at age 34 with progressive worsening. Analysis of the maternal DNA revealed that she carries the p.Gln316* mutation, but not the frameshift mutation, indicating that the mutations in the proband are on opposite alleles.

      DiseaseAssertion: Cerebellar ataxia

      FamilyInfo:

      CasePresentingHPOs: HP:0001288, HP:0007979, HP:0008003, HP:0007338, HP:0001251, HP:0002064, HP:0006895, HP:0001348 (Gait disturbance, Gaze-evoked horizontal nystagmus, Jerky ocular pursuit movements, Hypermetric saccades, Ataxia, Spastic gait, Lower limb hypertonia, Brisk reflexes

      CaseHPOFreeText: Difficulty writing, cerebellar dysarthria, downgoing plantar responses, ataxia on finger chase and heel-shin slide, Mild spastic paraplegia Cervical dystonia

      CasePreviousTesting: No weakness. Normal sensory examination. An MRI brain scan revealed mild cerebellar atrophy. Ophthalmological examinations were normal. Nerve conduction studies and EMG did not show evidence of a peripheral neuropathy. Laboratory testing including vitamin E, metabolic screening, albumin, cholesterol, alpha-fetoprotein, lactate, acanthocytes, copper, ceruloplasmin, and coeliac screen was normal or negative. Genetic testing for Friedreich, spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 12, 14 and 17, dentatorubral-pallidoluysian atrophy, autosomal recessive spastic ataxia of Charlevoix-Saguenay and SPG7 were negative.

      GenotypingMethod: Exome sequencing. Sanger sequencing was performed for confirmation of the variants and for segregation analyses using standard techniques. Altogether, 117 708 variants (single nucleotide variants and small deletions/insertions/indels) were detected. Initial filtering for a gene panel of movement disorders revealed no mutations.Variants were filtered for variant type, rarirty (MAF <0.5%) and conservation (>0.75, phyloP). Paternal DNA unavailable.

      MultipleGeneVariants:

      (1) GeneName: GDAP2

      (1) Variant: c.946C>T; p.(Gln316*)

      (1) ClinVarID or CAID: CA1031513

      (1) gnomAD: Total AF 0.00006711 (gnomAD v4.1, https://gnomad.broadinstitute.org/variant/1-117896840-G-A?dataset=gnomad_r4)

      (2) GeneName: GDAP2

      (2) Variant: c.1305dup p.(Ser436fs*36)

      (2) ClinVarID or CAID: CA913189981

      (2) gnomAD: Total AF 0.000001301, gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-117878149-A-AC?dataset=gnomad_r4)