Patient3: IOPD Group, 11days old

CasePresentingHPOs:

HPOsFreeText: LDH = 664 U/L, CK = 809 U/L, ALT = 48 U/L, AST = 117 U/L, Mann-Whitney Test = 3

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo:

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)

ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

gnomAD: 0.0001240, https://gnomad.broadinstitute.org/variant/17-78086721-C-A

Patient9: IOPD Group, 14days old

CasePresentingHPOs:

HPOsFreeText: LDH = 597 U/L, CK = 998 U/L, ALT = 43 U/L, AST = 102 U/L, Mann-Whitney Test = 3

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo:

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)

ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

gnomAD: 0.0001240, https://gnomad.broadinstitute.org/variant/17-78086721-C-A

Patient1: Female, northern China

CasePresentingHPOs:

HPOsFreeText: IOPD

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo:

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.2662G>T (p.Glu888Ter)

ClinVar: 578595, https://www.ncbi.nlm.nih.gov/clinvar/variation/578595/

gnomAD: 1.65e-05, http://exac.broadinstitute.org/variant/17-78092467-G-T

Variant2: NM_000152.4(GAA):c.1927G>A (p.Gly643Arg)

ClinVar: 4023, https://www.ncbi.nlm.nih.gov/clinvar/variation/4023/

CasePDC-1: Female, Taiwan, Birth diagnosis

HPOsFreeText: 4MU enzyme activity at 1.15, MS/MS ennzyme activity at 1.2

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

CaseAddInfo: Patient is either a carrier or has a pseudodeficency allele, Second allele is wildtype

Case21HPOsFreeText: 20 mg/kg GAA treatment, GAA activity at 0.8 U/g, GAA activity at 8.9% lower limit of normal

CaseAddInfo: Late Onset Pompe Disease

CaseGenotypingMethod: Method not described, only that the diagnosis was "confirmed … based on 2 GAA gene mutations"

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 https://gnomad.broadinstitute.org/variant/17-78078341-T-G

No information given to identify where the variant is

Variant2: NM_000152.4: IVS15+2T>A

ClinVar:

gnomAD:

CaseAddInfo:

CaseLOPD-11: 8.3 years diagnosis

HPOsFreeText: GAA activity 2.0 (nmol · h−1 · mg−1), Mean percentage of normal 2.8%

GenotypingMethod: Newborn Screening Panels

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Chromosomal code not provided

Variant2: NP_000143.2:p.Q743∗ 

ClinVar: N/A

gnomAD: N/A

CaseAddInfo: Late Onset Pompe Disease

CasePD/VOUS-7: 3 weeks diagnosis

HPOsFreeText: GAA activity 3.43 (nmol · h−1 · mg−1), Mean percentage of normal 4.8%

GenotypingMethod: Newborn Screening Panels

Variant1: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

Variant2: NM_000152.4:c.2065G>A (p.Glu689Lys)

ClinVar: 4030 https://www.ncbi.nlm.nih.gov/clinvar/variation/4030/

gnomAD: East Asian 0.2355, Overall 0.05524 http://gnomad.broadinstitute.org/variant/17-78087041-G-A

Multiple interpretations of p.G615R possible

Variant3: NP_000143.2:p.G615R

CAID: PA113309 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NP_000143.2%3Ap.G615R

gnomAD: N/A

CaseAddInfo: Patient has one pseudodeficency allele and one allele of uncertain significance, Nomenclature claims Variant 1 and 2 are in cis

Case5: Male, 65 years onset, 72 years diagnosis, Italy

HPOsFreeText: See Group Phenotypes, ERT started at 72, GAA Activity at ~6 pmol/min/mg before ERT and ~10.5 after

GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.525delT (p.Glu176Argfs*45)

ClinVar: 4033 https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

gnomAD: European (Non-Finnish) 1.880e-4, Overall 9.959e-5 http://gnomad.broadinstitute.org/variant/17-78078909-CT-C

CaseAddInfo: Late Onset Pompe Disease

Patient1: Female 26yo

CasePresentingHPOs: HP:0003077

HPOsFreeText: LOPD

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 5year follow-up MRI, 15yr disease duration, ERT lasted for 67mo

CasePMIDs: PMID: 25614309

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.-32-13T>G

Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

Variant2: IVS9 G > C no ClinVar or CAID

Patient12: Female, 66yo

CasePresentingHPOs: HP:0003077, HP:0000822

HPOsFreeText: LOPD

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 7yr disease duration, ERT lasted 33mo

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.-32-13T>G

Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4(GAA):c.525delT (p.Glu176Argfs)

ClinVar: 4033, https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

gnomAD: 0.00009959, http://gnomad.broadinstitute.org/variant/17-78078909-CT-C

CaseP3-GAA: male, ethnicity = European, country origin = Italy

CasePresentingHPOs:

HPOsFreeText: enzyme activity = 1.97

CaseNotHPOs: HP:0010899, HP:0010916, HP:0003236

CaseAddInfo: known psuedodeficiency alleles (c.1726G>A and c.2065G>A)

CasePreviousTesting: initial and confirmatory DBS, biochemical tests

CaseGenotypingMethod: mutation analyses

Variant1: NM_000152.4(GAA):c.-32-13T>G

Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: n/a

NM_015338:c.566-5T>

Unable to identify variant for following reasons: 1) NM_015338 is for ASXL1 not ITGA2B 2) c.566 is not a exon boundary in ITGA2B Mane transcript 3) T> is not standard notation, is this a deletion of the T or something else?

NM_017489:c.415+10->G

Unable to identify variant for following reasons: 1) NM_017489 is for TERF1 not ITGA2B 2) c.415 is not a exon boundary in ITGA2B Mane transcript 3) ->G is not standard notation, is this a substitution to G of whatever is normally there or is it an insertion of G or something else?

CaseGM01565: Female, 16 years report, Caucasian, Europe

CasePresentingHPOs: HP:0003153 (Cystathioninuria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is a homozygote for this variant.

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.

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

CaseGM01454: Male, 7 years report, Asian, China

CasePresentingHPOs: HP:0003153 (Cystathioninuria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is a homozygote for this variant.

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.

Variant: CTH, 2-BP DEL, 940CT AKA: NM_001902.5:c.784_785del (p.Leu262Thrfs*21)

ClinVar: 2937 https://www.ncbi.nlm.nih.gov/clinvar/variation/2937/

gnomAD: East Asian 1.088e-4, Overall 7.960e-6 https://gnomad.broadinstitute.org/variant/1-70897822-ACT-A

found c.444dup in allele registry

according to Mutalyzer, for correct HGVS notation, the correct position was 2 nucleotides over. The aa consequence also looked the same as the article reported.

Case22 7yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0011342

(Lens dislocation, Mild intellectual disability, Mild developmental delay)

HPOsFreeText Patient had marfanoid features and was diagnosed on the basis of dislocated lens and mild 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.

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2(CBS):c.919G>A (p.Gly307Ser), 2. NM_000071.2(CBS):c.536_553del18 (p.Asp179_Leu184del), comp het

ClinVar 1. 117, 2. 198388

gnomAD 1. MAF=0.00041539(Other), no homozygotes, 2. MAF= 0.00002683(European(non-Finnish)), no homozygotes

CaseAddInfo patient also carries a common 68bp insertion, 88ins68, variant that does not cause hyperhomocysteinemia.

CasePMIDs n/a

Case16 3yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256

(Lens dislocation, Mild intellectual disability)

HPOsFreeText Diagnosis was based on dislocated lens and marfanoid features. 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 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.

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

Case5 14yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Diagnosis was based on dislocated lenses. Plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

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 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. NM_000071.2(CBS):c.325T>C (p.Cys109Arg), compound heterozygous

ClinVar 1. 120, 2. 212878

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.0001631(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case23 5yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0002751, HP:0000766

(Lens dislocation, Mild intellectual disability, Kyphoscoliosis, Abnormality of the sternum)

HPOsFreeText Patient was diagnosed on the basis of dislocated lenses. 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.

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2(CBS):c.430G>A (p.Glu144Lys), 2. IVS1+1G>A, compound heterozygous

ClinVar 1. 122, 2. n/a

CAID 2. need more info

gnomAD 1. MAF=0.00009799(South Asian), no homozygotes, 2. n/a

CaseAddInfo n/a

CasePMIDs n/a

FamilyLabel Family 1

Family1PresentingHPOs n/a

HPOsFreeText plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

FamilyNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CountryOrigin n/a

Ethnicity Anglo-Celtic

Race n/a

Family1PreviousTesting 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.

FamilyMethod1 PCR

FamilyMethod2 Sanger

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

ProbandLabel Case 1

Variant NM_000071.2(CBS):c.833T>C (p.Ile278Thr), homozygous

ClinVar 120

gnomAD MAF=0.001432(European(non-Finnish)), no homozygotes

FamilyAddInfo n/a

FamilyPMIDs n/a

Case13 8yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0000767

(Lens dislocation, Pectus excavatum)

HPOsFreeText borderline intellectual disability. 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 had a partial response to the treatment. Homocystine levels were sharply reduced on pyridoxine and folate treatment, but did not levels did not fall below 20μmol (nv <60μmol) on this treatment alone.

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.

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2(CBS):c.430G>A (p.Glu144Lys), 2. NM_000071.2(CBS):c.1111G>A (p.Val371Met), compound heterozygous

ClinVar 1. 122, 2. 212862

gnomAD 1. MAF=0.00009799(South Asian), no homozygotes, 2. MAF= 0.00006219(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

FamilyLabel Family 2

Family2PresentingHPOs n/a

HPOsFreeText plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

FamilyNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText no other sequelae

CountryOrigin n/a

Ethnicity Anglo-Celtic

Race n/a

Family2PreviousTesting 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.

FamilyMethod1 PCR

FamilyMethod2 Sanger

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

ProbandLabel Case 3

Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. NM_000071.2(CBS):c.302T>C (p.Leu101Pro), compound heterozygous

ClinVar 1. 120, 2. 189185

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. not in gnomAD

FamilyAddInfo n/a

FamilyPMIDs n/a

CaseDII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 970 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

CaseAII-4: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 2085 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband for Family A

Variant1: NM_000277.3(PAH):c.165del (p.Phe55fs)

ClinVar: 611 https://www.ncbi.nlm.nih.gov/clinvar/variation/611/

gnomAD: 0.00002639, https://gnomad.broadinstitute.org/variant/12-103306571-CA-C?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.143T>C (p.Leu48Ser)

ClinVar: 608 https://www.ncbi.nlm.nih.gov/clinvar/variation/608/

gnomAD: 0.001025, https://gnomad.broadinstitute.org/variant/12-102912816-A-G?dataset=gnomad_r3

CaseBI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 375 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.688G>A (p.Val230Ile)

ClinVar: 102784 https://www.ncbi.nlm.nih.gov/clinvar/variation/102784/

gnomAD: 0.0009025, https://gnomad.broadinstitute.org/variant/12-102855154-C-T?dataset=gnomad_r3

CaseEI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 430 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.1066-11G>A

ClinVar: 607 https://www.ncbi.nlm.nih.gov/clinvar/variation/607/

gnomAD: 0.0004116, https://gnomad.broadinstitute.org/variant/12-103237568-C-T

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

CaseAI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 330 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.143T>C (p.Leu48Ser)

ClinVar: 608 https://www.ncbi.nlm.nih.gov/clinvar/variation/608/

gnomAD: 0.001025, https://gnomad.broadinstitute.org/variant/12-102912816-A-G?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

CaseDI-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.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.898G>T (p.Ala300Ser)

ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

CaseAII-5: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 440 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.165del (p.Phe55fs)

ClinVar: 611 https://www.ncbi.nlm.nih.gov/clinvar/variation/611/

gnomAD: 0.00002639, https://gnomad.broadinstitute.org/variant/12-103306571-CA-C?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

CaseAII-3: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 370 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.165del (p.Phe55fs)

ClinVar: 611 https://www.ncbi.nlm.nih.gov/clinvar/variation/611/

gnomAD: 0.00002639, https://gnomad.broadinstitute.org/variant/12-103306571-CA-C?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

NonHumanModel: Mouse (Mus musculus)

GeneAlteration: A fragment covering exons 4-8 of the SLC1A3 locus was subcloned with the P290R seuqnece being inserted via PCR into the end of Exon 7. Thse clones were injected into blastocysts of C37BL/6N mice with these generatingfoster mice and chimeric mice being crossbred to excise the neomycin casette. Due to the high mortality rate, the surviving mice harboring the variant were backcrossed to 129/SvJ for a more robust mouse and higher survival rate for study.

ModelPhenotype: MP:0002064, MP:0001393, MP:0010387, MP:0008925, MP:0002182, MP:0000877, MP:0010170, MP:0014185 (Seizures, Ataxia, Abnormal Bergmann glial cell morphology, Increased cerebellar granule cell number, Abnormal astrocyte morphology, Abnormal Purkinje cell morphology, Abnormal glial cell apoptosis, Cerebellum atrophy)

ModelFreeText: Slower firing of purkinje neurons

HumanPhenotype: HP:0001251, HP:0002076, HP:0001250 (Ataxia, Migraine, Seizure)

HumanFreeText: N/A

ModelEvidence: The first set of mutant knock-in mice were subject to generalized seizures and death before the weaning period, requiring a backcross onto the 129/SvJ strain in order to reduce lethal seizure activity and delay the onset. Even so, mutant mice demonstrated significant phenotypes indicative of human Episodic Ataxia including epilepsy, ataxia, and reduced motor/gait coordination. In order to determine the pathogenc mechanism, cerebellar Bergmann glia cells were examined to find a pronounced age-dependent reduction of cell numbers between P10 and P20. Immunostaining showed decreased numbers of somata and expression, demonstrating that the EAAT1 mutants were subject to cell death. Granule cell migration was also impaired during development, coupled with invasion of reactive astrocytes into the molecular layer demonstrating attempted repair. Following from this change, Purkinje neurons were examined and found to have been reduced and the morphology altered in mutant mice. As the P290R variant is known to increase EAAT1 anion currents in heterologous expression systems, measurement of these currents in mouse Bergmann glia cells showed significantly increased current, decreased Cl- concentration, and a resulting higher TUNEL expression in these cells, indicating earlier apoptosis events of these cell types. Spiking activities and developmental acceleration is absent in these cell types, likely due to progressive deterioration. This was verified by an observation of cerebellar size, where mutant cerebellar tissue showed generalized degeneration compared to the WT mice.

ModelVariant: NM_004172.5(SLC1A3):c.869C>G (p.Pro290Arg)

ClinVar: 9441, https://www.ncbi.nlm.nih.gov/clinvar/variation/9441/

CaseF4P: 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 disrupts the WT donor site and is predicted to alter splicing

CasePreviousTesting: Blood phenylalanine before treatment was 1150 μmol/l, Blood tyrosine before treatment was 30 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(PAH):c.60+5G>A

ClinVar: 120281 https://www.ncbi.nlm.nih.gov/clinvar/variation/120281/

gnomAD: Not in gnomAD

CaseF5S: 21 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variant has been shown to abolish canonical splice donor site and lead to a null protein

CasePreviousTesting: Blood phenylalanine before treatment was 1698 μmol/l, Blood tyrosine before treatment was 37 μmol/l

CaseGenotypingMethod: N/A

Variant: NM_000277.3(PAH):c.842+1G>A

ClinVar: 599 https://www.ncbi.nlm.nih.gov/clinvar/variation/599/

gnomAD: 0.00007752, http://gnomad.broadinstitute.org/variant/12-103246592-C-T

CaseF5P: 18 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband for Family 5, Variant has been shown to abolish canonical splice donor site and lead to a null protein

CasePreviousTesting: Blood phenylalanine before treatment was 1260 μmol/l, Blood tyrosine before treatment was 36 μmol/l

CaseGenotypingMethod: N/A

Variant: NM_000277.3(PAH):c.842+1G>A

ClinVar: 599 https://www.ncbi.nlm.nih.gov/clinvar/variation/599/

gnomAD: 0.00007752, http://gnomad.broadinstitute.org/variant/12-103246592-C-T

CaseF1S: 5 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variant is demonstrated to activate a cryptic splice site and abolish the canon splice site leading to a premature termination and nonsense-mediated decay

CasePreviousTesting: Blood phenylalanine before treatment was 1431 μmol/l, Blood tyrosine before treatment was 35 μmol/l

CaseGenotypingMethod: N/A

Variant: NM_000277.3(PAH):c.169-2A>G

ClinVar: 555212 https://www.ncbi.nlm.nih.gov/clinvar/variation/555212/

gnomAD: 0.00003267, http://gnomad.broadinstitute.org/variant/12-103288698-T-C

Case: P.1017/ BIODEF 1035, male, Fars, 12.5 years (Dx)

CasePresentingHPOs: HP:0008297

Plasma Phe levels at 12.5 years 1116uM (per BIODEF database). Neopterin level at 1.52U.

CaseNOTHPOs:

CasePreviousTesting: n/a

CaseGenotypingMethod: PCR of D1 and direct sequencing.

Variant: NM_000281.3(PCBD1):c.313T>C (p.Ter105Gln)

ClinVar ID: 428616

Homozygous

gnomAD: MAF (South Asian)= 3.283E-5, hets only, no homozygous. http://gnomad.broadinstitute.org/variant/10-72643709-A-G

AddCaseInfo: The paper notes that the parents of all the individuals were tested. Consanguinity was not noted for parents, but may be likely due to the same variant.

VariantEvidence: No variant evidence was provided in this article. The mutation does change the termination codon and thus extends the protein by 16 amino acids.

Case16 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 4885(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 713(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 R402W variant destroys an MspI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. Likewise, the R128X variant destroys a Sau961 site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), 2. NM_000159.3(GCDH):c.382C>T (p.Arg128Ter), compound heterozygous

ClinVar 1. 2085, 2. 371176

gnomAD 1. MAF=0.0007566(European(Finnish)), no homozygotes, 2. MAF= 0.00002891(Latino), no homozygotes

CaseAddInfo Sibling, case 17, had a mild phenotype: static or improving dystonia, with maintained ability to walk without assistance. GC-MS measured glutarate of 6644(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 603(nv 2–14 mm/mol creatinine).

CasePMIDs n/a

Case42 sex unknown, Spain

CasePresentingHPOs HP:0006846, HP:0000707

(Acute encephalopathy, Neurological abnormality)

HPOsFreeText Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. 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 35(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 268(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 A433V variant creates an MwpI restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved.

Variant NM_000159.3(GCDH):c.1298C>T (p.Ala433Val), homozygous

ClinVar 556228

gnomAD MAF= 0.00003266(South Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs see notes on previous studies

Case1 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 3336(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 825(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 NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

ClinVar 2083

gnomAD MAF= 0.0004013(African), no homozygotes

CaseAddInfo Sibling(Case 2) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 2120mmol/mol creatinine and 3-OH-glutarate was 543mmol/mol creatinine.

CasePMIDs n/a

Case13 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 1288(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 75(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 R402W variant destroys a MspI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

Variant NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), homozygous

ClinVar 2085

gnomAD MAF= 0.0007566(European(Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

Case27 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 screening as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 2(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 18(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 10.

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 site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant NM_000159.3(GCDH):c.1198G>A (p.Val400Met), homozygous

ClinVar 2088

gnomAD MAF= 0.0002769(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

"proband disclosed a heterozygous 18 bp deletion (c.553_570del18) in GCDH (NM_000159) predicted to result in a six amino acids deletion (p.Gly185_- Ser190del)"

I don't see any patient carrying this variant in Table 1

Case10 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 778(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 264(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 Sibling (Case 11) was asymptomatic. GC-MS measured glutarate of 2083(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 262(nv 2–14 mm/mol creatinine)

CasePMIDs n/a

Case3 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 1773(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 340(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 NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

ClinVar 2083

gnomAD MAF= 0.0004013(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case29 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 5(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 114(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 V400M variant creates an NlaIII site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant NM_000159.3(GCDH):c.1198G>A (p.Val400Met), homozygous

ClinVar 2088

gnomAD MAF= 0.0002769(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case18 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 4097(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 212(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 R402W variant destroys an MspI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

Variant 1. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

ClinVar 1. 2085, 2. 370106

gnomAD 1. MAF=0.0007566(European(Finnish)), no homozygotes, 2. MAF= 0.00005646(Latino), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case# PB5, 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_000056.4(BCKDHB):c.574G>A (p.Gly192Arg)

ClinVar 96596

VariantEvidence none

CaseAddInfo consanguineous family

Case# PB6, 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_000056.4(BCKDHB):c.817A>C (p.Thr273Pro)

ClinVar 96610

VariantEvidence none

CaseAddInfo consanguineous family

Case# PB4, 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_000056.4(BCKDHB):c.502C>T (p.Arg168Cys)

ClinVar 96586

VariantEvidence none

CaseAddInfo consanguineous family

CasePMIDs previously studied in 17922217

Case# PA4

Variant NM_000709.3(BCKDHA):c.661_664delTACG (p.Tyr221Glnfs)

ClinVar 203638

Case# PA3

Variant NM_000709.3(BCKDHA):c.647-1G>C

ClinVar 431985

gnomAD 0.000009079( European (Non-Finnish)), 0.000004103 (Overall)

CasePMIDs described previously in 19715473

Case# PA1

Variant NM_000709.3(BCKDHA):c.347A>G (p.Asp116Gly)

ClinVar 93354

VariantEvidence none

for nucleotide coordinates add 84 or for codons add 28 to get the correct position on NM_001182.4 or just use the given coordinates on this old transcript NM_001201377.1

Case13 age/gender unknown, Caucasian, Germany

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Possible PDE: no trial of pyridoxine withdrawal performed and no antecedent affected.

CaseNotHPOs n/a

CasePreviousTesting pre-treatment testing: Pipecolic acid in plasma 53(nv 1-3.2µmol/liter), PA in urine 410µmol/mmol creati-nine(nv 0.55–24.1), AASA in plasma 14(nv<0.2µmol/liter), urine AASA 342(nv<1mmol/molcreatinine).

Variant NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), homozygous

ClinVar 17994

gnomAD not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case1 age/gender unknown, Caucasian, German

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Possible PDE: no trial of pyridoxine withdrawal performed and no antecedent affected

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 16(nv 0.4-4.9µmol/liter), AASA in plasma 3.9(nv<0.2µmol/liter), urine AASA 62(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

Variant 1. NM_001182.4(ALDH7A1):c.902A>T (p.Asn301Ile), 2. NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), compound heterozygous

ClinVar 1. 18001, 2. 17994

gnomAD neither in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case5: male, Lebanon, neonatal screening 7 days

CasePresentingHPOs: HP:0045045, HP:0002155

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Treatment of 150-200 mg L-carnitine/kg body weight and has shown normal development until 10 months.8 months: elevated serum triglycerides and GOT.

CaseNotHPOs:

CasePreviousTesting: Neonatal screening: elevated C5 acylcarnitine (0.51 umol/l and 0.72 umol/l; upper 99th percentile 0.29 umol/l) and C5/C2 acylcarnitine ratio (0.04 and 0.06; upper 99th percentile 0.02). 8 months: elevated serum triglycerides (673 mg/dl; ref <205) and GOT (57 U/l; ref <35).

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced. Sibling and parents: only exons 1, 4, and 10 were analyzed.

Variant: 1. NM_001609.3(ACADSB):c.1159G>A (p.Glu387Lys) 2. NM_001609.3(ACADSB):c.443C>T (p.Thr148Ile)

ClinVar: 1. 9203; 2. 9202

gnomAD: 1. Latino 0.0004797, Overall 0.0002404, no homozygotes; 2. South Asian 0.002678; Overall 0.0008097, no homozygotes

VariantEvidence: In vitro expression of c.1159G>A in E. coli shows no protein on Western blot, reduced enzymatic activity to 2% and defects in protein folding and stability. c. 443C>T decreases ACADSB enzymatic activity to 2.8% of wild type in vitro (PMID: 20547083).

CaseAddInfo: 3 year old brother had a similar metabolite profile, but was not picked up by newborn screening (different cut-off values were used). Parents were normal. Patient also had c.38G>A polymorphism.

CasePMIDs:

CaseOS-104_II-1: Male, Birth onset, Turkey

CasePresentingHPOs: HP:0001992, HP:0001324, HP:0002317 (Organic aciduria, Muscular hypotonia, Unsteady gait)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001263, HP:0001252 (Global developmental delay, Muscle weakness)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous, Two younger brothers are unaffected, The variant results in a frameshift that extends the WT protein to 408 AAs and affects the C-terminal peptidase domain

CasePreviousTesting: GS-MS analysis identified urinary organic acids dominated by N-aceylated AAs, supported by NMR spectroscopy of urine samples with serum samples being negative; Metabolite pattern of brother was unremarkable; Values of excreted AAs are in Table 1; Ultrasound, electromyography, and NMR tomography of the musculature from the lower extremities showed unremarkable results; Routine histological, histochemical, enzyme histochemical, and immunohistochemical studies did not reveal any significant myopathological abnormalities

CaseGenotypingMethod: Genomic DNA was extracted from blood samples or after EBV transformation of peripheral blood lymphocytes. Exons and exon-intron boundaries were amplified and bidirectionally sequenced.

Variant: NM_000666.3(ACY1):c.1102_1103AC[3] (p.Pro369fs)

ClinVar: 18109, https://www.ncbi.nlm.nih.gov/clinvar/variation/18109/

gnomAD: Not in gnomAD

CaseOS-120_II-1: Female, Birth onset, German/Italian

CasePresentingHPOs: HP:0001992, HP:0011343 (Organic aciduria, Moderate global developmental delay)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Younger brother is unaffected; Proband is confirmed compound heterozygous as mother is heterozygous for R353C but father is unavailable

CasePreviousTesting: GS-MS analysis identified urinary organic acids dominated by N-aceylated AAs, supported by NMR spectroscopy of urine samples with serum samples being negative; Values of excreted AAs are in Table 1; Neuropediatric evaluation performed

CaseGenotypingMethod: Genomic DNA was extracted from blood samples or after EBV transformation of peripheral blood lymphocytes. Exons and exon-intron boundaries were amplified and bidirectionally sequenced.

Variant1: NM_000666.3(ACY1):c.699A>C (p.Glu233Asp)

ClinVar: 18111, https://www.ncbi.nlm.nih.gov/clinvar/variation/18111/

gnomAD: 0.0001846, https://gnomad.broadinstitute.org/variant/3-52021204-A-C

Variant2: 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

Case#: Patient 2, caucasian, 3 days (onset)

CasePresentingHPOs:

HPOFreeText: 3 days: hypoglycemia, poor feeding, lethargy, hypothermia. MRI: bilateral areas of subacute ischemia, increased T1 signal in lentiform nuclei consistent with global hypoxia. 1 year MRI: evolving areas of ischemia, thinning of gyri, delayed myelination of corpus callosum. 4 years: developmental delay, epilepsy. 6 years: unable to crawl or walk recurrent ear infections, chronic sinusitis, left eye extropia, microcephaly.

CaseNotHPOs: Normal neonatal EEG

CasePreviousTesting: 3 days: increased 2-methylbutyrylglycine (urine), 2-methylbutyrylcarnitine in plasma (C5-carnitine 1.4-2.4 uM, ref <0.4 uM)., elevated short chain carnitine to free carnitine (1.0, ref <0.5), normal blood amino acids. SBCAD enzyme activity in fibroblasts: 0.1 nmol/min/mg, ref. 0.16-0.29 nmol/min/mg).

CaseGenotypingMethod: Genomic DNA sequencing of all exons and part of flanking introns.

Variant: 1. NM_001609.3(ACADSB):c.303+3A>G 2. NM_001609.3(ACADSB):c.763C>T (p.Leu255Phe)

ClinVar: 1. 448980 2. 9200

gnomAD: 1. Not in gnomAD 2. Not in gnomAD

VariantEvidence: Skipping of exon 3 confirmed by mRNA analysis and minigene assay.This leads to a shifted reading frame with a PTC and likely NMD (when mRNA from patient 2's fibroblasts, who is het. for the variant, was analyzed, they saw no product from the mutant allele). CIS OR TRANS??

CaseAddInfo: Sister was also diagnosed with SBCADD prenatally and has been treated since birth. She has no clinical symptoms.

CasePMIDs: 10832746

Case#: Patient 1, Somalia, birth

CasePresentingHPOs: HP:0002104, HP:0001250, HP:0001263, HP:0008947

HPOFreeText: At birth, GC/MS of urine showed elevated 2-methylbutyrylglycine and 2-ethylhydracrylic acid, mildly elevated lactate. Plasma carnitine profile normal. NBS blood spot: high normal acylcarnitine profile (0.39 uM C5-acylcarnitine, ref <0.4 uM). 6 weeks: apena. 6 months: seizures, decline around 10 months, normal CT cerebrum. 7 months: protein-restricted diet. 8 months: normal EEG, infantile spasms. 9 months: global developmental delay, hypotonia. 10 months: sparse eye contact.

CaseNotHPOs: Normal chromosome analysis, cytomegalovirus (CMV) negative, normal hearing and vision, no skin changes.

CasePreviousTesting: SBCAD enzyme activity in fibroblasts: 0.17 +/- 0.01 nmol/min/mg, ref. 0.54-0.79 nmol/min/mg).

CaseGenotypingMethod: Genomic DNA sequencing of all exons and part of flanking introns.

Variant: NM_001609.3(ACADSB):c.303+3A>G

ClinVar: 448980

gnomAD: Not in gnomAD

VariantEvidence: Skipping of exon 3 confirmed by mRNA analysis and minigene assay.This leads to a shifted reading frame with a PTC and likely NMD (when mRNA from patient 2's fibroblasts, who is het. for the variant, was analyzed, they saw no product from the mutant allele).

CaseAddInfo:

CaseJE: Male, 10 yrs report,

CasePresentingHPOs: HP:0002131, HP:0004374, HP:0001319, HP:0001270, HP:0001350, HP:0002076, HP:0010547, HP:0001272, HP:0002381, HP:0002181, HP:0011182, HP:0045084, HP:0001289, HP:0002078, HP:0007034, HP:0007772, HP:0011289 (Episodic ataxia, Hemiplegia/hemiparesis, Neonatal hypotonia, Motor delay, Slurred speech, Migraine, Muscle flaccidity, Cerebellar atrophy, Aphasia, Cerebral edema, Interictal epileptiform activity, Limb myoclonus, Confusion, Truncal ataxia, Generalized hyperreflexia, Impaired smooth pursuit, EEG with temporal sharp slow waves)

HPOsFreeText: Left visual field neglect, Episodic left hemifield distortion

CaseNotHPOs: HP:0000639, HP:0000570, HP:0007670, HP:0000267 (Nystagmus, Impaired saccades, Abnormal vestibulo-ocular reflex, Cranial asymmetry)

NotHPOsFreeText: N/A

CaseAddInfo: Variant is confirmed heterozygous de novo via parental testing and confirmed paternity; No family member has any neurological signs or symptoms

CasePreviousTesting: Previously screened for CACNA1A and ATP1A2 with negative results; Episodic migraine attacks led to progressive right-sided headache and left-sided symptoms such as weakness and visual field neglect; Comprehensive metabolic workup revealed no abnormality in the CSF, serum, and urine; MRI showed a diffuse right-sided cortical hyperintensity most prominent in fluid-attenuated inversion recovery (FLAIR); EEG showed subclinical seizure activity in the left frontal temporal cortex and diffuse slowing on the right

CaseGenotypingMethod: DNA was extracted from blood samples. All exons and flanking intronic regions of SLC1A3 were PCR-amplified and directly sequenced. These were confirmed via resequencing.

Variant: NM_004172.5(SLC1A3):c.869C>G (p.Pro290Arg)

ClinVar: 9441, https://www.ncbi.nlm.nih.gov/clinvar/variation/9441/

gnomAD: Not in gnomAD

Variant: NM_002225.3:c.749G>C

VariantEvidence: This variant is located in the coil region of the protein where hydrogen bonding is limited, thus the variant would not have significant effects on bonding. This along with the mild phenotype in Patient 5 suggests a mild genotype-phenotype correlation for this variant

CaseV1 Male, 6yr report, Dutch

CasePresentingHPOs HP:0025116, HP:0001941, HP:0002098, HP:0000737, HP:0010818, HP:0010851, HP:0000486, HP:0002464, HP:0001288, HP:0000750, HP:0000238, HP:0001263, HP:0100021

(Fetal distress, Acidosis, Respiratory distress, Irritability, Generalized tonic seizures, EEG with burst suppression, Squint, Spastic dysarthria, Gait difficulties, Speech delay, Hydrocephalus, Developmental delay, Cerebral palsy)

HPOsFreeText born at 35wk gestation. (neonatal, pre-treatment:) apgar score 1min:6, 5min:7; acidosis, respiratory distress, irritability, generalized tonic fits(onset at 1h old), burst suppression EEG, resistant to ACD's. (4do:) first pyridoxine trial, trial dose/route=50mg i/v, complete cessation of seizures, apnoea, hypotonia/sleepiness, hypotension, initial maintenance daily dose=50mg. (infancy/childhood:) squint, spastic dysarthria, gait problems, speech delay/difficulties, IQ:60-70, hydrocephalus on MRI requiring ventriculoperitoneal shunt. (PMID:16159904:) developmental delay, cerebral palsy

CaseNotHPOs HP:0001557, HP:0003270, HP:0002013, HP:0011169, HP:0001336, HP:0002521, HP:0025116

(Abnormal Intrauterine movements, Abdominal distension, Vomiting, Clonic seizures, Myoclonic jerk, Hypsarrhythmia, Fetal distress)

NotHPOsFreeText (neonatal, pre-treatment:) abdominal distension, clonic or myoclonic jerks, hypsarryhythmia, or other EEG changes. (infancy/childhood:) recurrence of seizures with febrile illness. (PMID:16159904:) intrauterine seizures, signs of fetal distress, for example, meconium stained amniotic fluid or abnormal cardiotocography

CasePreviousTesting Administration of pyridoxine relieved patient's seizures. CSF pipecolic acid: 6.9, 1.5(nv<0.15μM), plasma pipecolic acid: 5.3(nv<2.5μM), CSF AASA: 1(nv <0.1μM), plasma AASA: 2.4(nv<0.2μM), urine AASA: 12(nv<1 mmol/mol creatinine).

Variant 1. NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), 2. NM_001182.4(ALDH7A1):c.328C>T (p.Arg110Ter), compound heterozygous

ClinVar 1. 17994, 2. 17995

gnomAD 1.MAF= 0.0006123(European(Non-Finnish)), no homozygotes, 2. MAF=0.0001385(Other), no homozygotes

CaseAddInfo nonconsanguineous parents

CasePMIDs 17721876, 17088338, 16159904

FamilyLabel Family H

FamilyHPresentingHPOs HP:0001557, HP:0001941, HP:0002098, HP:0003270, HP:0002013, HP:0001336, HP:0010851, HP:0000750

(Abnormal intrauterine movements, Acidosis, Respiratory distress, Abdominal distension, Vomiting, Myoclonic jerks, EEG with burst suppression, Speech delay)

HPOsFreeText born after 40wks gestation. (neonatal, pre-treatment:) apgar score at 1min:9, 5min:9, acidosis, respiratory distress, abdominal distension, vomiting, onset of myoclonic jerks at 12h, EEG burst suppression. (2d:) introduced to pyridoxine therapy, trial dose/route of 100mg i/v, complete cessation of seizures, ventilated, initial daily dose of 100mg. (infancy/childhood:) speech delay, IQ: 60-70, no seizures on withdrawal from therapy

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity Turkish

Race n/a

FamilyHPreviousTesting Administration of pyridoxine relieved patient's seizures.

ProbandLabel H1

Variant NM_001182.4(ALDH7A1):c.518-1G>C, homozygous

ClinVar 17994

gnomAD MAF=0.0006123(European(non-Finnish)), no homozygotes

FamilyAddInfo 1st cousin parents

FamilyPMIDs n/a

CaseP1 Male, 4.5yr report, Austrian

CasePresentingHPOs HP:0010818, HP:0010851, HP:0001290, HP:0011343, HP:0007359, HP:0001942, HP:0002376, HP:0001290

(Generalized tonic seizures, EEG with burst suppression, Hypotonia, moderate GDD, focal seizures, Metabolic acidosis, Developmental regression, Hypotonia)

HPOsFreeText born 40wk gestation. (neonatal, pre-treatment) apgar scores at 1min:8, 5min:9, 10min: 10, generalized tonic fits at <1d old and burst suppression EEG. (3d:) introduced pyridoxine therapy, 100mg I/v trial dose/route, complete cessation of seizures, apnoea(3d), hypotonia, sleepiness, initial maintenance daily dose of 10 mg/kg. (infancy/childhood:) hypotonia, moderate IQ delay. (4d:) withdrew from pyridoxine trial then focal seizures recurrenced 3 weeks after(definite PDE). (PMID: 0894227) gestational toxicosis, birth weight 3,260g, myoclonic jerks of both arms with hours of birth.Paroxysms of polyspike-wave-activity on EEG, normal cranial imaging,CSF analysis

CaseNotHPOs n/a

CasePreviousTesting Administration of pyridoxine relieved patient's seizures. CSF pipecolic acid: 3.4(nv<0.15μM), urine AASA: 168 before treatment(nv<1 mmol/mol creatinine). Blood lactate: 4.0mM and CSF lactate: 4.2mM (nv <2.5mM). (PMID:17068770:)post treatment testing: Pipecolic acid in plasma 4.7(nv 0.7-2.6mmol/liter), AASA in plasma 2.6(nv<0.2mmol/liter), urine AASA 17(nv<1mmol/molcreatinine). (PMID: 0894227) CSF analysis, organic acids in urine, amino acids in serum, and VLCFAs were normal. Plasma PA at 1st week 49µmol/L(before treatment)(nv 1-3.2), at 1-6mo 14.3µmol/L, 6-12mo 10.1µmol/L, CSF PA at 0-1yr 3.38µmol/L.

Variant NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), homozygous

ClinVar 17994

gnomAD MAF= 0.0006123(European(Non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs 10894227 (Patient 2), 17068770 (Patient 11)

FamilyLabel Family C

FamilyCPresentingHPOs HP:0001941, HP:0002098, HP:0000737, HP:0011169, HP:0010818, HP:0001336, HP:0000750

(Acidosis, Respiratory distress, Irritability, Clonic seizures, Generalized tonic seizures, Myoclonic jerks, Speech delay)

HPOsFreeText (neonatal, pre-treatment:) acidosis, respiratory distress, irritability, clonic seizures, generalized tonic seizures, myoclonic jerks. no apnoea, hypotonia, sleepness, or hypotension during pyridoxine therapy. (infancy/childhood:) speech delay.

FamilyNotHPOs HP:0003270, HP:0002013, HP:0001290, HP:0010851, HP:0002521

(Abdominal distension, Vomiting, Hypotonia, EEG with burst suppression, Hypsarrhythmia)

NotHPOsFreeText (neonatal, pre-treatment:) abdominal distension, vomiting, hypotonia, EEG with burst suppression, hypsarrhythmia

CountryOrigin n/a

Ethnicity Turkish

Race n/a

FamilyCPreviousTesting n/a

ProbandLabel C1

Variant NM_001182.4(ALDH7A1):c.1597delG (p.Ala533Profs), homozygous

ClinVar 17999

gnomAD not in gnomAD

FamilyAddInfo 1st cousin parents

FamilyPMIDs n/a

Case1: Amish

HPOsFreeText: GA1 confirmed

Case (Level 2)

CasePreviousTesting: GA1 confirmed

CaseMethod1: PCR

CaseMethod2: MaeII restriction digest

CaseGenotypingMethod: same as Amish group

Variant: NM_000159.3(GCDH):c.1262C>T (p.Ala421Val)

ClinVar: 2082

gnomAD: 0.0002867 (European non-Finnish)

CaseAddInfo: homozygous, founder allele in Amish of Lancaster County from immigrant from Switzerland to US in early 18th century. 4 non-Amish patients were found heterozygous for this allele with central European ancestry.

Case#: GA5, Southern Italy, 40 years (onset), gender unknown

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

CaseHPOsFreeText: Presented with visual disturbances at age 40 years. Plasma ornithine levels could be normalized by diet alone. Not responsive to Vitamin B6 treatment.

CaseNotHPOs: Neonatal encephalopathy

CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 805 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.1307T>A (p.Ile436Asn)

ClinVar: 56115

gnomAD: The maximum population minor allele frequency in gnomAD = 0.00002662 (European non-Finnish); no homozygotes in any population.

VariantEvidence: The variant was expressed in S. cerevisae with a deletion of CargB, the year ortholog of OAT, that cannot grow in media with ornithine as the sole nitrogen source. Whereas expression of wild type OAT allows yeast to grow in media with ornithine as the sole nitrogen source, no growth was observed when the variant was expressed. OAT enzymatic activity was measured and was <10% normal, and OAT protein was barely detectable on Western blot.

Case#: GA3, Turkey, 5 years (onset), gender unknown

CaseHPOs: HP:0012026 (hyperornithinemia)

CaseHPOsFreeText: Presented with visual disturbances at 5 years of age. No further details.

CaseNotHPOs: Neonatal encephalopathy

CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 650umol/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.991C>T (p.Arg331Ter) (homozygous)

ClinVar: 56141

gnomAD: The maximum population minor allele frequency in gnomAD is 0.0001446 (Latino); no homozygotes in any population.

Family#: GA-07, Lebanese Maronite

FamilyHPOs: HP:0012026

FamilyHPOText: “Clinical presentation typical of gyrate atrophy”; no further details.

FamilyGenotypingMethod: RNAse A protection assay using 2 probes to cover the entire OAT cDNA, narrowed the site of the variant to the 5’ end of the gene. DNA sequence analysis revealed c.3G>A (p.Met1?). Parents are confirmed heterozygous, based on RFLP analysis.

FamilyPreviousTesting: Elevated plasma ornithine; Fibroblast OAT activity was undetectable

Variant: NM_000274.3(OAT):c.3G>A (p.Met1?)

ClinVar: 146

gnomAD: Not in gnomAD

Proband: GA-07, Case 7, female, Lebanese, 32 (at report)

CasePreviousTesting: Plasma ornithine, on normal diet: 771uM/l (normal 75+/-25). Fibroblast OAT activity was undetectable (ornithine value from Kaiser-Kupfer, M. I., and D. Valle. 1986. Progress in Retinal Research. p179-206)

CaseAddInfo: Parents are confirmed heterozygotes.

Sibling: GA-07, Case 16, male, Lebanese, 33 (at report)

SiblingPreviousTesting: Plasma ornithine, on normal diet: 800uM/l (normal 75+/-25). Fibroblast OAT activity was undetectable (ornithine value from Kaiser-Kupfer, M. I., and D. Valle. 1986. Progress in Retinal Research. p179-206)

Points: 1 point

Case1: Male, 3 months diagnosis/death, Egypt, African

CasePresentingHPOs: HP:0001999, HP:0011968, HP:0001531, HP:0001270, HP:0001252, HP:0003468, HP:0001636, HP:0001274 (Dysmorphic facial features, Poor feeding, Failure to thrive in infancy, Motor delay, Muscle hypotonia, Abnormal vertebrae, Tetraology of Fallot, Agenesis of corpus callosum)

HPOsFreeText: Agenesis of the cingulate gyrus

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: Parents are consanguinous, Proband is homozygous for this mutation, Died a few days after hospital admission in infancy

CasePreviousTesting: Increased levels of S-2-carboxypropyl-cysteamine and S-2-carboxypropyl-cysteine, Fibroblast and liver homogenates of patient 1 showed normal hydratase activities towards methacrylyl-CoA (as well as crotonyl-CoA and tiglyl-CoA),

CasePMIDs: 7122152

CaseGenotypingMethod: After confirming low HICBH activity in fibroblasts of the patients, the gene was analyzed at the genomic level and the mRNA level in both patients using sequence analysis.

Variant: NM_014362.3:c.220-9T>G

ClinVar: 1144 https://www.ncbi.nlm.nih.gov/clinvar/variation/1144/

gnomAD: Not in gnomAD

Case2: Male, Caucasian, 9 months onset

CasePresentingHPOs: HP:0011968, HP:0001270, HP:0001251, HP:0002376, HP:0002121, HP:0000737, HP:0002317, HP:0002599, HP:0002078, HP:0012389, HP:0001310, HP:0001337, HP:0001254, HP:0001942, HP:0002329, HP:0001308, HP:0002599, HP:0001332, HP:0002181, HP:0002134 (Poor feeding, Delayed motor milestones, Ataxia, Developmental regression, Absence seizures, Irritability, Unsteady gait, Head titubation, Truncal ataxia, Appendicular hypotonia, Dysmetria, Tremor, Lethargy, Metabolic acidosis, Drowsiness, Tongue fasciculation, Head titubation, Dystonia, Cerebral edema, Abnormality of the basal ganglia)

HPOsFreeText: Head bobbing at 4 months, Rolled over at 5 mo but lost the ability at 10 mo, Reaching out and grasping objects at 4 mo but lost the ability at 13 mo, Eye rolling episodes at 9 months, Lost ability to finger feed at 10 months, Inability to sit unsupported, At 14 months blood pH was 7.29 with a base deficit of 15.8 mmol/L, Sluggish papillary responses, Pooling of secretions in the mouth, No improvement on treatment with thiamine or a combination of vitamin C, vitamin E, and ubiquinone, Signal abnormalities in the globus pallidus and the midbrain

CaseNotHPOs: HP:0000639, HP:0002151, HP:0001987, HP:0003116, HP:0012443 (Nystagmus, Increased serum lactate, Hyperammonemia, Abnormal echocardiogram, Abnormality of brain morphology)

NotHPOsFreeText: N/A

CaseAddInfo: Parents were nonconsanguinous, Proband is compound heterozygous for these mutations with parental testing

CasePreviousTesting: Pyruvate dehydrogenase and pyruvate carboxylase in cultured human skin fibroblasts, Activities of respiratory chain complexes in a muscle biopsy, Marked reduction of complex I (patient 0.089, controls 0.104–0.268) and a borderline reduction of complex IV (patient 0.013, controls 0.014–0.034), Organic acid analysis during ketotic episodes showed excessive excretion of 3-hydroxybutyrate and acetoacetate and moderate excretion of lactate, 2-hydroxyisovalerate, 2-oxoisocaproate, dicarboxylic acids (C6, C8, C10), and methylmalonate, with normal levels of methylcitrate as opposed to normal levels when well, Urine amino acid analysis, Elevated levels of hydroxy-C4-carnitine (patient 0.45-1.73 μM, controls <0.4 μM) even when not ketotic

CaseGenotypingMethod: After confirming low HICBH activity in fibroblasts of the patients, the gene was analyzed at the genomic level and the mRNA level in both patients using sequence analysis.

Variant1: NM_014362.4:c.365A>G (p.Tyr122Cys)

ClinVar: 1145 https://www.ncbi.nlm.nih.gov/clinvar/variation/1145/

gnomAD: Latino 4.338e-4, Overall 6.373e-5 https://gnomad.broadinstitute.org/variant/2-191155151-T-C

Variant2: NM_014362.3:c.79-3C>G

ClinVar: 1146 https://www.ncbi.nlm.nih.gov/clinvar/variation/1146/

gnomAD: Not in gnomAD

Case2267(g) Caucasian, Hispanic

CasePresentingHPOs HP:0003571 (Propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting none reported

Variant NM_000532.4(PCCB):c.1218_1231delGGGCATCATCCGGCinsTAGAGCACAGGA (p.Gly407Argfs)

ClinVar 38875

gnomAD not in gnomAD

CaseAddInfo parents tested heterozygous

CasePMIDs n/a

Case467 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

NonHumanModel: Mouse (Mus musculus)

GeneAlteration: Mutations were induced in mice germline cells at a rate near 10^-3 per locus via an alkylating agent called ethylnitrosourea. Inbred BTBR males were treated with this agent and bred to normal BTBR females. Three hundred and fifty progeny were screened for mutations that did not complement the previous model PAH_enu1 and if present bred to a previous homozygote and tested for hyperphenylalaninemia. A PHE clearance test was performed in questionable cases. For those that tested positive the carrier parents were mated to a normal BTBR partner to establish a cogenic mutant line. Western blot confirmed reduced to absent CRM in liver.

ModelPhenotype: HP:0007513, HP:0000707, HP:0005982, HP:0100610, HP:0004923, HP:0001510, HP:0000252 (Generalized hypopigmentation, Abnormality of the nervous system, Reduced phenylalanine hydroxylase activity, Maternal hyperphenylalaninemia, Hyperphenylalaninemia, Growth delay, Microcephaly)

ModelFreeText: Serum PHE concentrations were 15x wild-type for PAH_enu2 (23.1 +/- 6.9 mg/dl, 1.5 +/- 0.5 reference) and 14x wild-type for PAH_enu3 (20.3 +/- 5.9 mg/dl, 1.5 +/- 0.5 reference), PAH activity was reduced to <1% wild-type for PAH_enu2 (0 +/- 2 delta O.D. x 10^3/min/mg protein, 40 +/- 6 reference) and <10% wild-type for PAH_enu3 (5 +/- 5 delta O.D. x 10^3/min/mg protein, 40 +/- 6 reference)

HumanPhenotype: HP:0007513, HP:0000707, HP:0005982, HP:0100610, HP:0004923, HP:0000252 (Generalized hypopigmentation, Abnormality of the nervous system, Reduced phenylalanine hydroxylase activity, Maternal hyperphenylalaninemia, Hyperphenylalaninemia, Microcephaly)

HumanFreeText: N/A

ModelEvidence: PAH_enu2 has been further characterized many times and results from a missense variant in PAH (PMID: 9119379). PAH_enu3 has also been further characterized and results from a canonical splicing variant in PAH (PMID:11161825). Both models fully recapitulate the phenotypes we expect to see in phenylketonuria, including the quintessential elevated PHE levels and significantly decreased PAH activity. Also of note is the progressive hypopigmentation, microcephaly, growth delay, and neurological abnormalities which are all seen in human probands without proper intervention. Maternal hyperphenylalaninemia is also recapitulated, with no pups surviving beyond several hours with standard breeding diet when born to a mother with the homozygous genotype. Diets low in PKU resulted in less severe symptoms, similar to low protein diets in human probands.

ModelVariant1: NM_000277.3(PAH):c.788T>C (p.Phe263Ser)

ClinVar: 619150 https://www.ncbi.nlm.nih.gov/clinvar/variation/619150/

ModelVariant2: NM_000277.3(PAH):c.1199+2T>G

ClinVar: 557365 https://www.ncbi.nlm.nih.gov/clinvar/variation/557365/

Case5: Female, 3.5 (report), European

CasePresentingHPOs: HP:0002194, HP:0000750, HP:0002370, HP:0002136, HP:0002066, HP:0002360, HP:0025401, HP:0012168, HP:0000252, HP:0000316, HP:0000426, HP:0000369, HP:0000347, HP:0002299, HP:0006801

HPOFreeText: Normal neonatal course. By 8 months could not crawl, subsequent gross motor development delayed. Speech and language delay. By 3.5 years showed balance problems, poor coordination, abnormal wide based gait with ataxia. Sleep disturbance , staring, behavioral issues since 1 year. Dysmorphic features noted at 3.5 years. Brain dysgenesis and partial seizure disorder.

CaseNotHPOs: No skeletal abnormaliites, no organomegaly.

CasePreviousTesting: Followup C5 carnitine 2.58 nM/ml (ref <0.63). 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. Chromosome and fragile X testing normal as well as sequencing of exons 2 and 3 of MECP2. Plasma amino acids normal as well as Angelmann syndrome testing and microarray testing.

CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

Variant: NM_001609.3(ACADSB):c.303+1G>A (homozygous)

ClinVar: 203367

gnomAD: Other 0.0005549

VariantEvidence: Canonical splice site variant. Discrupts canonical splicing signal of intron 3.

CaseAddInfo:

CasePMIDs:

Case2: European

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 1.89 nM/ml (ref <0.63). 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: 1. NM_001609.3(ACADSB):c.443C>T (p.Thr148Ile) 2. NM_001609.3(ACADSB):c.1159G>A (p.Glu387Lys)

ClinVar: 1. 9202 2. 9203

gnomAD: 1. South Asian 0.002678 2. Latino 0.0004797

VariantEvidence: 1. Decreases ACADSB enzymatic activity to 2.8% of wild type in vitro 2. In vitro expression of c.1159G>A in E. coli shows no protein on Western blot, reduced enzymatic activity to 2% and defects in protein folding and stabilit

CaseAddInfo: No info on cis or trans. Also heterozygous for p.R13K polymorphism.

CasePMIDs:

Case4:

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 2.58 nM/ml (ref <0.63). 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.303+1G>A (homozygous)

ClinVar: 203367

gnomAD: Other 0.0005549

VariantEvidence: Canonical splice site variant. Discrupts canonical splicing signal of intron 3.

CaseAddInfo:

CasePMIDs:

CaseSA3P: Female, 16 months onset, European

CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001987 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Hyperammonemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is confirmed de novo via parental teting and confirmed paternity

CasePreviousTesting: Protein/leucine restriction was effective at reducing symptoms

CaseGenotypingMethod: Genomic DNA was prepared from all patients via peripheral blood leukocytes. The GLUD1 gene exons 1-13 and the flanking intronic regions were PCR-amplified and directly sequenced. All variants were confirmed via restriction enzyme analysis. Additionally, paternity testing was performed by HLA typing and by southern blot analysis of DNA fragments as well as PCR analysis of STRs.

Variant: NM_005271.5(GLUD1):c.965G>A (p.Arg322His)

ClinVar: 16129, https://www.ncbi.nlm.nih.gov/clinvar/variation/16129/

gnomAD: Not in gnomAD

CaseSA5P: Female, 3 months onset, European

CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001249, HP:0001250 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Intellectual disability, Seizure)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001987 (Hyperammonemia)

NotHPOsFreeText: N/A

CaseAddInfo: Has father with confirmed variant and similar phenotypes

CasePreviousTesting: Leucine load test showed leucine sensitivity; Protein/leucine restriction and dioxazide was effective at reducing symptoms

CaseGenotypingMethod: Genomic DNA was prepared from all patients via peripheral blood leukocytes. The GLUD1 gene exons 1-13 and the flanking intronic regions were PCR-amplified and directly sequenced. All variants were confirmed via restriction enzyme analysis. Additionally, paternity testing was performed by HLA typing and by southern blot analysis of DNA fragments as well as PCR analysis of STRs.

Variant: NM_005271.5(GLUD1):c.965G>A (p.Arg322His)

ClinVar: 16129, https://www.ncbi.nlm.nih.gov/clinvar/variation/16129/

gnomAD: Not in gnomAD

CaseSA2P: Female, 3 months onset, European

CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001987 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Hyperammonemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is confirmed de novo via parental teting and confirmed paternity

CasePreviousTesting: Leucine load test showed leucine sensitivity in some patients; Protein/leucine restriction was effective at reducing symptoms

CaseGenotypingMethod: Genomic DNA was prepared from all patients via peripheral blood leukocytes. The GLUD1 gene exons 1-13 and the flanking intronic regions were PCR-amplified and directly sequenced. All variants were confirmed via restriction enzyme analysis. Additionally, paternity testing was performed by HLA typing and by southern blot analysis of DNA fragments as well as PCR analysis of STRs.

Variant: NM_005271.5(GLUD1):c.965G>A (p.Arg322His)

ClinVar: 16129, https://www.ncbi.nlm.nih.gov/clinvar/variation/16129/

gnomAD: Not in gnomAD

CaseF-4 female, 2mo onset, Ethnicity: Southern Indian, Muslim

CasePresentingHPOs HP:0006846, HP:0001254, HP:0001987, HP:0002154, HP:0045045, HP:0003571

(Acute encephalopathy, Lethargy, Hyperammonemia, Elevated blood glycine, Elevated acylcarnitines, Propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting Also screened for variants in PCCA

Variant NM_000532.4(PCCB):c.1540C>T (p.Arg514Ter)

ClinVar 217893

gnomAD MAF=0.00005015(South Asian), no homozygotes

CaseAddInfo consanguineous, abnormality in family history noted

CasePMIDs n/a

CaseF-25 female, 4do onset, Ethnicity: North Indian, Muslim

CasePresentingHPOs HP:0006846, HP:0001254, HP:0002098, HP:0001942, HP:0045045, HP:0003571

(Acute encephalopathy, Lethargy, Respiratory distress, Poor feeding, Metabolic acidosis, Elevated acylcarnitines, Propionicacidemia)

HPOsFreeText Serum ammonia 86.4micromolar

CaseNotHPOs n/a

CasePreviousTesting Also screened for variants in PCCA

Variant NM_000532.4(PCCB):c.1498+2T>C

ClinVar 217895

gnomAD not in gnomAD

CaseAddInfo consanguineous, no abnormalities in family history noted

CasePMIDs n/a

CaseF-2 male, 14mo onset, Ethnicity: North Indian, Hindu

CasePresentingHPOs HP:0001263, HP:0003571

(Developmental delay, Propionicacidemia)

HPOsFreeText normal plasma amino acids, acylcarnitines 13.9(normal <3.6nmol/mL), normal development by 6.5 years

CaseNotHPOs HP:0001942, HP:0001987

(Metabolic acidosis, Hyperammonemia)

CasePreviousTesting Also screened for variants in PCCA

Variant NM_000532.4(PCCB):c.1210G>A (p.Glu404Lys)

ClinVar 217891

gnomAD MAF= 0.00003266(South Asian), no homozygotes

CaseAddInfo nonconsanguineous, no abnormality in family history noted

CasePMIDs n/a

Case: BIODEF 306, male, Caucasian, 7 days (per BIODEF website)

CasePresentingHPOs: HP:0008297, HP:0040210

Increased primapterin levels in urine.

CaseNOTHPOs:

CasePreviousTesting: n/a

CaseGenotypingMethod: Assumed PCR of exons 2-4 of PCBD1 followed by direct sequencing. Psuedogenes were not assessed.

Variant: NM_000281.3(PCBD1):c.289G>A (p.Glu97Lys)

ClinVar ID: 91907

Homozygous

gnomAD: MAF (Euro-NF)= 2.320E-5 in hets only, no homozygous. http://gnomad.broadinstitute.org/variant/10-72643733-C-T

AddCaseInfo: Parents noted as consanguineous on the BIODEF website.

VariantEvidence: Expression of recombinant protein in bacteria revealed that the E97K are present in the insoluble fraction compared to wildtype which is found in the soluble. The little amount retained of each in the soluble fraction showed that they retained activity. Dehydratase activity of the patients duodenal mucosa cells showed reduced activity of he E97K (17% activity) mutant compared to wildtype , indicating that this mutation severely reduces the activity of PCBD1.

VariantEvidence: Human HEK293 cells were transfected with either wild-type or mutant protein and cloned, with mRNA and protein levels being determined by PCR and western blotting. The mutant protein levels were just on the threshold of being detected, while the wild-type was over-expressed. This further exemplifies the pathogenicity of the gene.

Variant: NM_018960.4:c.296G>A (p.Arg99His)

Case 1 (Variant Evidence)

VariantEvidence: This variant was expressed in E. coli cells and investigated for protein levels. After the standard incubation time/temperature (15-20 min, 25 deg C) there was no detectable activity. Only after incubation for 60 min at 30 deg C was any measurable amount of sarcosine present, and only then at less than 1% of normal levels.

Variant: NM_018960.5(GNMT):c.422A>G (p.Asn141Ser)

ClinVar: 218931 https://www.ncbi.nlm.nih.gov/clinvar/variation/218931/

gnomAD: not in gnomAD

CaseCA4: Male, 6 months death

CasePresentingHPOs: HP:0001644, HP:0001508 (Dilated cardiomyopathy, Failure to thrive)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Cardiac transplant 11 months after presentation; Variant also found in mother and grandmother

CasePreviousTesting: N/A

CaseGenotypingMethod: The TAZ gene was PCR amplified in three fragments and directly sequenced in obligate heterozygotes, III.2, a heterozygous carrier, and III.4.

Variant: NM_000116.5(TAZ):c.589G>A (p.Gly197Arg)

ClinVar: 11105, https://www.ncbi.nlm.nih.gov/clinvar/variation/11105/

gnomAD: Not in gnomAD

Case8: Female

CasePresentingHPOs: HP:0001270, HP:0001252, HP:0011342, HP:0007479 (Motor delay, Muscular hypotonia, Mild motor developmental delay, Congenital nonbullous ichthyosiform erythroderma)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Consanguineity is suspected, Proband is homozygous

CasePreviousTesting: Patient fibroblasts were analyzed for mutations in SLC25A21 and activities of KATII with no abnormalities; Urine AAA and KAA were elevated. Oxidation of radiolabeled AAA in fibroblasts was deficient.

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

CasePMIDs: 1112064, 1112065

Variant: NM_018706.7(DHTKD1):c.2134C>T (p.Arg712Ter)

ClinVar: 572241 https://www.ncbi.nlm.nih.gov/clinvar/variation/572241/

gnomAD: 0.00003267, https://gnomad.broadinstitute.org/variant/10-12149994-C-T

FamilyBJ1: Sweden

FamilyPresentingHPOs: HP:0003235, HP:0011344, HP:0001410, HP:0001508, HP:0001252, HP:0000256, HP:0002007, HP:0000316, HP:0001533, HP:0001250, HP:0002463, HP:0003323, HP:0003202, HP:0002910 (Hypermethioninemia, Severe global developmental delay, Decreased liver function, Failure to thrive, Muscular hypotonia, Macrocephaly, Frontal bossing, Hypertelorism, Slender build, Seizure, Language impairment, Progressive muscle weakness, Skeletal muscle atrophy, Elevated hepatic transaminase)

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: The siblings were subject to whole exome sequencing. Variants were extracted, aligned, and filtered to build a list of candidate genes. These were filtered through a series of restrictions until only five candidate genes were left, with ADK being the only one related to methionine metabolism. To confirm the results, Exon 10 of ADK was Sanger sequenced in the family members and the variant was confirmed in a heterozygous state in both parents.

FamilyPreviousTesting: Parents are nonconsanguineous and healthy; Maximum plasma Met values were 455 and 886 μmol/liter, respectively (reference range: 15–35 μmol/liter); Elevated AdoMet and AdoHcy; Sequency analysis of AHCY and enzyme activity was negative for SAHH deficiency; More detailed test values in Table 1

FamilyAddInfo: N/A

Variant: NM_006721.4(ADK):c.953C>A (p.Ala318Glu)

ClinVar: 29603, https://www.ncbi.nlm.nih.gov/clinvar/variation/29603/

gnomAD: 0.00001761, https://gnomad.broadinstitute.org/variant/10-76430016-C-A

Affected: 2

Unaffected: 0

Segregations: 1

AddSegregationInfo: Not enough info

CaseOS-138_II-1: Female, 4 yrs report, Asian

CasePresentingHPOs: HP:0001992, HP:0002373, HP:0001263 (Organic aciduria, Febrile seizure (within the age range of 3 months to 6 years), Global developmental delay)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

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

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

Variant: NM_000666.3(ACY1):c.589C>T (p.Arg197Trp)

ClinVar: 18113, https://www.ncbi.nlm.nih.gov/clinvar/variation/18113/

gnomAD: 0.00001764, https://gnomad.broadinstitute.org/variant/3-52021009-C-T

CaseOS-146_II-1: Male, 5 yrs report, Romani

CasePresentingHPOs: HP:0001992, HP:0000954, HP:0000431, HP:0000316, HP:0040194, HP:0004322, HP:0001250, HP:0010819, HP:0032792, HP:0002121, HP:0000752, HP:0002342 (Organic aciduria, Single transverse palmar crease, Wide nasal bridge, Hypertelorism, Increased head circumference, Short stature, Seizure, Atonic seizure, Tonic seizure, Generalized non-motor (absence) seizure, Hyperactivity, Moderate Intellectual disability)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are healthy consanguineous cousins, Two cousins and a niece of the mother have epilepsy, Proband is homozygous for this variant

CasePreviousTesting: Routine urine screening for organic acidurias by gas chromatography–mass spectrometry showed markedly increased urinary excretion of several N-acetylated amino acids; Cerebral MRI was normal at the ages of 17 months and 2.5 years

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

Variant: 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

CaseSE5: 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

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

CaseC1: Female, Arab, Israel

CasePresentingHPOs: HP:0010896, HP:0010897, HP:0001638 (Hypersarcosinemia, Hypersarcosinuria, Cardiomyopathy)

HPOsFreeText: Elevated blood Sarcosine (345 μmol/l; reference 0-9), Elevated urine Sarcosine (481 μmol/mmol; reference 0-36)

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous and first cousins, sister has the same genotype

CasePreviousTesting: N/A

CaseGenotypingMethod: DNA was extracted from the probands and immediate family. The whole coding region and the exon-intron boundaries of the SARDH gene was then amplified and sequenced.

Variant: NM_007101.3:c.211G>T (p.Val71Phe)

ClinVar: 39448 https://www.ncbi.nlm.nih.gov/clinvar/variation/39448/

gnomAD: Not in gnomAD

CaseF2: Female, 6 yrs report, Italy

CasePresentingHPOs: HP:0004923 (Hyperphenylalaninemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents do not appear to be tested, DNA sequence analysis "shows the sense sequence expected of compound heterozygotes with two comigrating bands seen"

CasePreviousTesting: Pre-treatment phenylalanine levels determined soon after birth were above 20 mg / 100 ml, Proband has been under treatment since birth and currently tolerates less than 20 mg Phe/kg bodyweight per day

CaseGenotypingMethod: DNA as isolated from leukocytes and haplotype analysis performed. Enzymatic digestion of PCR-amplified DNA fragments was performed and DGGE analysis of all 13 exons and flanking introns were carried out. The resulting samples containing abberant bands were sequenced and cleaved by MaeI and MaeIII for analysis.

Variant1: NM_000277.3(PAH):c.620A>G (p.Asn207Ser)

ClinVar: 102765 https://www.ncbi.nlm.nih.gov/clinvar/variation/102765/

gnomAD: Not in gnomAD

Variant2: NM_000277.3(PAH):c.842C>T (p.Pro281Leu)

ClinVar: 589 https://www.ncbi.nlm.nih.gov/clinvar/variation/589/

gnomAD: 0.0002016, https://gnomad.broadinstitute.org/variant/12-103246593-G-A

CaseF1: Male, 6 yrs report, Italy

CasePresentingHPOs: HP:0004923 (Hyperphenylalaninemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents were confirmed heterozygous, Splicing variant is predicted to lead to a null protein

CasePreviousTesting: Pre-treatment phenylalanine levels determined soon after birth were above 20 mg / 100 ml, Proband has been under treatment since birth and currently tolerates less than 20 mg Phe/kg bodyweight per day

CaseGenotypingMethod: DNA as isolated from leukocytes and haplotype analysis performed. Enzymatic digestion of PCR-amplified DNA fragments was performed and DGGE analysis of all 13 exons and flanking introns were carried out. The resulting samples containing abberant bands were sequenced and cleaved by MaeI and MaeIII for analysis.

Variant1: NM_000277.2(PAH):c.611A>G (p.Tyr204Cys)

ClinVar: 590 https://www.ncbi.nlm.nih.gov/clinvar/variation/590

gnomAD: 0.0001632, https://gnomad.broadinstitute.org/variant/12-103249009-T-C

Variant2: NM_000277.2(PAH):c.442-2A>C

ClinVar: 120276 https://www.ncbi.nlm.nih.gov/clinvar/variation/120276

gnomAD: Not in gnomAD

RescueModel: Mouse (Mus musculus)

GeneAlteration: PAH_enu2 mice were purchased and bred to obtain the homozygotic mice for this study. Original Generation Method: Mutations were induced in mice germline cells at a rate near 10^-3 per locus via an alkylating agent called ethylnitrosourea. Inbred BTBR males were treated with this agent and bred to normal BTBR females. Three hundred and fifty progeny were screened for mutations that did not complement the previous model PAH_enu1 and if present bred to a previous homozygote and tested for hyperphenylalaninemia. A PHE clearance test was performed in questionable cases. For those that tested positive the carrier parents were mated to a normal BTBR partner to establish a cogenic mutant line. Western blot confirmed reduced to absent CRM in liver.

RescuePhenotype: HP:0007513, HP:0004923, HP:0005982, HP:0100610 (Generalized hypopigmentation, Hyperphenylalaninemia, Reduced phenylalanine hydroxylase activity, Maternal hyperphenylalaninemia)

RescueMethod: The human PAH expression vector plasmid pAAV2-EF-hPAH-WPRE was created by subcloning a full-length human PAH cDNA into a preexisitng parent vector by substitution with eGFP cDNA. Alos included is an EF promoter, woodchuck hepatitis virus post-transcriptional element, and bovine growth hormone poly (A) signal. The rep2/cap2 plasmid or rep2/cap8 plasmid was used to package the vector and produce the final rAAV2/2-hPAH and rAAV2/8-hPAH vectors by triple plasmid transfection. Five-to-six week old PAH_enu2 mice were anesthetized with ketamine-xylazine and infused with viral particles of rAAV2/2-hPAH or rAAV2/8-hPAH through the hepatic portal vein or tail vein.

RescueEvidence: PAH activity in the livers of treated mice six weeks after treatment recovered to 58.43±5.73% and 89.25±8.79% of the wild-type activity in female and male PAH_enu2 mice respectively compared to <1% WT in untreated mice. Plasma phenylalanine concentration in female PAH_enu2 mice infused with rAAV2/8-hPAH vectors decreased markedly to 110±34.5 µM at two weeks from 2,891±336.2 µM and showed continued significant phenylalanine clearance for six month after rAAV2/8-hPAH infusion. Male PAH_enu2 showed a similar reduction, though they started at a lower base concentration of 1,800.6±233.7 µM. The fur color of treated mice also changed from greyish to black from one week after delivery with sustained fur color changes over the entire six month period. Investiation of effects on pregnant mice revealed a complete recovery of fetus length and body weight compared to the untreated mice (1.746±0.203 cm and 774±144 mg for untreated VS 2.081±0.269 cm and 916±67 mg for treated). Spontaneous abortion rate also normalized to 4.55±5.89% from 30.95±14.27%. The rAAV-hPAH genome was not found in the placentae or fetuses nor did the genome of fetuses affect the development parameters.

ModelVariant: NM_000277.3(PAH):c.788T>C (p.Phe263Ser)

ClinVar: 619150 https://www.ncbi.nlm.nih.gov/clinvar/variation/619150/

Case12a: Male, Afghanistan

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0002804, HP:0001558, HP:0001622, HP:0001623, HP:0003798 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Arthrogryposis, Decreased fetal movement, Preterm delivery, Breech presentation, Nemaline bodies)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in 2 months, Has 2 siblings with same genotype/phenotype

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.1099_1100delAA (p.Asn367Glnfs*11)

ClinVar: 162218 https://www.ncbi.nlm.nih.gov/clinvar/variation/162218/

gnomAD: South Asian 4.575e-4, Overall 5.625e-5 https://gnomad.broadinstitute.org/variant/3-69168405-GTT-G

Case14a: Female, Australia

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0001622, HP:0002804, HP:0003798, HP:0001558, HP:0000602 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Nemaline bodies, Decreased fetal movements, Ophthalmoplegia)

HPOsFreeText: Atrophic myofibers, Percutaneous endoscopic gastrostomy performed, Nocturnal noninvasive ventilation

CaseNotHPOs: HP:0001627, HP:0002540 (Cardiac abnormality, Inability to walk)

NotHPOsFreeText: N/A

CaseAddInfo: Typical congenital nemaline myopathy, Alive at 10 yrs, Parents are not consanguineous

CasePreviousTesting: N/A

CaseGenotypingMethod: Linkage analysis combined with homozygosity mapping was used to identify candidate chromosomal loci. Whole exome sequencing in this family revealed likely pathogenic mutations in LMOD3 which agreed with the aforementioned analysis and was consistent with autosomal recessive inheritance.

Variant1: NM_198271.4:c.1103_1105del (p.Asn368del)

ClinVar: 162216 https://www.ncbi.nlm.nih.gov/clinvar/variation/162216/

gnomAD: Not in gnomAD

Variant2: NM_198271.4:c.1201C>T (p.Arg401Ter)

ClinVar: 162217 https://www.ncbi.nlm.nih.gov/clinvar/variation/162217/

gnomAD: African 4.137e-5, Overall 7.135e-6 https://gnomad.broadinstitute.org/variant/3-69168305-G-A

Case#: Patient 3, 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.1430T>G (homozygous)

ClinVar: 93994

gnomAD: European (Non-Finnish) 8.971e-6, Overall 4.065e-6.

VariantEvidence: Mutation is present in the catalytic domain and would expect a defect in catalytic function (Alamut software analysis).

FamilyLabel 38/39 Fam

Family38/39PresentingHPOs n/a

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity Turkish

Race n/a

Family38/39PreviousTesting Diagnosed by selective metabolic screen

ProbandLabel 38

Variant NM_000532.4(PCCB):c.1534C>T (p.Arg512Cys), homozygous

ClinVar 38879

gnomAD MAF= 0.00005440(East Asian), no homozygotes

FamilyAddInfo parental consanguinity

FamilyPMIDs n/a

Case8 Male, 9.8yo report, Ethnicity:Turkish

CasePresentingHPOs HP:0012523, HP:0001508, HP:0002013, HP:0008947, HP:0002789, HP:0002045, HP:0002014, HP:0003571

(propionicacidemia, oral aversion, failure to thrive, vomiting, infantile hypotonia, tachypnea, hypothermia, diarrhea)

HPOsFreeText feeding refusal, failure to thrive, vomiting, hypotonia, tachypnea, hypothermia, diarrhea (4do). 73 IQ on Culture Free Test.

CaseNotHPOs n/a

CasePreviousTesting Diagnosed by selective metabolic screening

Variant NM_000532.4:c.429+3_6delAAGT (p.Asp125_Lys143del), homozygous

ClinVar n/a

CAID to register

gnomAD not in gnomAD

CaseAddInfo parental consanguinity

CasePMIDs n/a

CaseES: Female, 1 yr onset

CasePresentingHPOs: HP:0002312, HP:0002131, HP:0002719, HP:0002078, HP:0002066, HP:0100560, HP:0002345, HP:0008376, HP:0000666, HP:0001348, HP:0002342, HP:0410217, HP:0012237 (Clumsiness, Episodic ataxia, Recurrent infections, Truncal ataxia, Gait ataxia, Upper limb asymmetry, Action tremor, Dysarthic speech, Horizontal nystagmus, Brisk reflexes, Moderate intellectual disability, Reduced blood 5-methyltetrahydrofolate level, Urocanic aciduria)

HPOsFreeText: Urocanis acid levels 158-202 mmol/mol creatinine (reference <10)

CaseNotHPOs: HP:0000496, HP:0001324, HP:0002160, HP:0001903 (Abnormal ocular movements, Muscle weakness, Hyperhomocystinemia, Anemia)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are healthy and nonconsanguineous, Steady improvement after mid-life, Proband is confirmed compound heterozygous by parental confirmation (father heterozygous for Variant 2)

CasePreviousTesting: Cranial MRI and neurophysiological studies, including electroencephalography, electroretinography, visual and brainstem evoked potentials, electromyography, nerve conduction velocities, fundus oculi and cardiological examinations, gave normal results; Cognitive evaluation rated her IQ at 54; Routine laboratory analyses including serum amino transferases, creatinine, urea and other parameters were normal; Screening for inborn errors of metabolism, including plasma and urine amino acids (no histidine accumulation), blood lactate, sialotransferrin isoelectricfocusing, creatine deficiency syndromes, purine and pyrimidine defects, and organic acidurias, gave normal results; Hypothyroidism and coeliac disease were also excluded; Biochemical and/or genetic screening for early onset forms of inherited ataxia gave normal results; Deficiencies in 5-methyltetrahydrofolate, neopterin and biopterin deficiencies were seen, together with an evident reduction in homovanillic acid (HVA) and the HVA:5-hydroxyindolacetic acid ratio; Other parameters determined in cerebrospinal fluid (CSF), such as glucose, proteins, cells and amino acids were normal.

CaseGenotypingMethod: Genomic DNA was obtained from peripheral white blood cells from the proband and her father. Mutation analysis of UROC1 was performed via direct sequencing and PCR amplification of the 20 exons and flanking exon-intronic sequences. In-silico analysis and modeling was performed on the variants.

Variant1: NM_144639.3(UROC1):c.209T>C (p.Leu70Pro)

ClinVar: 408 https://www.ncbi.nlm.nih.gov/clinvar/variation/408/

gnomAD: 0.00005647, https://gnomad.broadinstitute.org/variant/3-126229555-A-G

Variant2: NM_144639.3(UROC1):c.1348C>T (p.Arg450Cys)

ClinVar: 407, https://www.ncbi.nlm.nih.gov/clinvar/variation/407/

gnomAD: 0.00008012, https://gnomad.broadinstitute.org/variant/3-126216984-G-A

CaseFI2: Male, Turkey, Birth onset

CasePresentingHPOs: HP:0009800, HP:0001195, HP:0000773, HP:0003026, HP:0001650, HP:0003561, HP:0001518, HP:0000252, HP:0004887, HP:0001274, HP:0001250, HP:0000411, HP:0007957, HP:0007495, HP:0000963, HP:0000973, HP:0100678, HP:0010648, HP:0001382, HP:0009815, HP:0001181, HP:0010557, HP:0001374, HP:0012330, HP:0030750, HP:0040187 (Maternal diabetes, Single umbilical artery, Short ribs, Short long bone, Aortic valve stenosis, Birth length less than 3rd percentile, Small for gestational age, Microcephaly, Respiratory failure requiring assisted ventilation, Agenesis of corpus callosum, Seizures, Protruding ear, Corneal opacity, Prematurely aged appearance, Thin skin, Cutis laxa, Premature skin wrinkling, Dermal translucency, Joint hypermobility, Aplasia/hypoplasia of the extremities, Adducted thumb, Overlapping fingers, Congenital hip dislocation, Pyelonephritis, Grade III preterm intraventricular hemorrhage, Neonatal sepsis)

HPOsFreeText: Intrauterine growth restriction birth length: 38 cm (< 3rd percentile), birth weight 1370 g (< 3rd percentile) and microcephaly (OFC at birth was 29.5 cm (3rd–10th percentile)). APGAR scores were 5, 9, and 9 after 1, 5, and 10 min, respectively; Typical facial gestalt

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are first-degree cousins that had three healthy daughters and three early abortions

CasePreviousTesting: N/A

CaseGenotypingMethod: Familial DNA was extracted from peripheral blood samples. Direct sequencing of PYCR1 and exons 2-18 of ALDH18A1 was performed in the affected individual with a homozygous single-basepair deletion found predicted to lead to a frameshift and premature stop codon.

Variant: NM_002860.4(ALDH18A1):c.2131del (p.Leu711fs)

ClinVar: 156546 https://www.ncbi.nlm.nih.gov/clinvar/variation/156546/

gnomAD: Not in gnomAD

Case: Patient 4/ BIODEF 263, female, 1 week

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

At 1 week old plasma showed Phe levels at 258 umol/L. Repeat screening at 9 days old showed Phe levels at 900 umol/L. Amino acid quantitation of plasma showd a Phe level of 1200 umol/L. Urine analysis showed low BH4, high neopterin, low biopterin, and the presence of primapterin. A diet of low protein and phenylalanine were begun, and continue with 100 mg/kg of phenylalanine per day. Patient is 6 years old and developing normally.

CaseNOTHPOs:

CasePreviousTesting: n/a 

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

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

ClinVar ID: 16799

Homozygous

gnomAD: n/a

AddCaseInfo: No information about the family.

VariantEvidence: Expression of recombinant protein in bacteria revealed that both the Q98X variants are present in the insoluble fraction compared to wildtype which is found in the soluble. the little amount retained of each in the soluble fraction showed that they retained activity.

Case: Patient 3/ BIODEF 216, male, Morrocan, 1 month

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

HyperPhe presented a 1 month old with plasma levels of 1850 umol/L. A low Phe diet was initiated for 8 months. Urinary pterin profile showed high neopterin, low biopterin, and elevated primapterin. The diet was ceased at 2 years old, and the child has normal Phe levels (110 umol/L).

CaseNOTHPOs:

CasePreviousTesting: n/a

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

Variant: NM_000281.3(PCBD1):c.289G>A (p.Glu97Lys)

ClinVar ID: 91907

Homozygous

gnomAD: MAF (Euro-NF)= 2.320E-5 in hets only, no homozygous. http://gnomad.broadinstitute.org/variant/10-72643733-C-T

AddCaseInfo: Parents are consanguineous. Older brother (by 17 years) presented with HyperPhe in the neonatal period, but no information on whether he was a carrier of the mutation.

VariantEvidence: Expression of recombinant protein in bacteria revealed that the E97K are present in the insoluble fraction compared to wildtype which is found in the soluble. the little amount retained of each in the soluble fraction showed that they retained activity. Per Ayling et al., 2000 (PMID:10924272), another patient (BIODEF 306) that was homozygous for the same E97K mutation, showed reduced activity of PCBD1 from duodenal mucosa cells compared to wildtype (17% activity), indicating that this mutation severely reduces the activity of PCBD1.

NonHumanModel: Mouse (Mus musculus)

GeneAlteration: Two constructs were created, containing with the WT human GDH sequence or the H507Y variant along with the rat insulin promotoe and human growth hormone genomic DNA sequence to stabilize the construct and drive β-cell-specific transcription of the cDNA sequence. These were microinjected into fertilized eggs of B6SJLF1 mice, transferred into pseudopregnant females, and PCR-amplified/sequenced to confirm the succesful insertion of the transgene. Offspring were crossed with C57BL/6 mice and generated two lines of mutant along with one line of WT transgenic mice: TG-1, TG-2, and huGDH.

ModelPhenotype: MP:0000189, MP:0008770, MP:0002079, MP:0005309 (hypoglycemia, decreased survivor rate, increased circulating insulin level, hyperammonemia)