Case35: 5 y (at biopsy), Hispanic

Case 35 (Level 2)

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

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case33: 9 mo (at biopsy), Hispanic

Case 33 (Level 2)

CasePreviousTesting: same as group. found 1.0 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case32: 10 y (at biopsy), Arab

Case 32 (Level 2)

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

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 1880

CAID: CA249728

gnomAD: 0.0004777 (European- Finnish)

CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.

Case34: 3.5 wks (at biopsy), White/Hispanic

Case 34 (Level 2)

CasePreviousTesting: same as group. found 1.6 nmol/mg protein/18 h propionate incorporation, 1.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Variant NM_000709.3:c.1267C>T(p.Gln423Ter)

CAID CA406015497

Patient12: Group 2

CasePresentingHPOs: same as group 2

CasePreviousTesting: same as group 2

CaseGenotypingMethod: same as group 2

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

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

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

Variant2: NM_001159508.1:c.870_871insG

CAID: CA913184835, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913184835

gnomAD: n/a

CaseAHN15.1: Australia, White

CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants segregate with the disease

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

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

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

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

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

Variant2: NM_001003841.3:c.850G>A (p.Gly284Arg)

CAID: CA3182918, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182918

gnomAD: 0.00005440, https://gnomad.broadinstitute.org/variant/5-1214143-G-A

Case# Pat4, F, Chinese, 5day onset

CasePresentingHPOs HP:0008344, HP:0002013, HP:0011968, HP:0001250, HP:0001276, HP:0001279

CasePreviousTesting Tested serum BCAAs

CaseMethod1 PCR

CaseMethod2 Direct

CaseGenotypingMethod exons and flanking intronic regions of the BCKDHA, BCKDHB and DBT genes were amplified using PCR and sequenced

Variant NM_000709.3:c.178G>T, NM_000709.3:c.491T>C

CAID CA406004676(c.178), CA406010453(c.491)

CaseAddInfo mutations confirmed in parents by Sanger sequencing, Her elder brother was healthy. This patient presented with lethargy and feeding difficulty when she was 5 days old. She was admitted because of unconsciousness at the age of 5 months, and she was diagnosed with MSUD accompanied by metabolic acidosis, liver damage and hypermyotonia. Cerebral MRI showed abnormal signals in the left and right globus pallidus. Clinical improvement as well as improvement in the laboratory test results was observed after treatment. She is now 3 years and 11 months old with severe psychomotor retardation. She is still unable to walk or speak.

Case#: 3, female, 12 days (onset), 4 y (current- this differs than what is in table 1), Chinese

CasePresentingHPOs: HP: 0008344, HP: 0012088, HP:0011968, HP: 0002013, HP:0011344, HP: 0002543, HP: 0012751 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, vomiting, severe global developmental delay, abnormal globus pallidus, abnormal basal ganglia)

HPOsFreeText: Bilateral damage to capsula interna and externa, Blood ammonia: 205 uM, Hemoglobin: 118 g/L, Leucin: 891.90 uM, Valine: 502.50 uM, Isoleucine: 165.99 uM, Alloisoleucine: 90.12 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: 2 different variants, unsure of cis or trans

CasePreviousTesting: n/a

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000709.3(BCKDHA):c.178G>T (p.Glu60Ter), NM_000709.3(BCKDHA):c.1214_1219dupCCAACC (p.Asn406Leu407insProGln)

ClinVar: n/a

CAID: CA406004676 , CA658820662

gnomAD: neither in gnomAD

Case#: 6, male, 18 m (onset), 2 y 6 m (current), Chinese

CasePresentingHPOs: HP: 0008344, HP; 0012088, HP: 0011342, HP: 0001332, HP:0002543, HP: 0012751, HP:0012747 (elevated A keto acids in urine, abnormal urinary odor, mild global developmental delay, dystonia, abnormal globus pallidus, abnormal basal ganglia, abnormal brainstem MRI signal intensity)

HPOsFreeText: damage to cerebellar dentate nucleus, damage to corpora quadrigemina, damage to frontal lobe, damage to insular cortex, Isoleucine: 167.13 uM, Alloisoleucine: 44.88 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: unsure cis or trans

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_183050.3:c.767A>G (p.Tyr256Cys), NM_183050.3:c.768C>G (p.Tyr256Ter)

ClinVar: neither found

CAID: CA364659935, CA142287564

gnomAD: 0.000008820 (European, non-Finnish), not found

Case#: 8, male, 13 days (onset), 1 y 6 m (current), Chinese

CasePresentingHPOs: HP: 0008344, HP:0012088, HP:0011968, HP:0001254, HP:0002415, HP: 0006989 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, lethargy, leukodystrophy, dysplastic corpus callosum)

FreeTextHPOs: blood ammonia: 96 uM, hemoglobin: 98 g/L, leucin: 1047.24 uM, isoleucine: 261.09 uM, alloisoleucine: 127.05 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: homozygous mutation

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_001918.3:c.1A>G (p.Met1Val)

ClinVar: not found

CAID: CA969877

gnomAD: not found

Case#: 1, male, 3 days (onset), 2 y 8 mo (current), Chinese

CasePresentingHPOs: HP:0008344 HP: 0012088, HP: 0001250, HP: 0011968, HP: 0001941, HP: 0001943, HP: 0001987, HP: 0001903, HP:0012751, HP:0002543, HP: 0001276, HP:0011343 (elevated A keto acids in urine, abnormal urinary odor, seizures, feeding difficulties, acidosis, hypoglycemia, hyperammonemia, anemia, abnormal basal ganglia MRI signal intensity, abnormal globus pallidus signals, hypertonia, moderate global developmental delay)

HPOsFreeText: Blood ammonia: 75 uM, Valine: 532.83 uM, Isoleucine: 384.90 uM, Alloisoleucine: 213.09 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: variants also found in parents

Case (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000709.3(BCKDHA): IVS6+1delG (can't search this format of an intronic mutations, how do I change it?)

ClinVar: not sure how to search for BCKDHA IVS6 + 1delG

CAID:

gnomAD:

Variant2: NM_000709.3(BCKDHA):c.740A>G (p.His247Arg)

ClinVar: not found

CAID: CA406012849

gnomAD: not in gnomAD

There are two variants listed for every patient except, one. The text said that all the mutations found were also found in the parents so does that mean they would be in trans?

(didn't see this template at first, so still need to apply it to the other entries)

Case4: Male, Chinese, 2.8 y (end of study)

HPOsFreeText: poor neurologic outcome, neonatal onset

NotHPOsFreeText: not responsive to vitamin B12

Case4 (Level 2):

CasePreviousTesting: NBS

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 552079

CAID: CA3847064

gnomAD: 0.0002008 (East Asian)

CaseAddInfo: homozygous mutations

Case5: Female, Chinese, 1.6 y (onset)

HPOsFreeText: 1.6 y onset

NotHPOsFreeText: Not responsive to vitamin B12

Case5 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 203846

CAID: CA312764

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: homozygous mutations, lost to follow up

Case3: Female, Chinese, 4 mo (end of study)

HPOsFreeText: Responsive to vitamin B12

Case3 (Level 2):

CasePreviousTesting: NBS

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000255.3:c.599T>C (p.Ille200Thr)

ClinVar: n/a

CAID: CA364404381

gnomAD: n/a

CaseAddInfo: homozygous mutations, asymptomatic

Case2: Male, Chinese, 3 mo (age at death)

HPOsFreeText: Neonatal onset

NotHPOsFreeText: Not responsive to vitamin B12

Case2 (Level 2):

CasePreviousTesting: NBS (newborn screening)

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000255.3:c.482G>T (p.Gly161Val)

ClinVar: n/a

CAID: CA364404636

gnomAD: n/a

CaseAddInfo: homozygous mutations, novel mutation

Case#: Hou 2016 Proband, M, 7 days (onset), Taiwan (Amis Tribe)

CasePresentingHPOs: HP:0004396, HP:0030842, HP:0040181, HP:0002045 (continue)

HPOsFreeText:

CaseNotHPOs: .

CasePreviousTesting: Hemoglobin 1.36 mM (normal 1.4-2.17 mM); 613x10^9 platelets/L (normal 150-400x10^9); glucose 2.16 mM (normal 3.3-5.5 mM). Valine 1026 uM (normal 84.07-354 uM); leucine/isoleucine 829.41 uM (normal 56.82-287 uM).

CaseGenotypingMethod: Direct sequencing and duplex PCR of DBT.

Variant: 1. NM_001918.3(DBT):c.1282-4142_*(434_435)del; . NM_001918.3:c.650dup

ClinVar: 1. 11951

CAID: 2. CA658820832

gnomAD: 1. Not in gnomAD; Not in gnomAD

VariantEvidence: The deletion includes the 3' half of intron 10, the entire coding region of the terminal exon 11, and the 5' part of the 3' UTR of DBT.

CaseAddInfo: The 4.7 kb deletion had been previously reported in Paiwan tribe in Taiwan.

Patient5: Male, 11mo, sibling to patient 4

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 6.0 μmol l−1, IVA incorp (%) = 64, IVG in urine mmol permol creatinine = 955, Ammonium (μmol l−1) = 65, pH = 7.41, Protein intake (g kg−1 per day) = 1.5, treated with carnitine supplements, PDI/IQ in follow-up = 85

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS at 10 days old

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_001159508.1:c.1214T>C

CAID: CA268781818, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA268781818

gnomAD: 0.000003977, http://gnomad.broadinstitute.org/variant/15-40710485-T-C

Variant2: NM_001159508.1:c.500T>C

CAID: CA391717541, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391717541

gnomAD: n/a

Case# Patient 16, Female, 2mo diagnosis

Variant NM_000320.2:c.277G>A (p.Gly93Ser)

CAID CA356450231

This variant was mentioned as being previously published (PMID: 12559846). Structural changes for this variant were analyzed by calculating RMSD and predicted this variant to result in a severe phenotype. However, this type of prediction is not used by the LD VCEP.

Unable to annotate on article.

Case#: Konstantinidis Case 2

DiseaseAssertion: optic atrophy

FamilyInfo: none provided

CasePresentingHPOs: none, tests performed on blastocyst

CaseHPOFreeText:

CaseNotHPOs: none

CaseNotHPOFreeText:

PreviouslyPublished: n/a

Variant: c.182A > G

ClinVar: 511815

CAID: CA2758946

SupplementalData: n/a

Case#: Hudson Proband II:5, 66yo, female, UK

DiseaseAssertion: OA plus

FamilyInfo: Pedigree (Fig 1) shows 6 segregations

CasePresentingHPOs: HP:0007663, HP:0001288, HP:0001730, HP:0000746, HP:0002367, HP:0000648, HP:0000544, HP:0001488, HP:0001349, HP:0002066, HP:0001315, HP:0003236, HP:0033568, HP:0001272, HP:0002120

CaseHPOFreeText: slowly progressive deterioration in her visual acuity, a progressive gait disturbance of 20 years duration, and a 5-year history of deteriorating hearing, acute paranoid delusions, low mood, just able to perceive light, bilateral optic atrophy, plantar responses flexor, elevated serum creatine kinase (417 U/l, normal <190 U/l) with a normal fasting blood glucose and lactate, mild cortical disturbance, prominent small-vessel ischaemic lesions in the cerebral white matter bilaterally. Muscle biopsy of the index case (II:5) revealed features that were diagnostic of mitochondrial myopathy

CaseNotHPOs: HP:0001627, HP:0031983

CaseNotHPOFreeText:

PreviouslyPublished: n/a

PreviousTesting: The entire mitochondrial genome-coding region was amplified and found (m.8839G>A) in the MTATP6 gene. No sequence variants were identified in the coding region or flanking exon–intron boundaries for POLG1, PEO1, POLG2 and SLC25A4.

GenotypingMethod: The 30 coding exons and intron–exon junctions of the OPA1 gene were sequenced using a set of 30 primer pairs

Variant: c.1800C>G (p.Ser600Arg)

ClinVar: 30461

CAID: CA10575554

SupplementalData:

annotating here since this is a PDF

Case#: Yamagishi Case 2, female, 10m at dx

DiseaseAssertion: Hurler

FamilyInfo:

CasePresentingHPOs:

CaseHPOFreeText: mental delay. height=70cm

CaseNotHPOs: HP:0002240

CaseNotHPOFreeText: cardiac involvement

PreviouslyPublished: n/a

Variant: 704ins5/704ins homozygous

ClinVar: 11921

CAID: CA256123

SupplementalData: n/a

annotating here since this is a PDF

Case#: Yamagishi Case 3, female, 3y4m at dx

DiseaseAssertion: Hurler/Scheie

FamilyInfo: Case 4 is this patient's sibling. Same genotype and similar phenotype

CasePresentingHPOs: HP:0001433

CaseHPOFreeText: height=90cm (-1.2SD)

CaseNotHPOs:

CaseNotHPOFreeText: mental delay. cardiac involvement

PreviouslyPublished: n/a

Variant: 704ins5; R89Q

ClinVar: 11921; 11922

CAID: CA256123; CA256124

SupplementalData: n/a

annotating here since this is a PDF

Case#: Yamagishi Case 1, female, 3y1m at dx

DiseaseAssertion: Hurler

FamilyInfo: consanguinity

CasePresentingHPOs: HP:0002240

CaseHPOFreeText: mental delay. height=89cm (-1.5SD)

CaseNotHPOs:

CaseNotHPOFreeText: cardiac involvement

PreviouslyPublished: n/a

Variant: 704ins5/704ins homozygous

ClinVar: 11921

CAID: CA256123

SupplementalData: n/a

Case#: N5214, F, 62 y.o., Italian

CasePresentingHPOs: HP:0007354, HP:0002015, HP:0001260, HP:0002380, HP:0003690, HP:0003202

CaseNotHPOs: HP:0100543

CaseGenotypingMethod: Sanger sequencing

Variant: NM_006000.3(TUBA4A):c.1045A>T p.Thr349Ser

CAID: CA350723588

CaseAddInfo: While most cases were found to be negative during pre-screening for known mutations, some cases were positive for mutations in SOD1 (n=4), C9orf72 (n=12), TARDBP (n=4), & FUS/TLS (n=1) genes. Whether this case tested positive for any of these is not specified.

Case#: B1103, M, 57 y.o., Italian

CasePresentingHPOs: HP:0007354, HP:0003202, HP:0007340

CaseNotHPOs: HP:0100543

CaseGenotypingMethod: Sanger sequencing

Variant: NM_006000.3(TUBA4A):c.226+4A>G IVS2+4A>G

CAID: CA2018007638

CaseAddInfo: While most cases were found to be negative during pre-screening for known mutations, some cases were positive for mutations in SOD1 (n=4), C9orf72 (n=12), TARDBP (n=4), & FUS/TLS (n=1) genes. Whether this case tested positive for any of these is not specified.

FamilyLabel: Van Driest Family

Family#PresentingHPOs: HP:0001639 (hypertrophic cardiomyopathy)

FamilyNotHPOs:

CountryOrigin:

Ethnicity:

Race:

Family#PreviousTesting: Three highly polymorphic markers for each of 9 known HC genes (MYH7, TNNT2, TNNI, TPM1, MYL3, MYL2, MBPC, ACTC, and PRKAG2) were PCR-amplified for haplotype analysis. Only 3 candidate genes, MYL3, TNNT2, and TPM1, were shared by proband, affected siblings, and father.

Family#Method1: (other) PCR amplification of all protein-coding exons and splice junctions of the 3 candidate genes from genomic DNA was analyzed using DHPLC (denaturing high-performance liquid chromatography).

Family#Method2: Cycle sequencing was performed on all DHPLC amplicons with abnormal elution profiles (exon 5 of TPM1).

Family#GenotypingMethod: DHPLC screening followed by cycle sequencing of TPM1 exon 5.

Affected: 4

Unaffected:

Segregations: 3 (Figure 1)

PublishedLOD: N/A

eLOD: N/A; < 4 segregations

AddSegregationInfo:

ProbandLabel: III-1

Variant: NM_001018005.2(TPM1):c.554T>G (p.Leu185Arg)

ClinVar: 31881

CAID: CA019057

gnomAD: 15-63060930-T-G has no data in gnomAD v4.0.0

FamilyAddInfo: TPM1 variant reported as c.T610G (p.L185R), using coding positions relative to GeneBank accession M19713.1?

FamilyPMIDs:

Case#: III-1

CasePresentingHPOs: HP:0001639 (hypertrophic cardiomyopathy); HP:0001645 (sudden cardiac death)

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: None for the proband

CaseMethod1:

CaseMethod2:

CaseGenotypingMethod: DNA extracted from paraffin-embedded spleen tissue, taken at autopsy, was subjected to PCR-amplification of TPM1 exon 5 followed by cycle sequencing to confirm presence of the familial TPM1 variant.

Variant: NM_001018005.2(TPM1):c.554T>G (p.Leu185Arg)

ClinVar: 31881

CAID: CA019057

gnomAD: 15-63060930-T-G has no data in gnomAD v4.0.0

VariantEvidence: Chang, et al. 2005 (PMID:16043485) demonstrated in ATPase activity assays that myofibrils reconstituted with L185R mutant tropomyosin had an increased sensitivity to calcium compared to wild-type tropomyosin-reconstituted myofibrils.

CaseAddInfo: No other genes were screened for mutations in this proband.

CasePMIDs:

Case# Pt1, female, 16yo diagnosis, French

CasePresentingHPOs HP:0001433, HP:0001263, HP:0001252, HP:0001395, HP:0000744, HP:0000718, HP:0000713, HP:0001397, HP:0003651, HP:0012465, HP:0001999, HP:0003155, HP:0003124, HP:0010837, HP:0011967, HP:0012852 (Hepatosplenomgaly, Psychomotor delay, Hypotonia, Hepatic fibrosis, Low tolerance to frustration, Aggressiveness, Agitation, Hepatic steatosis, Foamy histiocytes, Increased liver iron, Dysmorphic facies, Elevated alkaline phosphatase, High cholesterol, Decreased ceruloplasmin, Copper deficiency, Hepatic bridging fibrosis)

HPOsFreeText Hepatospenomegaly and cholestasis(spontaneously resolved) (neonate); Elevated liver enzymes, psychomotor delay, hypotonia(6mo); liver cytolysis, portal-to-portal bridging fibrosis without regenerative nodules, fatty hepatocytes, foamy histiocytes, and iron overload(4yo); behavioral issues, dysmorphic features, elevated relative exchangeable and urinary copper and other metabolic abnormalities(13yo);enlarged portal tracts and liver tissue abnormalities (Fig1)

CaseNotHPOs HP:0200032 (Kayser-Fleischer ring)

CasePreviousTesting Negative for NPC and Wilson disease(ATP7B variants) as well as TMEM199 variants. Metabolic results: ASAT 56 U/L, ALAT 45 U/L [N < 40 U/L]; ALP 196 U/L [N < 119 U/L], cholesterol 5.50 mmol/L [N < 5.20 mmol/L], ceruloplasmin 0.55 μmol/L [N = 2–4.5 μmol/L], total copper 5.44 μmol/L [N = 12.5–22.5 μmol/L], y-gutamyltransferase, bilirubin, CK, glucose, lactic acid, plasma amino acids, urinary organic acids, and lysosomal acid lipase were normal, Bis(Monoacylglycero)Phosphate was also elevated.

CaseMethod1 Direct sequencing

CaseMethod2 n/a

CaseGenotypingMethod Sequenced CCDC115 and TMEM199 in patients and parents

Variant (1) NM_032357.3(CCDC115):c.92T>C (p.Leu31Ser) (2) NM_032357.3:c.19C>T(p.Arg7Ter)

ClinVar (1) 218967 (2) n/a

CAID (2) CA1871401

gnomAD (1) 0.00002384(European (Non-Finnish)), 0.00001086(Total) (2) 0.00002691(European (Non-Finnish)), 0.00001220(Total)

VariantEvidence see note on Fig 2

CaseAddInfo nonconsanguineous

CasePMIDs 26833332

Case# Pt2, male, 20yo report, French

CasePresentingHPOs HP:0200123, HP:0003155, HP:0003236, HP:0003124, HP:0003141, HP:0010837, HP:0006580, HP:0012852, HP:0025321 (Chronic Hepatitis, Elevated alkaline phosphatase, Elevated CK, High cholesterol, Elevated LDL cholesterol, Decreased ceruloplasmin, Portal fibrosis, Hepatic bridging fibrosis, Liver copper accumulation)

CaseNotHPOs HP:0002240, HP:0001744, HP:0001999, HP:0200032 (Hepatomegaly, Splenomegaly, Dysmorphic facies, Kayser-Fleischer ring)

CasePreviousTesting Negative for NPC and Wilson disease(ATP7B variants) as well as TMEM199 variants. Metabolic workup: ALAT 154 U/L, ASAT 137 U/L [N < 40 U/L] for >6 months, GGT was normal, ALP 218 U/L [N < 119 U/L], CK 519 U/L [N < 190 U/L], cholesterol 8.16 mmol/L [N < 5.7 mmol/L], ceruloplasmin 0.54 μmol/L [N = 2–4.5 μmol/L], normal urinary copper, REC 19% [N = 3.0–8.1%], liver copper 2.47 μmol/g, [N = 0.3–0.9 μmol/g]

CaseMethod1 Direct sequencing

CaseMethod2 n/a

CaseGenotypingMethod Sequenced CCDC115 and TMEM199 in patients and parents

Variant (1) NM_032357.3(CCDC115):c.92T>C (p.Leu31Ser) (2) NM_032357.3:c.38T>C(p.Leu13Pro)

ClinVar (1) 218967 (2) n/a

CAID (2) CA348488009

gnomAD (1) 0.00002384(European (Non-Finnish)), 0.00001086(Total) (2) n/a

VariantEvidence see note on Fig 2

CaseAddInfo nonconsanguineous

CasePMIDs 26833332

Case# Pt3, male, 16yo diagnosis, French

CasePresentingHPOs HP:0009062, HP:0001433, HP:0001396, HP:0003124, HP:0012852, HP:0001414, HP:0011924, HP:0001409, HP:0001394, HP:0011343, HP:0002342, HP:0003236, HP:0001315, HP:0010837, HP:0010836 (Infantile axial hypotonia, Hepatosplenomegaly, Cholestasis, High cholesterol, Hepatic bridging fibrosis, Microvesicular hepatic steatosis, Mitochondrial complex III deficiency, Portal hypertension, Cirrhosis, Moderate global developmental delay, Moderate ID, Elevated CK, Absent deep tendon reflexes Decreased ceruloplasmin, Abnormal copper homeostasis)

HPOsFreeText Hepatosplenomegaly and choleostasis reported at birth. Enlarged portal tracts, focal portal inflammation, loss of interlobular ducts in 1/3 of portal tracts and proliferation of bile ductules, lobular steatosis

CaseNotHPOs HP:0003200 (Ragged red fibers)

NotHPOsFreeText foamy hepatoocytes, bile plug

CasePreviousTesting Negative for NPC, Gaucher and Wilson disease(ATP7B variants) as well as TMEM199 variants. Excluded acid lipase deficiency. Negative for disease causing variants in any known genes involved in mitochondrial metabolism. Ruled out type IV glycogen storage disease. Metabolic results: cholesterol 9.92 mmol/L [N < 5.2 mmol/L], ceruloplasmin 0.09 g/L [N = 0.2–0.5 g/L], REC 18% [N = 3.0–8.1%], normal serum(4.16 μmol/L) and exchangeable copper(0.75 μmol/L). Glycogen and cytochrome oxidases were normal.

CaseMethod1 Exome sequencing

CaseMethod2 n/a

CaseGenotypingMethod Exome sequenced patient DNA, direct sequenced CCDC115 and TMEM199 in parents

Variant (1) NM_032357.3(CCDC115):c.92T>C (p.Leu31Ser) (2) NM_032357.3:c.19C>T(p.Arg7Ter)

ClinVar (1) 218967 (2) n/a

CAID (2) CA1871401

gnomAD (1) 0.00002384(European (Non-Finnish)), 0.00001086(Total) (2) 0.00002691(European (Non-Finnish)), 0.00001220(Total)

VariantEvidence see note on Fig 2

CaseAddInfo nonconsanguineous

CasePMIDs 26833332

Patients 2, 4, and 5 are all homozygous for this variant. Previously published in PMID: 22718273

Case# Subject 3-1, male, 11yo, Pakistani

CasePresentingHPOs HP:0000750, HP:0011342, HP:0000286, HP:0000431, HP:0000490, HP:0000717, HP:0007302, HP:0000218, HP:0001500, HP:0001837, HP:0002650, HP:0001249, HP:0001252, HP:0000717 (Speech delay, Mild global developmental delay, Epicanthus, Broad nasal bridge, Deep set eyes, Bipolar disorder, High palate, Broad fingers, Broad toes, Scoliosis, Intellectual Disability, Hypotonia, Autism)

HPOFreeText: mild speech/motor/cognitive delay, mild prominence of lateral ventricles, mild scoliosis, mild-moderate hypotonia

CaseNotHPOs HP:0002376, HP:0001250 (Developmental regression, Seizures)

NotHPOFreeText: Ventillator dependence

CasePreviousTesting Variants previously reported with a minor allele frequency > 1% were excluded. WES for additional compound-heterozygous, X-linked, or heterozygous de novo variants was negative.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES on all families, confirmed heterozygous/compound heterozygous with Sanger. Sanger on individuals with an affected family member. Parents confirmed heterozygous for childrens' variants

Variant NM_001163435.2:c.1652T>C(p.Leu551Pro), homozygous

ClinVar n/a

CAID CA357822100

gnomAD n/a

VariantEvidence n/a

CaseAddInfo consanguinity

CasePMIDs n/a

Case#: GC20578

PresentingHPOs:HP:0000666, HP:0000486, HP:0000540, HP:0001103

PresentingHPOsText: Horizontal nystagmus, strabismus, difficulties with near vision, bilateral central macular disturbance.

CaseNotHPOs: HP:0007642, HP:0031605

CaseNotHPOsText: No night blindness, no fundus abnormalities

CasePreviousTesting: "Previous extensive genetic testing results were negative"

CaseGenotypingMethod1: WES

CaseGenotypingMethod1: Confirmed by bidirectional Sanger sequencing.

Variant: NM_002075.3: c.124C>T (p.Arg42Ter), homozygous

ClinVar: Not in ClinVar

CAID: CA6417419

gnomAD: Pop max MAF 0.00006706 (Latino). No homozygotes.

gnomAD

CaseVI-4: Male, 3.5 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0002540, HP:0002970 (Hypophosphatemic rickets, Inability to walk, Genu varum)

HPOsFreeText: -3.76 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted de novo and confirmed by parental testing, Proband is hemizygous for this mutation

CasePreviousTesting: Calcium levels (9.8 mg/dL), Decreased serum phosphate levels (2.8 mg/dL; reference 3.8-6.5), Elevated serum ALP (925 IU/L; reference 90-325), 25OHD3 levels (35 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (62.2 ng/L), TPR levels (69.7), Decreased TmP/GFR levels (1.95; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.1217G>T (p.Cys406Phe)

CAID: CA412573391 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.1217G%3ET

gnomAD: Not in gnomAD

3 individuals with this variant, but they are previously reported. PMIDs: 20417570, 20157015

Case# P7, 2yo report

CasePresentingHPOs HP:0005528, HP:0001873

CasePreviousTesting genes related to MDS/inherited bone marrow failure syndromes was performed in patients, negative for this patient

CaseMethod1 NGS

CaseMethod2 Sanger

CaseGenotypingMethod NGS then variant confirmed with Sanger

Variant NM_152703.4(SAMD9L):c.2640C>A (p.His880Gln)

ClinVar 242372

CaseAddInfo transient monosomy 7 with somatic mutation of new variant NM_152703.3:c.3951_3955del (p.Ser1317ArgfsTer21) - CA658820702

This paper uses in silico predictors to evaluate variants. Prediction is severe for this variant.

ExperimentName: Mutt mice have a FBXO11 S244L mutation

NonHumanModel: mouse (mus musculus)

GeneAlteration: ENU (ethylnitrosourea) was used to induce random mutatgeneiss in the mouse (PMID: 10932191). Animals were screened based on the development of otitis media. Sequencing of the mouse genome uncovered a single point mutation in the FBXO11 gene resulting in a Ser244Leu protein change. This mutation occurs in the region between the F-box and CASH domain. The Ser at amino acid position 244 is conserved across several species.

ModelPhenotype: HP:0000708

Also cleft palate and craniofacial abnormalities

HumanPhenotype: HP:0000708

ModelEvidence: The Mutt mutant mice have a point mutation in FBXO11, S244L. Heterozygous Mutt mice displayed reduced startle reflex at postnatal day 48. They also showed mild cranialfacila abnormalities including a shortened face. The Mutt homozygtote mice demonstrated perinatal lethality within the first day after birth in 17% of mice, but was much less severe than the Jeff mutant mice. the Jeff mice. Furthermore, that homozygotes mice had mild cleft palate and variable facial clefting, and the surviving homozygotes went on to develop craniofacial abnormalities including short face as well as reduced hearing.

ModelVariant: NM_001190274.1:c.983C>T (p. Ser328Leu) equivalent to ENST00000402508.5:c.731C>T (p. Ser244Leu)

CA ID: CA346766144

550+3A>C: Minigene analysis showed aberrant splicing in nearly 100% of mutated minigene construct transcripts, confirmed exon 3 splicing disruption

686-7C>G: RT-PCR and fragment analysis. Both patient sample results show 2 peaks (WT shows only 1)—reference transcript peak and a peak corresponding to a 6 bp longer transcript using a de novo created acceptor splice site. Aberrant and normal transcript proportion was roughly equal, which corresponds to complete impairment caused by the variant. The variant preserves a reading frame and leads to incorporation of additional two amino acids (proline-alanine) into the polypeptide chain

Variants: c.550+3A>C; c.686-7C>G

CAIDs: CA2573332696;

This variant is mentioned in reference to previously published papers that report IEMs

This variant is mentioned as a reference to a previous publication (PMID: 20157015) which has already been included in the VCI.

CA3281947

Case# Subject 3, F, 5mo onset, Hispanic

CasePresentingHPOs HP:0002910, HP:0001942, HP:0003201, HP:0001664, HP:0002878, HP:0001663, HP:0001249, HP:0001250, HP:0008619, HP:0100295, HP:0001260, HP:0004756, HP:0001259, HP:0012734, HP:0002151, HP:0003236, HP:0002307, HP:0000252, HP:0004322, HP:0004325, HP:0002058, HP:0002136

HPOcont: Elevated Transaminases, Metabolic acidosis, Rhabdomyolysis, Torsade de pointes, Respiratory Failure, Ventricular fibrillation, Intellectual Disability, Seizures, Bilateral sensorineural hearing impairment, Muscle fiber atrophy, Dysarthria, Ventricular tachycardia, Coma, Ketotic hypoglycemia, Elevated Lactate, Elevated CPK, Drooling, Microcephaly, Short Stature, Low body weight, Myopathic facies, Broad-based gait

HPOFreeText: (5 months) coma, metabolic acidosis and rhabdomyolysis. (24 years) torsade de pointes, respiratory and multiorgan failure, ventricular fibrillation, epilepsy, bilateral sensorineural hearing loss, intellectual disability and atrophic muscle fibers. She was ambulatory, some speech, drooling, myopathic facies, and wide-based gait. "Height and weight below the 5th percentile for age (weight 42.9 kg, height 147 cm), head circumference below 5th percentile for age (51.4 cm)."

CaseNotHPOs HP:0002540, HP:0001987

NotHPOcont: Non-ambulatory, Hyperammonemia

CasePreviousTesting CPK elevated to 8,000 U/I on first episode, then 22,000 U/I during most severe episode.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, parents confirmed heterozygotes

CasePMIDs n/a

Case: Family D/Prendiville Patient 4, male, 12yo, American, Causasian

CasePresentingHPOs: HP:0100651, HP:0000953, HP:0000998, HP:0005912, HP:0001993

CasePresentingHPOsFreeText: Hyperpigmentation onset at 10yo; located on proximal anterior thighs initially, but spread to chest, lower back, abdomen, thighs, and posterior lower legs. Decreased IgM.

CaseNOTHPOs: HP:0002716, HP:0001433, HP:0003493, HP:0001999, HP:0004322, HP:0001738

CaseNOTHPOSFreeText: inflammatory symptoms

CasePreviousTesting: ADAMTS14, C10orf27, CDH23, EIF4EBP2, LRRC2, KIAA1274, NODAL, NPFFR1, PCBD1, PPA1, PRF1, SLC29A3, SGPL1, UNC5B were sequenced since they were positional candidate genes

CaseGenotypingMethod: homozygosity mapping (50K SNP array), candidate gene sequencing

Variant: M116R homozygous

ClinVarID: or CAID: CA114353

gnomAD: This missense variant, p.M116R, is present in gnomAD v4.0.0 with a MAF=0.0001517 (179/1180030 alleles) in the European NF population and 0 homozygotes. Downscoring for homozygosity since parents are consanguineous.

AddCaseInfo: consanguineous parents

PreviouslyPublished: 17461801

VariantEvidence: Functional studies in Xenopus oocytes expressing M116R displayed a near-total loss of transport activity compared to WT SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated mistrafficking of the mutant protein to the ER or Gogli apparatus (Kang et al. 2010; PMID: 20595384).

Case: Family A/Prendiville Patient 1, male, 14yo at report, East Indian

CasePresentingHPOs: HP:0004322, HP:0000343, HP:0030084, HP:0001993, HP:5000011, HP:0003261, HP:0000953, HP:0000998, HP:0000520, HP:0001433, HP:0012094, HP:0430023, HP:0003565, HP:0001935, HP:0012343, HP:0040303, HP:0100651, HP:0004322, HP:0001999, HP:0100534, HP:0000670, HP:0000767, HP:0031664, HP:0002716, HP:0001763, HP:0001698

CasePresentingHPOsFreeText: hyperpigmentation onset at 15yo; located on chin, axillae, back, abdomen. inner thigh, inguinal folds, genitalia. Pancreatomegaly. Orbital thickening and EOM infiltrate on MR/CT. Opacification of the maxillary sinuses. Posterior pericardial thickening. Thickened right atrial wall.

CaseNOTHPOs: HP:0001738

CaseNOTHPOSFreeText: inflammatory symptoms

CasePreviousTesting: ADAMTS14, C10orf27, CDH23, EIF4EBP2, LRRC2, KIAA1274, NODAL, NPFFR1, PCBD1, PPA1, PRF1, SLC29A3, SGPL1, UNC5B were sequenced since they were positional candidate genes

CaseGenotypingMethod: homozygosity mapping (50K SNP array), candidate gene sequencing

Variant: E444X homozygous

ClinVarID: or CAID: CA114350

gnomAD: This nonsense variant p.E444X, located in exon 6/6, is present in gnomAD v4.0.0 with a MAF=0.0002525 (23/91078 alleles) in the South Asian population and 1 homozygote. Downscoring this variant since NMD is not expected to occur and there is 1 homozygote in gnomAD.

AddCaseInfo: consanguinity not reported

PreviouslyPublished: 17461801

VariantEvidence: Functional studies in Xenopus oocytes expressing E444X displayed a partial reduction in nucleoside transport activity and impaired protein stability.

Case# Subject 10, female, 14yo, non-Hispanic

CasePresentingHPOs HP:0010535, HP:0002098, HP:0031064, HP:0000729, HP:0000750, HP:0001249, (Sleep apnea, Difficulty breathing, Impaired continence, Autism spectrum disorder, Speech delay, Intellectual disability)

HPOFreeText: Phenotypes described postnatally.

CaseNotHPOs HP:0001250, HP:0001252, HP:0000708, HP:0001285, HP:0007018, HP:0011968, HP:0000589, HP:0000648, HP:0000568, HP:0000659, HP:0000525, HP:0000581, HP:0000407, HP:0000453, HP:0410030, HP:0001629, HP:0001655, HP:0001643, HP:0010772, HP:0002020, HP:0002247, HP:0001734, HP:0002021, HP:0000076, HP:0000107, HP:0001159, HP:0001385, HP:0002650, HP:0002938, HP:0001511, HP:0011328, HP:0002007, HP:0000325, HP:0000534, HP:0000601, HP:0000316, HP:0000582, HP:0000494, HP:0045025, HP:0000286, HP:0000490, HP:0000598, HP:0004467, HP:0000414, HP:0000463, HP:0000319, HP:0012471, HP:0000160, HP:0000221, HP:0000164, HP:0000187, HP:0000218, HP:0000347, HP:0002557, HP:0003186, HP:0200055, HP:0004209, HP:0011297, HP:0001792, HP:0010490, HP:0000349, HP:0004532, HP:0000957 (Seizures, Hypotonia, Behavioral problems, Spastic quadriparesis, ADHD, Poor feeding, Coloboma, Optic atrophy, Microphthalmia, Peter's anomaly, Iris anomalies, Blepharophimosis, Sensorineural hearing loss, Choanal atresia, Cleft lip, Ventricular septal defect, Patent foramen ovale, Patent ductus arteriosus, Anomalous pulmonary venous return, Gastroesophageal reflux, Duodenal atresia, Annular pancreas, Pyloric stenosis, Vesicoureteral reflux, Cystic kidney, Syndactyly, Hip dysplasia, Scoliosis, Lumbar lordosis, Intrauterine growth retardation, Fontanel abnormality, Frontal bossing, Triangular face, Abnormal eyebrows, Hypotelorism, Hypertelorism, Upslanting palpebral fissures, Down-slanting palpebral fissures, Small palpebral fissures, Epicanthal folds, Deeply set eyes, Abnormal ears, Preauricular pits, Bulbous nose, Anteverted nares, Flat philtrum, Full lips, Small mouth, Furrowed tongue, Abnormal teeth, Broad alveolar ridges, High-arched palate, Micrognathia, Small nipples, Inverted nipples, Small hands, 5th finger clinodactyly, Digital Anomalies, Nail hypoplasia, Abnormal palmar creases, Widow's peak, Sacral hypertrichosis, Café Au Lait spots)

CasePreviousTesting Screen for variants involved with Autism, de novo RERE variant was only result

CaseMethod1 Exome sequencing

CaseMethod2 sanger

CaseGenotypingMethod exome sequencing confirmed with sanger in patient and parents by Krumm et al.

Variant NM_012102.3:c.2278C>T(p.Gln760Ter), de novo

ClinVar n/a

CAID CA338172916

gnomAD n/a

VariantEvidence n/a

CaseAddInfo both parents tested

CasePMIDs 25961944

Case#: (Biallelic affected sib) MM, female, 10 years (at age of blood draw) CaseHPOs: HP:0002024, HP:0002013, HP:0002570, HP:0002495, HP:0001284 (malabsorption, vomiting, steatorrhea, , impaired vibratory sensation, absent deep tendon reflexes)

CaseHPOsFreeText:: Diagnosed with FHBL at age 10 years; neurological symptoms stabilized on Vitamin E treatment. CasePreviousTesting: Total cholesterol 24mg/dl, no detectable triglyceride ot LDL-cholesterol, 21 mg/dl HDL cholesterol. Variant: Compound heterozygous: Variant 1: NM_000384.2:c.537+1G>T (paternal) Variant 2: NM_000384.2:c.1315C>T (p.Arg439Ter) (maternal)

ClinVar: N/A

CAID: Variant 1: CA345962364 ; Variant 2: CA052017

gnomAD: Variant 1: Not in gnomAD; Variant 2: 0.00002640 (Euro non-Finnish)

Case#: (Heterozygous sib) GM (II-5), male, 14 years (at blood draw), sib of proband CaseHPOs: HP:0003563 CaseHPOsFreeText: Asymptomatic CasePreviousTesting: Total cholesterol 97 mg/dl, triglyceride 59 mg/dl, LDL-cholesterol 29 mg/dl (<5th percentile), HDL cholesterol 56 mg/dl. ** Variant:** Heterozygous for NM_000384.2:c.537+1G>T (paternal)

CAID: CA345962364

Case#: (Heterozygous sib) JM (II-6), male, 7 years (at blood draw), sib of proband CaseHPOs: HP:0003563 CaseHPOsFreeText: Asymptomatic CasePreviousTesting: Total cholesterol 113 mg/dl, triglyceride 60 mg/dl, LDL-cholesterol 16 mg/dl (<5th percentile), HDL cholesterol 87 mg/dl) ** Variant:** Heterozygous for NM_000384.2:c.1315C>T (p.Arg439Ter) (maternal)

CAID: CA052017

Case#: Speigel Patient I-1, onset at birth, death at 10mo

DiseaseAssertion: Fatal infantile mitochondrial encephalomyopathy, hypertrophic cardiomyopathy and optic atrophy

FamilyInfo: Parents are healthy first-degree cousins with no visual or neurological complaints. Both parents were heterozygous for this OPA1 variant. Their optic discs did not look pale on dilated fundus examination and optical coherence tomography (OCT) imaging did not show any subclinical thinning of the retinal nerve fibre layer. The parents have two clinically unaffected sons who were 14 and 11 years old when last reviewed in clinic. The older son is heterozygous for the c.1601T>G OPA1 variant, whereas the other son only carries the wild-type OPA1 allele.

CasePresentingHPOs: HP:0001622, HP:0001531, HP:0008936, HP:0001276, HP:0002179, HP:0001612, HP:0000617, HP:0031964, HP:0012758, HP:0001639, HP:0002104

CaseHPOFreeText: elevated lactate levels, but a normal cerebrospinal fluid (CSF) lactate concentration. progressive, non-obstructive, generalised hypertrophic cardiomyopathy,

CaseNotHPOs: HP:0001635

CaseNotHPOFreeText: abnormal brain MRI

GenotypingMethod: genome-wide autozygosity mapping and next-generation exome sequencing

PreviouslyPublished: n/a

Variant: OPA1 NM_015560.2 c.1601T>G p.Leu534Arg

ClinVar:

CAID: CA357235

SupplementalData: n/a

Individual

Case#: NGI

Caseprevioustesting: SSCP Scan

Casemethod1: PCR, Sanger

Variant: NM_000268.3:c.1219C>T (nonsense)

CAID: CA021304

Caseaddinfo:

gnomad: no data

CasePt3 male, 4yo death, Italian

CasePresentingHPOs HP:0001987 (Hyperammonemia)

HPOsFreeText Severe hyperammonemia at 48h of life

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing: ammonia(348[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.1022T>C(p.Leu341Ser), 2. NM_001875.4:c.3784C>T(p.Arg1262Ter ) compound heterozygous

ClinVar n/a

CAID 1. CA350430554, 2. CA350438463

gnomAD 1. n/a, 2. 0.00004485(European (Finnish)), 0.000004062(Total)

VariantEvidence n/a

CaseAddInfo similarly affected brother died without diagnosis

CasePMIDs n/a

Case# Fam2Pat1, F, Turkish, 15yo onset

CasePresentingHPOs HP:0002061, HP:0002066, HP:0002070, HP:0001260, HP:0001310, HP:0000563, HP:0006986

CasePreviousTesting Neurologic examination revealed severe spasticity in the lower and mild spasticity in the upper extremities, hyperactive deep tendon reflexes, bilateral extensor plantar responses, and patellar clonus. The Hoffmann sign was positive. She had bilateral mild dysmetria and dysdiadochokinesia. Nerve conduction studies, EMG, sensory evoked potential tests, and MRI did not reveal any pathology

CaseMethod1 Whole Exome

Variant NM_001198869.1:c.1176G>A

CAID CA6093326

VariantEvidence premature stop codon

gnomAD 1.554e-05(European (Non-Finnish)), 8.513e-06(Overall)-Exac

Case: Family I Proband III-6, female, 20yo at report

CasePresentingHPOs: HP:0000953, HP:0000998, HP:0030053, HP:0001822, HP:0000365, HP:0001698, HP:0012385, HP:0034373, HP:0002619, HP:0000520, HP:0007380

CasePresentingHPOsFreeText: Dilated lateral scleral vasculature

CaseNOTHPOs: HP:0000823, HP:0001433, HP:0001256

CaseNOTHPOSFreeText:

CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3

Variant: G427S homozygous

ClinVarID: or CAID: 563/CA114349

gnomAD: The missense variant G427S is present in gnomAD v4.0.0 with a MAF=0.00005339 (4/74926 alleles) in the African/African American population and 0 homozygotes.

AddCaseInfo: Consanguineous parents, not genotyped. 3 additional affected family members

PreviouslyPublished: n/a

VariantEvidence: Functional studies in Xenopus oocytes demonstrated that G427S results in a total loss of transport activity (Kang et al. 2010; PMID: 20595384).

Case: Family E Proband EII-1, male, Arabic, Israeli, 17yo at report

CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0000054, HP:0000771, HP:0002619, HP:0001433, HP:0000520, HP:0012385, HP:0003565

CasePresentingHPOsFreeText: scrotal masses, dilated scleral vessels, maturation arrest in all tubules with few spermatids in 4% to 5% of the tubules on testicular biopsy

CaseNOTHPOs: HP:0008064, HP:0011025, HP:0000365, HP:0007380

CaseNOTHPOSFreeText:

CasePreviousTesting: direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: microarray, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

Variant: G437R homozygous

ClinVarID: or CAID: 565/CA114352

gnomAD: The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

AddCaseInfo: consanguineous, heterozygous, unaffected parents.

PreviouslyPublished: PMID: 18410979

VariantEvidence: Kang et al. (2010; PMID: 20595384) performed functional characterization of the G437R mutation in Xenopus oocytes and observed transport activity that was approximately half that of wildtype SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to wildtype, suggesting decreased stability.

Case#: Li 2018 sALS I42T, Chinese

MonDO:* MONDO:0005145 for sALS

CasePresentingHPOs: HP:0007354

CaseGenotypingMethod: Sanger sequencing. TUBA4A sequencing was performed using Sanger. No further details provided.

Variant: NM_006000.3(TUBA4A):c.125T>C (p.Ile42Thr)

CAID: CA2122537

gnomAD: 2-220116831-A-G; total overall AF (non-neuro) = 0.0001787 --> exceeds VCEP limit of 0.00005 therefore score at 0; TUBA4A_pI42T_gnomAD

Cultured fibroblasts from patients show that this variant results in altered organization of the mitochondrial network including a 20.5% reduction in mitochondrial volume compared to controls, a higher ratio of individual mitochondrial tubules to total mitochondrial length, unconnected mitochondria that consisted of small tubular structures (Fig. 3E) with few dichotomous branches and a small number of connection points, and fragmentation of the mitochondrial network (Fig. 4).

Case#: 10455, Female, Caucasian, 48 years (onset), 58 years (report)

CaseHPOs: HP:0000643, HP:0012048, HP:0000473 (Blepharospasm, oromandibular dystonia, cervical dystonia/torticollis)

CaseHPOFreeText: Segmental dystonia (BSP, oromandibular, lower face, cervical)

CaseNotHPOs:

CasePreviousTesting: Prior to WES, pathogenic variants in THAP1, GNAL, and Exon 5 of TOR1A were excluded by high resolution melt analysis.

CaseMethod1: WES

CaseMethod2: Confirmation by Sanger sequencing

Variant: NM_020821.2:c.9605C>G (p.Ala3202Gly)

ClinVar: NA

CAID: CA7594605

gnomAD 0.000009584 (European non-Finnish); no homozygotes

VariantEvidence: None

Case# SAL-584-005, Female, 67yo, Italian

CasePresentingHPOs HP:0001258, HP:0002070, HP:0001260, HP:0002066

CaseMethod1 Exome

CaseMethod2 Sanger

Variant NM_005186.3:c.188dup

CAID CA6092966

gnomAD 0.000009815

VariantEvidence null

CaseAddInfo in supplement, possibly consanguineous family

Case# Family R III:1, Female, 43yo, Bangladesh

CasePresentingHPOs HP:0002066, HP:0001257, HP:0002015, HP:0001260, HP:0001272

CaseMethod1 DNA SNP array

CaseMethod2 Exome sequencing

Variant NM_005186.3:c.337+1G>A

CAID CA381241741

VariantEvidence predicted null

The paper mentions this variant, but only in review of the cases that exist in the literature for Chinese MPS1 patients. Will annotate the case in the original publication.

variant in trans with c.5882G>A (p.Gly1961Glu)

Patient: ID1021

Variant: c.550G > A (p.Gly184Arg)

CAID: CA219267

Functional effect: Monoallelic expression (wt only). Observed in blood.

Patient: ID408

Variant: c.686-12A > G

CAID: CA2580612032

Functional effect: Normal exon inclusion *, use of de novo splice site: c.686-11. Observed in blood.

Family#PresentingHPOs HP:0001252, HP:0000486, HP:0200006, HP:0001344, HP:0001249, HP:0010813 (Hypotonia, Strabismus, Slanting of palpebral fissure, Absent speech, Intellectual disability, Double crown)

HPOFreeText: narrowing of ventricles

FamilyNotHPOs n/a

NotHPOFreeText: n/a

CountryOrigin Northern Israel

Ethnicity Arab-Moslem

Race n/a

Family#PreviousTesting Excluded off-target, heterozygous, synonymous and X chromosome variants. Also excluded varaints that were called fewer than x8 with MAF > 1% in ExAC. Metabolic analyses as well as muscle biopsy had normal results.

Family#Method1 WES

Family#Method2 Sanger

Family#GenotypingMethod WES confirmed with Sanger

Affected 2

Unaffected 2

Segregations 2

PublishedLOD n/a

eLOD n/a

AddSegregationInfo consanguineous

ProbandLabel Proband 2, male, 11yo diagnosis

CasePresentingHPOs HP:0000961, HP:0002098, HP:0006829, HP:0000237, HP:0000238, HP:0002079, HP:0000463, HP:0000218, HP:0000817, HP:0001250, HP:0000648, HP:0100702, HP:0000268, HP:0000338, HP:0000494, HP:0000520, HP:0002711, HP:0009092, HP:0000356, HP:0010864, HP:0002015, HP:0006532, HP:0001639, HP:0000276 (Cyanosis, Respiratory distress, Severe Hypotonia, Small anterior fontanelle, Hydrocephalus, Thin corpus callosum, Anteverted nares, High palate, Poor eye contact, Seizures, Optic nerve atrophy, Arachnoid cyst, Dolichocephaly, Hypomimic face, Downslanting palpebral fissures, Proptosis, Deep tongue groove, Gum ridge hypertrophy, Outer ear abnormality, Severe intellectual disability, Swallowing difficulties, Hypertrophic cardiomyopathy, Long face)

HPOFreeText: Neonatal cyanosis, no cry, respiratory distress, upper body hypotonia, small anterior fontanelle, lateral ventricle dilation, hydrocephalus, severe head lag, hypertrophic cardiomyopathy, thin corpus callosum, central hypotonia, anteverted nares, high palate, strabismus, and no eye contact. Convulsions, retro-cochlear defect-no response on left (2y), no expressive speech, partial atrophy of optic nerve and arachnoid cyst(5y), dolicocephaly, double crown, long face, decreased facial movement, downslanting palpebral fissures, mildly prominent eyes, deep grooves in tongue, gum hypertrophy, large simple auricles, small palms(7y). Diagnosis of severe ID, severe hypotonia, convulsions, swallowing abnormalities, recurrent pneumonia, small heart muscle fibers and primitive sarcomere structure at 11 years old.

CaseNotHPOs HP:0001507 (Growth abnormality)

NotHPOFreeText: n/a

Variant NM_001163435.2:c.1854del(p.Pro619GlnfsTer?)

ClinVar n/a

CAID CA658820911

gnomAD n/a

FamilyAddInfo variant absent in ~60,000 exomed individuals in Exac and in ~800 Moslem-Arab analyses. Affected sister who additionally presented with severe scoliosis, osteoporosis, narrow forehead, upslanted palpebral fissures, bushy eyebrows, flattened nose, porencephalic cyst, opistotonus, spenomegaly, prominent metopic suture and narrow high palate.

FamilyPMIDs n/a

additional phenotype and previous testing information to add to PMID 22875837 patient 1

MonDO: MONDO:0032706

Case: Chinese male. Onset at age 30 years with mild dysarthria with progressive worsening.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: No history of neurological disease and consanguinity was documented in the family. Delivery and perinatal events were unremarkable.

CasePresentingHPOs: HP:0001260, HP:0002141, HP:0002061, HP:0009046 (Dysarthria, Gait imbalance, Lower limb spasticity, Difficulty running

CaseHPOFreeText: Difficulty writing, Increase in bilateral knee reflexes

CaseNOTHPOs: HP:0003487 (Babinski sign)

CasePreviousTesting: His clinical examination displayed cerebellar ataxia with abnormal finger-to-nose and heel-knee-shin tests. Bilateral knee reflexes were symmetrical increased (+++) and Babinski signs were negative. Cranial nerves, muscle strength and sensory examinations were normal. Mild cognitive decline with a Mini-Mental State Examination (MMSE) of 24/30, a Scale for the Assessment and Rating of Ataxia (SARA) score of 17.5/40 and International Cooperative Ataxia Rating Scale (ICARS) score of 46/100. Brain MRI revealed cerebellar atrophy (Fig. 1A).

GenotypingMethod: WES with Sanger confirmation and co-segregation analysis. Genetic testing for spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 7, 12, 17 and dentatorubral-pallidoluysian atrophy (DRPLA) were negative.

VariantEvidence: Wildtype and mutant plasmids were transfected into SH-SY5Y cells. The mRNA level of frameshift variant p.Thr442fs7 was almost same with the level of wild-type, whereas nonsense variant p.Arg253 was even increased, thus they might escape NMD. As a result, p.Gln316 and p.Ser436fs36 mutant GDAP2 proteins were barely detectable, p.Thr442fs7, p.His400fs15 and p.Arg253 generated truncated proteins. Western blot analysis indicated that the GDAP2-Arg253 and GDAP2-Thr442fs*7 were C-terminal deletion mutants.

MultipleGeneVariants:

(1) GeneName: GDAP2

(1) Variant: c.757C>T (p.Arg253*)

(1) ClinVarID or CAID: CA1031554

(1) gnomAD: Total AF 0.00001860, gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-117899096-G-A?dataset=gnomad_r4)

(2) GeneName: GDAP2

(2) Variant: c.1323delC (p.Thr442fs*7)

(2) ClinVarID or CAID: CA2586967196

(2) gnomAD: not found in gnomAD v4.1

PMID: PMID:16043485

Gene: TPM1

Disease: hypertrophic cardiomyopathy 3

MonDO: MONDO:0007267

InheritancePattern: AD

CellLine: Human Mononuclear Myoblast

CellEFO: CL:0000056

GeneFunction: GO:0007015 (Actin Filament Organization)

GeneAlteration: A wild-type C-terminal EGFP-tagged β-TM fusion gene was generated by amplifying TPM2 and cloning it into a vector while introducing XhoI and EcoRI restriction sites. All mutant constructs were formed by site-directed mutagenesis and cloning into E. coli. These constructs were sequenced to verify the correct coding sequence and introduction of the mutations. They were then introduced to human myoblast cells and mouse C2C12 cells via transfection.

FunctionalEvidence: The expression of these TPM2 mutants in cultured cells demonstrated several morphological abnormalities reminiscent of those seen in nemaline myopathy patients. In the human myoblasts/differentiated cells, these included various types of aggregates including nuclear, cytoplasmic, endogenous, and perinuclear. Large accumulations of actin along with clouds around the nucleus and cytoplasm with unorganized structure were also present. Poor incorporation of stress fibers, what appeared to be disorganized sarcomeric structure, and rod-like structures both intranuclear and in the myotubes in particular all demonstrate clear similarities to those phenotypes seen in nemaline myopathy, namely the presence of nemaline rods, disorganized sarcomeres, and z-disc abnormalities. These two groups of pathologies also seem to share the same mechanism, specifically the TPM2 mutations destabilizing the actin-myosin structures and causing accumulation and abnormal structures to form. Similarly, the modified C2C12 myoblasts/myotubes also displayed peripheral and perinuclear aggregates in both stages of development as well as diffuse cytoplasmic labeling of stress fibers. They had difficulty differentiating, as they appeared to be fused rather than elongated and multinucleated. This further supports the connection between the gene disruption and the pathologies that are demonstrated here.

CellVariant1: NM_003289.3:c.121G>A (p.Glu41Lys)

ClinVar: 12464 http://www.ncbi.nlm.nih.gov/clinvar/variation/12464

CellVariant2: NM_003289.3:c.142_144delAAG (p.Lys49del)

ClinVar: 12466 https://www.ncbi.nlm.nih.gov/clinvar/variation/12466/

CellVariant3: NM_003289.3:c.154_156dup (p.Gly52dup)

ClinVar: 140485 https://www.ncbi.nlm.nih.gov/clinvar/variation/140485/

CellVariant4: NM_003289.3:c.364G>A (p.Glu122Lys)

CAID: CA373367963 http://reg.genome.network/redmine/projects/registry/genboree_registry/by_caid?caid=CA373367963

CellVariant5: NM_003289.3:c.606C>G (p.Asn202Lys)

ClinVar: 12467 https://www.ncbi.nlm.nih.gov/clinvar/variation/12467/

Case#: Zahari_HA24

Demographics:

CasePresentingHPOs: HP:0003125 severe hemophiliac FVIII:C:<1%

CaseNotHPOs:

CasePreviousTesting: No

CaseMethod1:

CaseMethod2:

CaseGenotypingMethod: F8 coding regions (26 exons) including the intron/exon boundaries and the promoter regions were amplified using 26 sets of primers and subsequently sequenced.

Variant: NM_000132.3:c.3625C>T(p.Gln1209Ter)

ClinVar:

CAID: CA414895516

gnomAD: Not Found

VariantEvidence: The variant introduces a stop codon in exon 14 and premature truncation of the protein product. The variant is awarded default points

CaseAddInfo:

CasePMIDs:

unable to annotate in PDF.

Case: Farooq Family 1 Proband, Syrian, female, 11yo at report, onset at 5yo

CasePresentingHPOs: HP:0004322, HP:0001730, HP:0030044, HP:0000953, HP:0000998, HP:0000969, HP:0100651, HP:0030084, HP:0002240, HP:0001395,

CasePresentingHPOsFreeText: Hyperpigmentation on lower extremities symmetrically and bilaterally, later the genital area as well with edema.

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting:

CaseGenotypingMethod: All 6 exons including exon-intron boundaries of the SLC29A3 gene were amplified by PCR from the genomic DNA. Direct sequencing analysis. Restriction enzyme digest.

Variant: c.1+2T>G homozygous

ClinVarID: or CAID: 213676/CA377128556

gnomAD: This splice site variant, c.1+2T>G found in intron 1, is absent from gnomAD v2.1.1. It is present in gnomAD v4.0.0 with a MAF of 0.00001024 (3/292950 alleles) in the European NF population and 0 homozygotes, but there is low coverage so the AF is not reliable.

AddCaseInfo: consanguineous, heterozygous parents

PreviouslyPublished: n/a

VariantEvidence: n/a

unable to annotate in PDF.

Case: Farooq Family 2 Proband, Syrian, female, 16yo at report, onset at 1wk old

CasePresentingHPOs: HP:0030148, HP:0001629, HP:0033190, HP:0004322, HP:0012785, HP:0001730, HP:0002240, HP:0001395

CasePresentingHPOsFreeText: Hyperpigmentation on thighs and later genital area. Hearing started deteriorating progressively after an ear infection. Fasting blood glucose was elevated (350 mg/dl).

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting:

CaseGenotypingMethod: All 6 exons including exon-intron boundaries of the SLC29A3 gene were amplified by PCR from the genomic DNA. Direct sequencing analysis. Restriction enzyme digest.

Variant: p.R386Q homozygous

ClinVarID: or CAID: 39870/CA130660

gnomAD: The missense variant p.Arg386Gln is present in gnomAD v4.0.0 with a MAF=0.00003999 (3/75018 alleles) in the African/African American population and 0 homozygotes.

AddCaseInfo: Consanguineous, heterozygous parents. Proband's younger sister was also reported by the parents to be affected, but was not examined by the authors or genotyped.

PreviouslyPublished: n/a

VariantEvidence: n/a

Case: Individual 11, male, AOR= 14 years

CasePresentingHPOs: HP:0001263, HP:0000750, HP:0001256, HP:0000752, HP:0001575, HP:0000276, HP:0000286, HP:0000278, HP:0000347, HP:0001182, HP:0001763, HP:0001852, HP:0011330, HP:0001382, HP:0002719, HP:0000540, HP:0000486, HP:0002967, HP:0001065, HP:0001724, HP:0010499, HP:0000243

CasePresentingHPOText: Began walking at 24 months old.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0012443,

CasePreviousTesting: Array-CGH (244K Agilent) normal, Fragile X syndrome (FMR1 Repeat analysis) normal, Loeys-Dietz syndrome (TGFBR1 and TGFBR2) normal and Marfan syndrome (FBN1) normal

CaseGenotypingMethod: WES (Agilent CRE and HiSeq 4000), searching for variants in FBXO11 after identification of variant in I13, Sanger confirmation to show de novo status and absence in parents. Sample identity confirmed.

Variant: hg19:chr2: g.4806002 0C>G, c.1042- 1G>C, p.(?) OR NM_001190274.1:c.1042- 1G>C(p.=)

CA ID: CA346765998

de novo splice site mutation.

gnomAD: n/a

AddCaseInfo:

VariantEvidence: The c.1042-1G>C mutation is most likely a splice site mutation. The mutation arises in exon 9 (Intron 8), and likely would disrupt exon 9 transcription. Exon 9 does not transcirbe any of the funcitonal domains, but exon 10 comprises the NosD domain, which is 5' to the first CASH domain. No functional assays or variant evidence was provided, so I have downgraded the score.

Case: Individual 2, female, AOR= 8yo

CasePresentingHPOs: HP:0001263, HP:0000750, HP:0002342, HP:0007359, HP:0002500, HP:0001290, HP:0002360, HP:0000729, HP:0000739, HP:0025269, HP:0000490, HP:0001840, HP:0000486

CasePResentingHPOText: Began walking at 22 months, first words at 2yo,. Seizure onset at 7 yo and are focal, and occur nightly. Reduced white matter bulk on MRI. Referred to as having intoeing or pigeon-toed. Low APGAR scores, brief resuscitation required

CaseNOTHPOs: HP:0002376, HP:0000202, HP:0000924, HP:0002719,

CasePreviousTesting: ArrayCGH, Fragile X (FMR1), Angelman Syndrome (methylation & UBE3A), Rett syndrome (MECP2), Pitt-Hopkins Syndrome (TCF4), and extensive metabolic screening were all normal

CaseGenotypingMethod: Trio-WES performed through the DDD consortium, 2017 PMID:PMID: 28135719.

Variant: hg19:chr2: g.48066586T>A, c.414A>T, p.(Arg138Ser) or NM_001190274.1:c.414A>T

CA ID: CA346813374

de novo Trio-WES performed by DDD so maternity and paternity could be investigated with this method.

gnomAD: n/a

AddCaseInfo: Case was part of the DDD study 2017 PMID: 28135719,

VariantEvidence: Arg138 is located N-terminal to the F-box region of FBXO11, and is conserved across species. Pathogenicity algorithms showing varying predictions, from tolerated to damaging, thus indicating a VUS. No functional assays were performed to indicate the impact of the R138S mutation on FBXO11 function.

Variant is in trans with a complex allele

Proband KH8 was 20yo at report, has the Hurler phenotype, and has this variant in compound heterozygosity with 704ins5 (CTGCT)

Proband KH9 was 11yo at report, has the Hurler phenotype, and has this variant in compound heterozygosity with 704ins5 (CTGCT)

Proband KH4 was 6yo at report, has the Hurler phenotype, and has this variant in compound heterozygosity with 704ins5 (CTGCT)

Case#: Yamagishi Case 1, female, 3yo1mo, Japanese

DiseaseAssertion: MPS1-Hurler

FamilyInfo: consanguinity

CasePresentingHPOs: HP:0001510, HP:0002240

CaseHPOFreeText: mental delay, height -1.5SD

CaseNotHPOs:

CaseNotHPOFreeText: cardiac involvement

PreviouslyPublished: n/a

Variant: 704ins5 homozygous

ClinVar: 11921

CAID: CA256123

SupplementalData: n/a

Case#: Family IV-II:1, 58 years old, male

CaseHPOs: HP:0003563 (decreased LDL cholesterol)

CaseHPOsFreeText: Type 2 diabetes and severe non-alcoholic steatohepatitis (NASH) with pre-cirrhotic lesions and well differentiated hepatocellular carcinoma (HCC) diagnosed on liver biopsy

CasePreviousTesting: TC 120 mg/dl, LDL-C 50 mg/dl, HDL-C 55 mg/dl, TG 89 mg/dl (see additional values in Table 1) ApoB100 19 mg/dl (normal range 49-88) (Supplemental data)

Variant: NM_000384.2:c.11153C>G (p.Ser3718Ter), heterozygous

CAID: CA345983128

gnomAD: Absent

Variant evidence: APOB- p.Ser3718* mutations lead to the formation of expected truncated ApoB forms (ApoB-81) of 418 kDa (Fig. 1C, right panel) that can be secreted by the liver and lipidated.

CaseAddInfo: Son of Family IV-I:1

Case#: Family II-II:1, 41 year old, male

CaseHPOs: HP:0003563, HP:0001397 (decreased LDL cholesterol, hepatic steatosis)

CaseHPOsFreeText: Prediabetes

CasePreviousTesting: TC 113 mg/dl, LDL-C 38 mg/dl, HDL-C 69 mg/dl, TG 32 mg/dl (see additional values in Table 1). ApoB100 22 mg/dl (normal range 49-88) (Supplemental data). Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

CaseGenotypingMethod: Next generation sequencing panel for high-throughput sequencing of the coding regions of genes previously linked to FHBL (APOB, PCSK9, ANGPTL3) and ABL (MTTP, SAR1B). Sanger sequencing was performed for validation.

Variant: NM_000384.2:c.7711C>T (p.Gln2571Ter), heterozygous

CAID: CA43502110

gnomAD: Absent

Family#: Family III

PresentingHPOs: HP:0003563 (decreased LDL cholesterol)

PresentingHPOsFreeText: FHBL diagnosis was based on low levels of fasting calculated plasma LDL-C < 50 mg/dL without lipid lowering therapy. Affected relatives were diagnosed by LDL-C < 80 mg/dL and/or ApoB <50 mg/dL.

FamilyMethod1: Next generation sequencing

FamilyGenotypingMethod: Next generation sequencing panel for high-throughput sequencing of the coding regions of genes previously linked to FHBL (APOB, PCSK9, ANGPTL3) and ABL (MTTP, SAR1B). Sanger sequencing was performed for validation and co-segregation analysis among family members.

ProbandLabel: Family III-II:2

Variant: NM_000384.2:c.8799C>A (p.Cys2933*), heterozygous

CAID: CA345993342

gnomAD: Absent

Case#: Severe MPS1 patients, 6 individuals with this genotype

DiseaseAssertion: Severe MPS I

FamilyInfo: n/a

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: n/a

GenotypingMethod: n/a

PreviouslyPublished: possible

Variant: R628X/R628X

ClinVar: 550421

CAID: CA2802462

SupplementalData: Table S1 also lists this variant one time in compound heterozygosity with Q70X

Case#: Patient 2.1.1, male, 4yo, Indian

DiseaseAssertion: MPS1

FamilyInfo: No family history reported, but said not to be consanguineous

CasePresentingHPOs:

CaseHPOFreeText: Distended abdomen, developmental delay

CaseNotHPOs:

CaseNotHPOFreeText:

GenotypingMethod: NGS, Sanger

PreviouslyPublished:

Variant: c.1882C > T p. Arg628Ter homozygous

ClinVar: 550421

CAID: CA2802462

SupplementalData: n/a

Case#: Family 5 Case 1, male, 43yo, south France

DiseaseAssertion: OA plus

FamilyInfo: mother and brother also had optic atrophy, but further details such as genotype and more phenotype information were not confirmed

CasePresentingHPOs: HP:0000648, HP:0000508, HP:0000365, HP:0001251, HP:0002403, HP:0003326, HP:0009830, HP:0003200, HP:0000590, HP:0003688, HP:0003390,

CaseHPOFreeText: visual impairment since childhood, colic occlusion without any evident mechanical cause, impaired sensation to all modalities predominantly in the lower limbs, atrophy of the corpus callosum and brainstem and a mild cerebellar atrophy, bilateral basal ganglia hypointensity was detected at T2-weighted MRI scan

CaseNotHPOs:

CaseNotHPOFreeText:

PreviouslyPublished:

PreviousTesting: Direct sequencing of the complete coding region and the exon/intron boundaries of the genes POLG1, PEO1 (Twinkle) and SLC25A4 (ANT1). mtDNA multiple deletions present.

GenotypingMethod: genomic DNA was amplified by PCR with specific primers designed to amplify all exons and flanking intronic regions and sequenced. Southern blot analysis, long-range PCR, sequencing in both directions, and quantitation of mtDNA relative to nuclear DNA was performed on mtDNA

Variant: c.1635 C > G (p.S545R)

ClinVar: 30461

CAID: CA10575554

SupplementalData:

CaseF2:III-1: Female, Italy

CasePresentingHPOs: N/A

CaseAddInfo: Proband for F2

Case# II-1, F, 13yo diagnosis, European

CasePresentingHPOs HP:0001254, HP:0001137, HP:0025404, HP:0008936, HP:0002509, HP:0025430, HP:0003739, HP:0002353, HP:0001508, HP:0000297, HP:0010804, HP:0000218, HP:0000347, HP:0001212, HP:0001864, HP:0040082, HP:0012167, HP:0030820, HP:0000276, HP:0000268, HP:0000549, HP:0000678, HP:0012166, HP:0002465

HPOcont: Lethargy, Alternating esotropia, Abnormal visual fixation, Muscular hypotonia of the trunk, Limb hypertonia, High-pitched cry, Myoclonic spasms, EEG abnormality, Failure to thrive, Facial hypotonia, Tented upper lip vermilion, High palate, Micrognathia, Prominent fingertip pads, Clinodactyly of the 5th toe, Happy demeanor, Hair-pulling, Hooded eyelid, Long face, Dolichocephaly, Abnormal conjugate eye movement, Skin-picking, Poor speech

Free Text: "Birth weight, length and head circumference were 3.149 kg (−0.18SD), 51 cm (+0.99SD), and 33 cm (−0.74SD), respectively. Although she did not cry immediately and was described as sleepy and lethargic, her Apgar scores were 8 and 9 at 1 and 5 minutes, respectively. She has had poor weight gain throughout life. By 2 months of age, she developed alternating esotropia, poor visual fixation, truncal hypotonia, upper and lower extremity hypertonia and a high-pitched cry. She also had myoclonic jerks and jerky movements of her extremities. Her weight, height and head circumference were 4.6 kg (−1.57SD), 51 cm (−3.81 SD) and 39.2 cm (+0.06SD), respectively. A head CT scan detected no anatomical anomalies. An EEG showed excessively slow background without epileptiform activity. Despite intervention, her weight gain continued to fall off, and she was diagnosed with failure to thrive. She rolled over at age 6 months, sat unsupported at 1 year. A follow-up EEG at 14 months showed a slow dysrhythmic background compatible with a seizure predisposition and diffuse cerebral dysfunction. A brain MRI at 18 months of age showed normal anatomy and myelination. In the ensuing months, she demonstrated a happy disposition, low truncal muscle tone and distal hypertonia as well as a myopathic facial appearance, a tented upper lip, a high arched palate, micrognathia, prominent finger pads and mild fifth toe clinodactyly. At age 4 years and 1 month, a developmental assessment defined her overall functioning at no more than a 12-month-old equivalent; she was not autistic. At age 6 years and 11 months, she manifested sparse hair (trichotillomania), hooded eyelids, high arched palate, thin long face and mild micrognathia. At age 12 years, she walked with the support of splints. Her height, weight and head circumference were 127 cm (−3.64 SD), 22.6 kg (−4.06 SD), and 52 cm (−0.94SD), respectively. Her features included dolicocephaly, hooded eyelids, intermittently disconjugate gaze, sparse hair, high palate and crowded dentition. Developmental assessment documented behavioral difficulties including repetitive and self-stimulatory behaviors, sensory issues such as repetitively rubbing her hands on the floor and/or licking them and mouthing objects, rigidity, communication deficits, difficulties with emotional regulation and aggression when frustrated. Her aggression included the self-injurious behaviors of dermatillomania, biting and trichotillomania. She communicated with a few words, signs, gestures and a picture exchange communication system (PECS). She developed menses at age 13 years."

CasePreviousTesting "Family history was negative for intellectual disability, multiple congenital anomalies and recurrent miscarriages. Normal genetic investigations included a karyotype (550 band resolution), subtelomeric FISH, methylation studies of SNRPN, sequence analysis of UBE3A, and DMPK repeat analysis. Normal metabolic tests included transferrin isoelectric focussing, CSF amino acids and neurotransmitters, plasma amino acids, urine organic acids, urine purines and pyrimidines, serum acylcarnitines, blood ammonia and blood lactate. She also had normal audiological testing."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod SNP array and WES, confirmed with Sanger qt/rtPCR

Variant (1) NM_032504.1:c.3983-3_3994delinsA (p.Ser1328Argfs19), (2) NM_032504.1:c.2431C>T (p.Arg811)

CAID (1) CA658820714, (2) CA350137388

VariantEvidence skin fibroblasts from affected sister showed no unc80 mRNA.

CaseAddInfo nonconsanguineous, confirmed in trans. Affected sister with similar phenotypes died of respiratory distress at age 7.

Article is a PDF, so annotating here.

Case#: OAK 96

DiseaseAssertion: clinical dx of adOA based on ophthalmological examination

FamilyInfo:

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

GenotypingMethod: All 30 coding exons of the OPA1 gene were amplified from genomic DNA by means of PCR. PCR and RT-PCR products were sequenced employing BigDyeTerminator Chemistry (Applied Biosystems, Darmstadt, Germany) and separated on an ABI 3100 DNA Sequencer

PreviouslyPublished: n/a

Variant: c.1705+1G>T (p.V556fsX596)

CAID: CA10576007

SupplementalData:

AdditionalInfo: Generation of minigene constructs and heterologous expression in COS7 cells allowed for cDNA analysis of the c.1705+1G>T mutation. This revealed a deletion of the last 40 nucleotides in exon 17 resulting from a splicing event that involves a cryptic splice donor site within exon 17 resulting in a frameshift and premature translation termination (p.V556fsX596).

Case: Zampieri SD9, Female

DiseaseAssertion: Sandhoff Disease

FamilyInfo: patient's genotype was confirmed in parents

CasePresentingHPOs: HP:0000007, HP:0033978

CaseHPOFreeText: neurological symptoms (unspecified)

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: Patients presented with neurological symptoms and diagnosis was confirmed by the demonstration of reduced Hex A and Hex B activity in peripheral white blood cells or cultured fibroblasts.

GenotypingMethod: PCR

PreviouslyPublished: n/a

SupplementalData: n/a

Variant: c.850C>T (p.R284X) same on both alleles

CAID: CA116495

gnomAD: MAF: 0.0002286 South Asian, gnomAD variant ID: 5-74009409-C-T

VariantEvidence: PMID:8162015 previously reported this variant to be associated with the infantile form of SD. A fibroblast line from this patient with the infantile form of the disease was investigated for mutations by single strand conformation polymorphism analysis and direct sequencing of PCR products. A nonsense mutation was found which generated a stop codon at codon 284. The study investigated the steady-state level of mRNA produced by cells containing stop codons using a competitive polymerase chain reaction technique and found that at codon 284, the mRNA levels were 0.8%, as percent of normal per single gene dose.

NM_017819.3(TRMT10C):c.814A>G (p.Thr272Ala)

ClinVar 224317

CAID CA10575895

gnamAD n/a

Family CL-16: FamilyInfo: Japanese and German ancestry Proband II.2: had large aneurysm of sinuses of Valsalva and ascending aorta at ae 38 skin laxity on lower face and submandibular area during childhood but not noticeable in adulthood single palmar crease bilateral limited ability to supinate forearms inguinal hernia

II.3: died at age 26 of aortic dissection, no skin laxity

I.1, III.1: mildly dilated aortic root, mild aortic insufficiency, cutis laxa (face, submandibular, trunk, extremities) III.1: overall normal pulmonary function, prolonged wound healing I.1: inguinal hernia III.1: 12 year old male

VariantInfo: Direct sequence analysis of ELN in CL‐16, III.1 uncovered a 25 bp deletion in exon 30, 2114_2138del. This defect was present in all affected members of the family available for testing, including I.1 and II.2. The mutation was not found in II.1. CAID: CA322210

Family CL-13: Singaporean girl of chinese decent with no family history of cutis laxa.

MonDO: MONDO:0008504

Case: CL-13, II.1: 6 year old Asian female, Singaporean of Chinese decent with de novo variant.

DiseaseAssertion: Cutis Laxa

FamilyInfo: Parents do not harbor variant and are asymptomatic. No family history of cutis laxa.

CasePresentingHPOs: HP:0000973, HP:0001582, HP:0008070, HP:0040080, HP:0000343, HP:0005280, HP:0002616 (Cutis laxa, Redundant skin, Sparse hair, Anteverted ears, Depressed nasal bridge, Aortic root aneurysm)

CaseHPOFreeText: tear shaped eyes

CaseNOTHPOs: HP:0001659 (Aortic regurgitation)

CasePreviousTesting: At the age of 5 years 9 months an echocardiogram showed significant dilatation of the aortic root at the level of the sinuses of Valsalva with a measured diameter of 2.47 cm (normal <2.2 cm for her body surface area).

GenotypingMethod: DNA extracted from whole blood was amplified using PCR for each exon of ELN gene. Amplified products were sequenced bidirectionally using Sanger sequencing. A panel of 121 normal control individuals was genotyped for mutations 2114_2138del and 2159delC using denaturing high performance liquid chromatography.

Variant: ELN:c.2159delC, in exon30 ClinVarID: 16736 CAID: CA2580077344 gnomAD: Not found in gnomAD v.4.1

Case: Dawidziuk Proband, female, Polish, Caucasian, 10yo at report, onset at 22wks

CasePresentingHPOs: HP:0033044, HP:0034332, HP:0000817, HP:0002540, HP:0001263, HP:0002273, HP:0001252, HP:0000508, HP:0001272, HP:0002470, HP:0001298, HP:0004322, HP:0001344, HP:0100710, HP:5200044, HP:0000252, HP:0002061, HP:0000767

CasePresentingHPOsFreeText: lack of smile, “rounded” back, protruding shoulder blades, tendency to open the mouth and tilt the head back, cortico-subcortical atrophy of the cerebellum on MRI, enlargement of the 4th ventricle and widening of cerebellar sulci. Low COQ10 level tests showing 0.6 mg/l (normal range >0.67 mg/l); after 2-month treatment: 0.7 mg/l

Cardiac echocardiogram, complete blood count, electrolyte levels, CPK, liver and renal function tests, carnitine and acyl-carnitine, copper, thyroid function tests, lactate, blood amino acid profile, homocysteine, as well as urine for protein and organic acids, were within normal limits.

CaseNOTHPOs: HP:0025190, HP:0010865, HP:0001336, HP:0001250, HP:0000639, HP:0000514, HP:0000570, HP:0000657, HP:0001310, HP:0002174, HP:0002080, HP:0002353,

CaseNOTHPOSFreeText: family history of neurodevelopmental disorders. The supratentorial structures are normal. Echocardiogram, abdominal ultrasonography, and ophthalmologic investigation were also uneventful. Encephalomyopathy

CasePreviousTesting: The aCGH analysis did not show any pathogenic copy number variations. Genetic panel excluded congenital Rett, Rett-like and Angelman's syndromes, microdeletion / microduplication syndromes and genetically based lysosomal diseases

CaseGenotypingMethod: Exome sequencing, Sanger sequencing of parents to confirm biallelic origin

Variant: c.681+1G>A; c.352G>A (p.Gly118Ser) confirmed in trans

ClinVarID: or CAID: CA386577420; CA244466459

gnomAD: The splice-site variant, c.681+1G>A in exon /7, is present in gnomAD v4.1.0 with a MAF=0.00002229 (1/44868 alleles) in the East Asian population and 0 homozygotes. The missense variant, p.Gly118Ser, is present in gnomAD v4.1.0 with a MAF=0.0001650 (1/6062 alleles) in the Middle Eastern population and 0 homozygotes.

AddCaseInfo: healthy, non-consanguineous parents

PreviouslyPublished: n/a

VariantEvidence: COQ5 mRNA (Supp.Fig.3) showed that its level is markedly diminished