T André 1 , C Bossard, B Gattegno, P F Plouin, G Benoit, S Richard
ArticleReferenceSequence: Not specified - Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3.
GenotypingMethod: N/A
SamplingMethod: N/A
unilateral PHEOs (Fig. 1a): her father (II:1) at age 73, her 34-year-old brother (III:2)
PatientID: III:2
KindredID: 1
Case: M, 34Y0M, Ethnicity Unknown
DiseaseAssertion: VHL
FamilyInfo: Look to proband (III:3) for extensive family info.
CohortInfo: Patients with the diagnosis of familial or sporadic PHEO and their relatives.
CasePresentingHPOs: HP:0002666; HP:0000107 (Pheochromocytoma, Renal cyst)
CaseHPOFreeText: Unilateral pheochromocytoma diagnosed at age 34.
CaseNotHPOs: HP:0005584 (Renal cell carcinoma)
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
PreviouslyPublished: N/A
SupplementalData: Figure 1
Variant: p.P138= (c.414A>G)
LegacyVariant: N/A
CaseProblemVariantFreeText: N/A
ClinVarID: 223206, https://www.ncbi.nlm.nih.gov/clinvar/variation/223206/
CAID: N/A
gnomAD: N/A
VariantEvidence: N/A
MutationType: missense_variant;transition
CivicName: P138= (c.414A>G)
MultipleGeneVariants: N/A
ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3
GenotypingMethod: PCR
SamplingMethod: DNA was isolated from peripheral blood using a commercial kit (QIAamp DNA Blood MaxiKit, Qiagen, France)
p.Leu188Val
PatientID: 1
KindredID: A
Case: M, 61Y0M, Ethnicity Unknown
DiseaseAssertion: assumed VHL
FamilyInfo: Positive: the patient’s sister also presented with the germline c.562C>G mutation, and metastatic lobular breast carcinoma. In a family pedigree, 10 additional members affected with cancer were displayed. This included both of their parents: father with lung cancer, mother with skin cancer, additional sister with breast cancer, brother with melanoma. Lastly, his two sons presented with skin cancer, however no description of their genotyping. See Fig. 3.
CasePresentingHPOs: HP:0006770; HP:0001028 (Clear cell renal cell carcinoma, hemangioma)
CaseHPOFreeText: He presented in 2012 (52Y) with worsening lower abdominal discomfort (CT scan revealed a right renal solid mass of renal cell carcinoma). A right renal nephrectomy was done, confirming ccRCC. 4 years later, new lung nodules and an enhancing lesion in the L1 vertebral body was found (metastatic ccRCC). Additionally, in 2020, a pancreatic lesion present on his scans was presumed to be a metastatic RCC lesion (consistent with an atypical hemangioma).
CaseNotHPOs: HP:0002666; HP:0009711 (Pheochromocytoma, retinal capillary hemangioblastoma)
CaseNotHPOFreeText: N/A
CasePreviousTesting: MAX/NF1/RET/SDHA/SHDB/SHDC/SDHD/SDHAF2/TMEM127 [133 genes evaluated by germline testing - Invitae]
PreviouslyPublished: N/A
SupplementalData: Yes
Variant: p.L188V (c.562C>G)
LegacyVariant: N/A
CaseProblemVariantFreeText: In 2013, somatic next generation sequencing (NGS) testing using a panel of 447 cancer genes (OncoPanel, BWH Pathology, MA, USA) was performed on the resected renal specimen. This revealed the following variants: VHL p.Leu188Val (c.562C>G), CHEK2 p.Val395Leu (c.1183G>C), VHL p.Ala149Thr (c.445G>A) variant, and several copy number losses including a large single-copy deletion in 3p. 6 years later, germline testing revealed a heterozygous germline VHL p.Leu188Val variant, a CHEK2 and ERCC4 mutation.
ClinVarID: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/
CAID: N/A
gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G
VariantEvidence: N/A
MutationType: missense_variant;transversion
CivicName: L188V (c.562C>G)
MultipleGeneVariants: Somatic, VHL, c.445G>A (p.Ala149Thr)
PatientID: V322
KindredID: V322
Case: Sex Unknown, Age Unknown, Ethnicity Unknown
DiseaseAssertion: Asymptomatic
FamilyInfo: N/A
CasePresentingHPOs: N/A
CaseHPOFreeText: N/A
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
PreviouslyPublished: N/A
SupplementalData: N/A
Variant: p.R167Q (c.500G>A)
LegacyVariant: N/A
CaseProblemVariantFreeText: N/A
ClinVarID: 2216 https://www.ncbi.nlm.nih.gov/clinvar/variation/2216/
CAID: N/A
gnomAD: 0.000003977 https://gnomad.broadinstitute.org/variant/3-10191507-G-A
VariantEvidence: N/A
MutationType: missense_variant;transition
CivicName: R167Q (c.500G>A)
MultipleGeneVariants: N/A
PatientID: V3
KindredID: V3
Case: Sex Unknown, Age Unknown, Ethnicity Unknown
DiseaseAssertion: VHL
FamilyInfo: N/A
CasePresentingHPOs: N/A
CaseHPOFreeText:N/A
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
PreviouslyPublished: 8956040
SupplementalData: N/A
Variant: p.R161* (c.481C>T)
CaseProblemVariantFreeText: N/A
LegacyVariant: N/A
ClinVarID: 2217 https://www.ncbi.nlm.nih.gov/clinvar/variation/2217/
CAID: N/A
gnomAD: N/A
VariantEvidence: N/A
MutationType: stop_gained
CivicName: R161* (c.481C>T)
MultipleGeneVariants: N/A
PatientID: 14
KindredID: 5
Case: Sex Unknown, 40Y0M, Indian
DiseaseAssertion: VHL
FamilyInfo: 2 other members of this family presented with the same variant. Patient 13 (Gen 2) presented with bilateral pheochromocytoma. Patient 12 (Gen 2) presented with bilateral pheochromocytoma and sympathetic paraganglioma.
CohortInfo: This retrospective study was conducted at Department of Endocrinology of a tertiary care health centre in Western India. Patients presented to our institute between 2008 and 2016 were included in the study. During the study period a total of 33 patients were suspected to have VHL syndrome based on clinical features among whom 31 patients were found to have mutation in VHL gene. All patients are of Asian Indian descent.
CasePresentingHPOs: HP:0002666 (Pheochromocytoma)
CaseHPOFreeText: Bilateral pheochromocytoma and sympathetic paraganglioma.
CaseNotHPOs: HP:0009711; HP:0010797; HP:0001737; HP:0005584; HP:0030405; HP:0002668 (Retinal capillary hemangioma, Hemangioblastoma, Pancreatic cysts, Renal cell carcinoma, Pancreatic endocrine tumor, Paraganglioma)
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
PreviouslyPublished: N/A
SupplementalData: N/A
Variant: p.L198P (c.593T>C)
LegacyVariant: N/A
CaseProblemVariantFreeText: N/A
ClinVarID: 223235, https://www.ncbi.nlm.nih.gov/clinvar/variation/223235/
CAID: N/A
gnomAD: N/A
VariantEvidence: N/A
MutationType: missense_variant;transition
CivicName: L198P (c.593T>C)
MultipleGeneVariants: N/A
PMID: 19399650
ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3
GenotypingMethod: Primers were selected and polymerase chain reactions (PCR) for every amplicon were established - PCR was carried out on a Eppendorf Mastercycler; WAVE-analysis hetero-duplex.
SamplingMethod: frozen tumor tissue; and whole blood leukocytes
The second, H125Y – previously unreported – was associated with the presence of a right pneumogastric nerve PGL diagnosed at 49 years.
PatientID: N/A
KindredID: 2
Case: Sex Unknown, 49Y0M, Ethnicity Unknown
DiseaseAssertion: Paraganglioma
FamilyInfo: N/A
CasePresentingHPOs: HP:0002668 (Paraganglioma)
CaseHPOFreeText: right pneumogastric nerve paraganglioma
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: SDHD/SDHB/SDHC
PreviouslyPublished: N/A
SupplementalData: N/A
Variant: p.H125Y (c.373C>T)
LegacyVariant: N/A
CaseProblemVariantFreeText: N/A
ClinVar: 411970 https://www.ncbi.nlm.nih.gov/clinvar/variation/411970/
CAID: N/A
gnomAD: 0.00001193 https://gnomad.broadinstitute.org/variant/3-10188230-C-T
VariantEvidence: N/A
MutationType: missense_transition
CivicName: H125Y (c.373C>T)
MultipleGeneVariants: N/A
Somatostatin receptor expression was investigated in vitro by immunohistochemistry in pancreatic tumor sections. On the basis of in vivo and in vitro findings, octreotide long-acting release treatment followed by 90Y-1,4,7,10-Tetraazacyclododecane-N, N′, N′’, N‴-tetraacetic acid (DOTA0)-Tyr3-octreotide led to a lack of progression in this patient although this result is a possibility which needs to be proved by further investigation and longer follow-up. The results of this study suggest that [111In-DTPA0] octreotide scintigraphy may be helpful in the routine work-up of VHL patients for diagnostic and therapeutic purposes.
ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3
GenotypingMethod: N/A (not stated)
SamplingMethod: tissue resection (paraffin-embedded sections of the pancreatic islet cell tumors)
PatientID: Carrier 1 (sister to proband 1)
KindredID: 1
Case: F, 29Y0M, Chinese
DiseaseAssertion: VHL
FamilyInfo: The family with PCCs includes 56 members of 4 generations, and is from Gansu Province. Among them, 7 extended over 3 generations were diagnosed as PCCs. One died before admission and another died due to a cardiovascular incident. Five were initially evaluated; evaluation included medical history, physical examination, abdominal ultrasonography, CT or MRI and laboratory tests. All 5 probands of this family underwent surgical resection. The tumors were benign under pathological examinations. There were no recurrence and malignant transformation over the period of up to 23-year follow-up. Twenty members, including 5 live patients and 15 direct relatives, accepted genetic examination.
CasePresentingHPOs: HP:0002666 (Pheochromocytoma)
CaseHPOFreeText: Bilateral PCC diagnosed at 17Y and did not have any other clinical presentations. Stated as having VHL type IIC.
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
PreviouslyPublished: N/A
SupplementalData: N/A
Variant: p.H125P (c.374A>C)
LegacyVariant: N/A
CaseProblemVariantFreeText: N/A
ClinVarID: 223201, https://www.ncbi.nlm.nih.gov/clinvar/variation/223201/
CAID: N/A
gnomAD: N/A
VariantEvidence: N/A
MutationType: missense_variant;transversion
CivicName: H125P (c.374A>C)
MultipleGeneVariants: N/A
PatientID: 5 (Aunt)
KindredID: 17
Case: F, 38Y0M, Ethnicity Unknown
DiseaseAssertion: VHL
FamilyInfo: 6 members of this family tested positive for the c.496_506del germline variant of the VHL gene. ID 4 presented with CNS hemangioblastoma, retinal angioma and renal and pancreatic abnormalities. ID 1, 25 and 8 were asymptomatic.ID 22 presented with CNS hemangioblastoma. 2 members were assumed to have the variant but were not genetically confirmed (ID 20 and ID 11). ID 11 and 20 presented with CNS hemangioblastoma.
CasePresentingHPOs: HP:0009711 (Retinal capillary hemangioma)
CaseHPOFreeText: This patient presented with retinal angioma (16Y).
CaseNotHPOs: HP:0005584; HP:0002666; HP:0010797; HP:0000077; HP:0001732 (Renal cell carcinoma, Pheochromocytoma, Hemangioblastoma, Abnormality of the kidney, Abnormality of the pancreas)
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
PreviouslyPublished: N/A
SupplementalData: Supplementary Table 1.
Variant: p.V166Sfs*4 (c.496_506del)
LegacyVariant: N/A
CaseProblemVariantFreeText: N/A
ClinVarID: 223229, https://www.ncbi.nlm.nih.gov/clinvar/variation/223229/
CAID: N/A
gnomAD: N/A
VariantEvidence: It is unclear from the publication if this variant is reported according to legacy (AF010238.1) or NM_000551.3 reference sequence. Clinical notes from the case confirm the reference sequence to be NM_000551.3.
MutationType: deletion; minus_2_frameshift_variant
CivicName: V166SFS*4 (c.496_506del)
MultipleGeneVariants: N/A
Table 2
No evidence of NM_000133.4:c.84T>G (p.Cys28Trp) in this paper.
Table I
No evidence of NM_000133.4:c.84T>G (p.Cys28Trp) in this paper.
Click here for additional data file.(2
NM_000133.4:c.128G>T (p.Arg43Leu) is mentioned in this paper, however, there is no case level data associated with the mentioned variant.
Variant 6 of 11
Variant1:NM_000203.3: c.1726A>G p.(Lys576Glu)
Variant1ClinVarID:3775044
rs617500716128464c.4120C > T28p.R1374C110.0000242A/M
Case:n.a.
DiseaseAssertion:VWD 2A/M
FamilyInfo:n.a.
ParentalGenotype(s):n.a.
CasePresentingHPOs:n.a.
CaseHPOFreeRext:n.a.
CaseNOTHPOs:n.a.
CaseNOTHPOFreeText:n.a.
CasePreviousTesting:n.a.
GenotypingMethod: n.a.
PreviouslyPublished: If applicable. n.a.
Gene:VWF
Variant: c.4120C > T
HGVS: NM_000552.5:c.4120C>T
ClinVarID:n.a.
CAID:n.a.
gnomAD:n.a.
rs617493956128641c.3943C > T28p.R1315C20.0000242A/M
Case: n.a.
DiseaseAssertion: VWD 2A/M
FamilyInfo:n.a.
ParentalGenotype(s):n.a.
CasePresentingHPOs:n.a.
CaseHPOFreeRext:n.a.
CaseNOTHPOs:n.a.
CaseNOTHPOFreeText:n.a.
CasePreviousTesting:n.a.
GenotypingMethod:n.a.
PreviouslyPublished: If applicable. n.a.
Gene:VWF
Variant:NM_000552.5(VWF):c.3943C>T (p.Arg1315Cys)
HGVS:NM_000552.5:c.3943C>T
ClinVarID:100310
CAID:n.a.
gnomAD:n.a.
2-years-old male
Case: 2 year old male at the time of genetic diagnosis, initially presenting with abnormal gait
DiseaseAssertion: Clinical exome sequencing showed the recurrent VWA1 founder mutation
FamilyInfo: no family history of neurological or musculoskeletal conditions
CasePresentingHPOs: HP:0001288 (abnormal gait), HP:0002359 (frequent falls), HP:0003701 (proximal muscle weakness)
CaseHPOFreeText: Gower's sign
Gene: VWA1
Variant: c.62_71dup (p.Gly25ArgfsTer74) (maternally inherited)
HGVS: NM_022834.5:c.62_71dup
ClinVar: 830327
gnomad: does not exist in database
MultipleGeneVariants: novel paternally inherited missense variant, c.212T>C (p.Leu71Pro)
DiseaseAssertion: Hypertrophic Cardiomyopathy
VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.
VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.
VariantAddInfo: Seen in one HCM probands
Variant: NM_000257.4(MYH7):c.715G>A (p.Asp239Asn)
ClinVar: 43100 https://www.ncbi.nlm.nih.gov/clinvar/variation/43100/
gnomAD: 0.00002891, http://gnomad.broadinstitute.org/variant/14-23900811-C-T
DiseaseAssertion: Hypertrophic Cardiomyopathy
VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.
VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.
VariantAddInfo: Seen in three HCM probands
Variant: NM_000257.4(MYH7):c.2681A>G (p.Glu894Gly)
ClinVarID: 42922 https://www.ncbi.nlm.nih.gov/clinvar/variation/42922/
gnomAD: Not in gnomAD
DiseaseAssertion: None
VariantPreviousTesting: Some combination of ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, ABCC9, CTF1, DES, EMD, LDB3, LMNA, MYH6, RBM20, SGCD, TAZ, TCAP, TTN, VCL, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, TTR, DSC2, DSG2, DSP, JUP, PKP2, RYR2, TMEM43, CASQ2 and RYR2 were tested via NGS.
VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.
Variant: NM_000257.4(MYH7):c.4399C>G (p.Leu1467Val)
ClinVar: 43015 https://www.ncbi.nlm.nih.gov/clinvar/variation/43015/
gnomAD: 0.001111, http://gnomad.broadinstitute.org/variant/14-23886482-G-C
DiseaseAssertion: Hypertrophic Cardiomyopathy
VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.
VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.
VariantAddInfo: Seen in two HCM probands
Variant: NM_000257.4(MYH7):c.1988G>A (p.Arg663His)
ClinVarID: 42875 https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/
gnomAD: 0.00003097, http://gnomad.broadinstitute.org/variant/14-23896042-C-T
DiseaseAssertion: Hypertrophic Cardiomyopathy
VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.
VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.
VariantAddInfo: Seen in one proband
Variant: NM_000257.4(MYH7):c.1063G>A (p.Ala355Thr)
ClinVarID: 42820 https://www.ncbi.nlm.nih.gov/clinvar/variation/42820/
gnomAD: Not in gnomAD
DiseaseAssertion: Hypertrophic Cardiomyopathy
VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, and TTR were all tested via NGS.
VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 760 HCM probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.
VariantAddInfo: Seen in two HCM probands
Variant: NM_000257.4(MYH7):c.2722C>G (p.Leu908Val)
ClinVar: 14097 https://www.ncbi.nlm.nih.gov/clinvar/variation/14097/
gnomAD: 0.00006482, http://gnomad.broadinstitute.org/variant/14-23893316-G-C
DiseaseAssertion: None
VariantPreviousTesting: Some combination of ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, ABCC9, CTF1, DES, EMD, LDB3, LMNA, MYH6, RBM20, SGCD, TAZ, TCAP, TTN, VCL, CAV3, GLA, MYL2, MYL3, MYOZ2, PRKAG2, TTR, DSC2, DSG2, DSP, JUP, PKP2, RYR2, TMEM43, CASQ2 and RYR2 were tested via NGS.
VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of probands for variants within exons and in +/- 10 nucleotides within the flanking introns of the genes provided above. These variants were then interpreted and filtered for pathogenicity.
Variant: NM_000257.4(MYH7):c.3803G>A (p.Arg1268His)
ClinVar: 42975 https://www.ncbi.nlm.nih.gov/clinvar/variation/42975/
gnomAD: 0.0009786, http://gnomad.broadinstitute.org/variant/14-23888742-C-T
index case
Case#: index case, III.4, female, 52 yrs,
DiseaseAssertion: HCM
FamilyInfo: Yes, III.3, IV.3 and IV.4 also diagnosed
CasePresentingHPOs: Cafe-au-lait spot, freckling, neurofibromas, heart murmur, left ventricular hypertrophy (HP:0000957, HP:0001480, HP:0001067, HP:0030148, HP:0001712)
CaseHPOFreeText: 20 mm IVS, 56% EF, 50 mmHg LVOTO, NSVT (VA)
CaseNotHPOs: N/A
CaseNotHPOFreeText: No AV, no ICD
CasePreviousTesting: N/A
CaseGenotypingMethod: ECG, cardiac magnetic resonance, physical examination, NGS tech
Variant: NM_000257.4(MYH7):c.1357C>T (p.Arg453Cys)
ClinVar: 14089 https://www.ncbi.nlm.nih.gov/clinvar/variation/14089/
CAID: N/A
gnomAD: absent
MultipleGeneVariants:
(1) NF1 Variant:
Variant: NM_000267.3(NF1):c.6709C>T (p.Arg2237Ter)
ClinVar: 230389 https://www.ncbi.nlm.nih.gov/clinvar/variation/230389/
CAID: N/A
gnomAD: absent
HCM147
CaseHCM147: 31 yrs report, Vietnam, Asian
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: Family history of Sudden Cardiac Death and Hypertrophic Cardiomyopathy, Has a 9 year old daughter with the same variant but no symptoms
CasePresentingHPOs: HP:0100749, HP:0006698, HP:0031295 (Chest pain, Dilatation of the ventricular cavity, Left atrial enlargement)
HPOsFreeText: Maximal LV thickness 32 mm
CaseNotHPOs: HP:0005110, HP:0001297, HP:0004756 (Atrial fibrillation, Stroke, Ventricular tachycardia)
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: The gene panel included 10 sarcomeric genes (MYH7, MYBPC3, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1, TNNC1, MYH6), 9 genes encoding Z-disk components and Ca2+ homeostasis factors (LDB3, CSRP3, TCAP, VCL, ACTN2, MYOZ2, NEXN, JPH2, PLN), and 4 genes involved in HCM phenocopies (GLA, LAMP2, PRKAG2, TTR), All probands had left ventricular wall thickness >= 15 mm and no other diseases that can cause secondary hypertrophy
CaseGenotypingMethod: The coding region, flanking sequences, and untranslated regions of each gene were enriched by LC-PCR, amplified, and sequenced on the Illumina MiSeq or MiniSeq platform. Identified variants were then filtered for pathogenicity and confirmed by Sanger sequencing.
Variant: NM_000257.4(MYH7):c.2156G>A (p.Arg719Gln)
ClinVar: 14107 https://www.ncbi.nlm.nih.gov/clinvar/variation/14107/
gnomAD: Not in gnomAD
9
CaseIX: Brazil, Caucasian
DiseaseAssertion: Hypertrophic cardiomyopathy
FamilyInfo: Family history of HCM
CasePresentingHPOs: HP:0001712, HP:0001639 (Left ventricular hypertrophy, Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: Only MYH7, MYBPC3, and TNNT2 were tested.
CaseGenotypingMethod: DNA was extracted from peripheral blood and the above genes were subject to PCR amplification and directly sequenced. The resulting sequences were compared with the reference and filtered for pathogenicity.
Variant: NM_000257.3:c.788T>C (p.Ile263Thr)
ClinVar: 43106 https://www.ncbi.nlm.nih.gov/clinvar/variation/43106/
gnomAD: European (Non-Finnish) 8.792e-6, Overall 3.977e-6 https://gnomad.broadinstitute.org/variant/14-23900635-A-G
WPW381
Case#: WPW381
DiseaseAssertion: WPW, LY non compaction cardiomyopathy
FamilyInfo: inherited
CasePresentingHPOs: Wolff-Parkinson-White syndrome, Left ventricular noncompaction cardiomyopathy (HP:0001716, HP:0011664)
CaseHPOFreeText: 0 ARIC, 0 THou, 8.12e-6 gnomAD, 8.24e-6 Exac, 0 esp6500, 34 CADD_phred, 0 pLI,
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: ECG, exome sequencing, gene analysis, burden analysis,
Variant: NM_000257.4(MYH7):c.728G>A (p.Arg243His)
ClinVar: 14126 https://www.ncbi.nlm.nih.gov/clinvar/variation/14126/
CAID: N/A
gnomAD: 0.00002891 Latino/Admixed American https://gnomad.broadinstitute.org/variant/14-23894525-C-T
Case404: Female, 0.083 years onset, Japan, Asian
DiseaseAssertion: Left ventricular noncompaction
CasePresentingHPOs: HP:0030682, HP:0025169 (Left ventricular noncompaction, Left ventricular systolic dysfunction)
HPOsFreeText: Left Ventricular Ejection Fraction at 48.9%, LVDD-Z score at 0.0408
CaseNotHPOs: HP:0011675, HP:0001635 (Arrhythmia, Heart failure)
NotHPOsFreeText: Congenital heart disease with significant hemodynamic changes
CaseAddInfo: No family history
CasePreviousTesting: Genes tested include the 8 sarcomere genes as well as 65 more listed in Table S1.
CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each of the probands. Next Generation Sequencing of 73 genes related to cardiac function was performed, incorporating PCR amplification, and any variants found were subjected to filtering for frequency and pathogenicity. Any variants suggested to be pathogenic were confirmed by Sanger sequencing afterwards.
Variant: NM_000257.3:c.67C>T (p.Arg23Trp)
ClinVar: 181295 https://www.ncbi.nlm.nih.gov/clinvar/variation/181295/
gnomAD: European (Finnish) 7.961e-5, Overall 2.475e-5 https://gnomad.broadinstitute.org/variant/14-23902875-G-A
Case391: Female, 0.83 years onset, Japan, Asian
DiseaseAssertion: Left ventricular noncompaction
CasePresentingHPOs: HP:0030682, HP:0025169, HP:0001635 (Left ventricular noncompaction, Left ventricular systolic dysfunction, Heart failure)
HPOsFreeText: Left Ventricular Ejection Fraction at 38%, LVDD-Z score at 2.6785
CaseNotHPOs: HP:0011675 (Arrhythmia)
NotHPOsFreeText: Congenital heart disease with significant hemodynamic changes
CaseAddInfo: No family history
CasePreviousTesting: Genes tested include the 8 sarcomere genes as well as 65 more listed in Table S1.
CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each of the probands. Next Generation Sequencing of 73 genes related to cardiac function was performed, incorporating PCR amplification, and any variants found were subjected to filtering for frequency and pathogenicity. Any variants suggested to be pathogenic were confirmed by Sanger sequencing afterwards.
Variant: NM_000257.3:c.5401G>A (p.Glu1801Lys)
ClinVar: 43069 https://www.ncbi.nlm.nih.gov/clinvar/variation/43069/
gnomAD: Not in gnomAD
Case362: Female, 0.0833 years onset, Japan, Asian
DiseaseAssertion: Left ventricular noncompaction
CasePresentingHPOs: HP:0030682, HP:0025169 (Left ventricular noncompaction, Left ventricular systolic dysfunction)
HPOsFreeText: Left Ventricular Ejection Fraction at 40%, LVDD-Z score at -0.823
CaseNotHPOs: HP:0011675, HP:0001635 (Arrhythmia, Heart failure)
NotHPOsFreeText: Congenital heart disease with significant hemodynamic changes
CaseAddInfo: No family history
CasePreviousTesting: Genes tested include the 8 sarcomere genes as well as 65 more listed in Table S1.
CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each of the probands. Next Generation Sequencing of 73 genes related to cardiac function was performed, incorporating PCR amplification, and any variants found were subjected to filtering for frequency and pathogenicity. Any variants suggested to be pathogenic were confirmed by Sanger sequencing afterwards.
Variant: NM_000257.3:c.689T>C (p.Phe230Ser)
ClinVar: 263543 https://www.ncbi.nlm.nih.gov/clinvar/variation/263543/
gnomAD: Not in gnomAD
12
Case: Patient 12, male, 7yo
CasePresentingHPOs: HP:0030682 (left ventricular noncompaction)
HPOsFreeText: CK = 1400U/l
CaseNotHPOs:
NotHPOsFreeText: no muscle symptoms, no respiratory or cardiac involvement
FamilyInfo: family history, pedigree in figure 1
DiseaseEntity: no assertion
InheritancePattern: no assertion
CasePreviousTesting: see below
CaseGenotypingMethod: 9 cases underwent targeted Sanger sequencing of MYH7, 12 cases underwent Motorplex analysis (NGS of 93 myopathy-related genes - PMID:25214167), all MYH7 variants confirmed via Sanger sequencing, segregation analysis performed on available family members, which cases received which sequencing technique is not specified
Variant: NM_000257.4(MYH7):c.5401G>A (p.Glu1801Lys)
ClinVar: 43069, https://www.ncbi.nlm.nih.gov/clinvar/variation/43069/
gnomAD: absent
21
Case: Patient 21, female, 40yo, symptom onset in adulthood
CasePresentingHPOs: HP:0009027, HP:0002460, HP:0003458, HP:0025115 (foot drop, distal muscle weakness, EMG: myopathic abnormalities, hyalin bodies)
HPOsFreeText: CK = 500 U/l
CaseNotHPOs: HP:0002650 (scoliosis)
NotHPOsFreeText: no respiratory or cardiac involvement
FamilyInfo: no family history
DiseaseEntity: no assertion
InheritancePattern: no assertion
CasePreviousTesting: see below
CaseGenotypingMethod: 9 cases underwent targeted Sanger sequencing of MYH7, 12 cases underwent Motorplex analysis (NGS of 93 myopathy-related genes - PMID:25214167), all MYH7 variants confirmed via Sanger sequencing, segregation analysis performed on available family members, which cases received which sequencing technique is not specified
Variant: NM_000257.4(MYH7):c.1322C>T (p.Thr441Met)
ClinVar: 14122, https://www.ncbi.nlm.nih.gov/clinvar/variation/14122/
gnomAD: 0.0002227, https://gnomad.broadinstitute.org/variant/14-23898249-G-A?dataset=gnomad_r2_1
Case: Australian
DiseaseAssertion: HCM
CaseHPOFreeText: maximum left ventricular wall thickness of ≥15 mm
CasePreviousTesting: electrocardiography, echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1)
CaseGenotypingMethod: DNA isolated from peripheral blood or buccal swabs, PCR, Sanger sequencing, segregation analysis, haplotype analysis of MYBPC3 and MYH7
Variant: NM_000257.3(MYH7):c.427C>T (p.Arg143Trp)
ClinVar: 164401, https://www.ncbi.nlm.nih.gov/clinvar/variation/164401/
gnomAD: 0.00002784, https://gnomad.broadinstitute.org/variant/14-23901923-G-A
Supplementary Data, Table 2
Case: Australian
DiseaseAssertion: HCM
CaseHPOFreeText: maximum left ventricular wall thickness of ≥15 mm
CasePreviousTesting: electrocardiography, echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1)
CaseGenotypingMethod: DNA isolated from peripheral blood or buccal swabs, PCR, Sanger sequencing, segregation analysis, haplotype analysis of MYBPC3 and MYH7
Variant: NM_000257.3(MYH7):c.1207C>T (p.Arg403Trp)
ClinVar: 14102, https://www.ncbi.nlm.nih.gov/clinvar/variation/14102/
gnomAD: n/a
Supplementary Data, Table 2
Variant noted to be present in 5 individuals
Variant: NM_000257.3(MYH7):c.2167C>T (p.Arg723Cys)
ClinVar: 14095, https://www.ncbi.nlm.nih.gov/clinvar/variation/14095/
gnomAD: 0.00001194, https://gnomad.broadinstitute.org/variant/14-23895023-G-A
Supplementary Data, Table 2
Variant noted to be present in 3 individuals
Variant: NM_000257.3(MYH7):c.2207T>C (p.Ile736Thr)
ClinVar: 164342, https://www.ncbi.nlm.nih.gov/clinvar/variation/164342/
gnomAD: n/a
Supplementary Data, Table 2
Variant noted to be present in 2 individuals
Variant: NM_000257.3(MYH7):c.1357C>T (p.Arg453Cys)
ClinVar: 14089, https://www.ncbi.nlm.nih.gov/clinvar/variation/14089/
gnomAD: n/a
Supplementary Data: S2 Table
Case 198: Spanish, 56, Male
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1
CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes
Variant: NM_000257.3(MYH7):c.2167C>T (p.Arg723Cys)
ClinVar: 14095, https://www.ncbi.nlm.nih.gov/clinvar/variation/14095/
gnomAD: 0.00001194, https://gnomad.broadinstitute.org/variant/14-23895023-G-A
Supplementary Data: S2 Table
Case 9: Spanish, 13yo, Female
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1
CaseGenotypingMethod: genomic DNA obtained from blood or saliva, PCR, Sanger Sequencing
Variant: NM_000257.3(MYH7):c.4124A>G (p.Tyr1375Cys)
ClinVar: 164293, https://www.ncbi.nlm.nih.gov/clinvar/variation/164293/
gnomAD: n/a
Supplementary Data: S2 Table
Case 65: Spanish, 35yo, Male
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1
CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes
Variant: NM_000257.3(MYH7):c.715G>A (p.Asp239Asn)
ClinVar: 43100, https://www.ncbi.nlm.nih.gov/clinvar/variation/43100/
gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23900811-C-T
MultipleGeneVariants:
(1) MYBPC3 Variant:
Variant: NM_000256.3(MYBPC3):c.3676C>T (p.Arg1226Cys)
ClinVar: 42731, https://www.ncbi.nlm.nih.gov/clinvar/variation/42731/
gnomAD: 0.00004815, https://gnomad.broadinstitute.org/variant/11-47353761-G-A
(2) TTN Variant:
Variant: NM_001267550.2(TTN):c.49175C>A (p.Ala16392Glu)
ClinVar: 405004, https://www.ncbi.nlm.nih.gov/clinvar/variation/405004/
gnomAD: 0.000004042, https://gnomad.broadinstitute.org/variant/2-179478949-G-T
Supplementary Data: S2 Table
Case 251: Spanish, 55yo, Female
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1
CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes
Variant: NM_000257.3(MYH7):c.3610G>C (p.Gly1204Arg)
ClinVar: 42966, https://www.ncbi.nlm.nih.gov/clinvar/variation/42966/
gnomAD: 0.000004008, https://gnomad.broadinstitute.org/variant/14-23889170-C-G
Supplementary Data: S2 Table
Case 10: Spanish, 69yo, Male
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1
CaseGenotypingMethod: genomic DNA obtained from blood or saliva, PCR, Sanger Sequencing
Variant: NM_000257.3(MYH7):c.4377G>T (p.Lys1459Asn)
ClinVar: 43012, https://www.ncbi.nlm.nih.gov/clinvar/variation/43012/
gnomAD: 0.0002937, https://gnomad.broadinstitute.org/variant/14-23886504-C-A
Supplementary Data: S2 Table
Case 130: Spanish, 14yo, Male
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1
CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes
Variant: NM_000257.3(MYH7):c.2167C>G (p.Arg723Gly)
ClinVar: 42885, https://www.ncbi.nlm.nih.gov/clinvar/variation/42885/
gnomAD: n/a
MultipleGeneVariants:
(1) TCAP Variant:
Variant: NM_003673.3(TCAP):c.97C>T (p.Arg33Trp)
ClinVar: 282451, https://www.ncbi.nlm.nih.gov/clinvar/variation/282451/
gnomAD: 0.00007092, https://gnomad.broadinstitute.org/variant/17-37821709-C-T
Supplementary Data: S2 Table
Case 67: Spanish, 40yo, Male
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePreviousTesting: Full Testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data table S1
CaseGenotypingMethod: genomic DNA obtained from blood or saliva, Next-gen sequencing panels of 55 or 78 genes
Variant: NM_000257.3(MYH7):c.2389G>A (p.Ala797Thr)
ClinVar: 42901, https://www.ncbi.nlm.nih.gov/clinvar/variation/42901/
gnomAD: 0.00002386, https://gnomad.broadinstitute.org/variant/14-23894525-C-T
MultipleGeneVariants:
(1) TTN Variant:
Variant: NM_133378.4(TTN):c.4396T>C (p.Phe1466Leu)
ClinVar: 166320, https://www.ncbi.nlm.nih.gov/clinvar/variation/166320/
gnomAD: 0.0006871, https://gnomad.broadinstitute.org/variant/2-179642515-A-G
MYH7 (3)
Case#: SF No. 29, GC Case No. 22, female, 79
DiseaseAssertion: hypertrophic cardiomyopathy, dilated cardiomyopathy
FamilyInfo: No
CasePresentingHPOs: N/A
CaseHPOFreeText: Colorectal cancer,
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: WES, Sanger sequencing,
Variant: NM_000257.3(MYH7):c.4522_4524delGAG (p.Glu1508del)
ClinVar: 43023 https://www.ncbi.nlm.nih.gov/clinvar/variation/43023/
CAID: N/A
gnomAD: absent
Supplementary Data: Online Table 2a
Case:
CasePreviousTesting: Full sarcomere testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, EMD, GLA, JPH2, JUP, LAMA4, LAMP2, LMNA, MYH6, MYPN, MYOZ1, MYOZ2, PKP2, PLN, PRKAG2, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43, TNNC1, TTN, VCL and LDB3)
CaseGenotypingMethod: DNA isolated from peripheral blood, targeted enrichment, next-gen sequencing with panel of 46 genes
Variant: NM_000257.3(MYH7):c.2710C>T (p.Arg904Cys)
ClinVar: 164316, https://www.ncbi.nlm.nih.gov/clinvar/variation/164316/
gnomAD: 0.000003977, https://gnomad.broadinstitute.org/variant/14-23893328-G-A
Supplementary Data: Online Table 1a
Case:
CasePresentingHPOs: HP:0001629 (Ebstein anomaly)
CasePreviousTesting: Full sarcomere testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, EMD, GLA, JPH2, JUP, LAMA4, LAMP2, LMNA, MYH6, MYPN, MYOZ1, MYOZ2, PKP2, PLN, PRKAG2, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43, TNNC1, TTN, VCL and LDB3)
CaseGenotypingMethod: DNA isolated from peripheral blood, targeted enrichment, next-gen sequencing with panel of 46 genes
Variant: NM_000257.3(MYH7):c.689T>C (p.Phe230Ser)
ClinVar: 263543, https://www.ncbi.nlm.nih.gov/clinvar/variation/263543/
gnomAD: n/a
Supplementary Data: Online Table 3
Case:
CasePreviousTesting: Full sarcomere testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, EMD, GLA, JPH2, JUP, LAMA4, LAMP2, LMNA, MYH6, MYPN, MYOZ1, MYOZ2, PKP2, PLN, PRKAG2, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43, TNNC1, TTN, VCL and LDB3)
CaseGenotypingMethod: DNA isolated from peripheral blood, targeted enrichment, next-gen sequencing with panel of 46 genes
Variant: NM_000257.3(MYH7):c.345C>T (p.Tyr115=)
ClinVar: 42962, https://www.ncbi.nlm.nih.gov/clinvar/variation/42962/
gnomAD: 0.0001061, https://gnomad.broadinstitute.org/variant/14-23902293-G-A
Supplementary Data table 1
Variant noted to be present in 4 individuals
Variant: NM_000257.3(MYH7):c.1816G>A (p.Val606Met)
ClinVar: 14091, https://www.ncbi.nlm.nih.gov/clinvar/variation/14091/
gnomAD: 0.000007070, https://gnomad.broadinstitute.org/variant/14-23896866-C-T
Supplementary Data table 1
Variant noted to be present in 2 individuals
Variant: NM_000257.3(MYH7):c.1987C>T (p.Arg663Cys)
ClinVar: 42874, https://www.ncbi.nlm.nih.gov/clinvar/variation/42874/
gnomAD: n/a
Supplementary Data table 1
Variant noted to be present in 3 individuals
Variant: NM_000257.3(MYH7):c.2156G>A (p.Arg719Gln)
ClinVar: 14107, https://www.ncbi.nlm.nih.gov/clinvar/variation/14107/
gnomAD: n/a
Supplementary Data table 1
Case:
DiseaseAssertion: hypertrophic cardiomyopathy
CaseHPOFreeText: maximal wall thickness (MWT) ≥15 mm
CasePreviousTesting: Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (TNNC1, CSRP3, TCAP, ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CAV3, CRYAB, CTNNA3, DES, DSC2, DSG2, DSP, EMD, FHL1, GLA, JPH2, JUP, LAMA4, LAMP2, LDB3, LMNA, MIB1, MYH6, MYOZ2, MYPN, NEXN, PKP2, PLN, PRDM16, PRKAG2, RBM20, SCN5A, TAZ, TMEM43, TNNC1, TTN, TTR, VCL), electrocardiography
CaseGenotypingMethod: direct sequencing of all coding intron-exon boundaries of 12 genes (prior to 2012), next-generation sequencing (post 2012)
Variant: NM_000257.3(MYH7):c.1532T>C (p.Ile511Thr)
ClinVar: 42848, https://www.ncbi.nlm.nih.gov/clinvar/variation/42848/
gnomAD: n/a
Supplementary Data table 1
Case:
DiseaseAssertion: hypertrophic cardiomyopathy
CaseHPOFreeText: maximal wall thickness (MWT) ≥15 mm
CasePreviousTesting: Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (TNNC1, CSRP3, TCAP, ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CAV3, CRYAB, CTNNA3, DES, DSC2, DSG2, DSP, EMD, FHL1, GLA, JPH2, JUP, LAMA4, LAMP2, LDB3, LMNA, MIB1, MYH6, MYOZ2, MYPN, NEXN, PKP2, PLN, PRDM16, PRKAG2, RBM20, SCN5A, TAZ, TMEM43, TNNC1, TTN, TTR, VCL), electrocardiography
CaseGenotypingMethod: direct sequencing of all coding intron-exon boundaries of 12 genes (prior to 2012), next-generation sequencing (post 2012)
Variant: NM_000257.3(MYH7):c.727C>T (p.Arg243Cys)
ClinVar: 43101, https://www.ncbi.nlm.nih.gov/clinvar/variation/43101/
gnomAD: 0.00003184, https://gnomad.broadinstitute.org/variant/14-23900799-G-A
CaseMYH7-29: N/A
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 1 other proband shares this genotype
CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.
Variant: NM_000257.3:c.1988G>A (p.Arg663His)
ClinVar: 42875 https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/
gnomAD: European (Non-Finnish) 3.097e-5, Overall 1.414e-5 https://gnomad.broadinstitute.org/variant/14-23896042-C-T
CaseMYH7-12: N/A
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 1 other proband shares this genotype
CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.
Variant: NM_000257.3:c.1358G>A (p.Arg453His)
ClinVar: 42838 https://www.ncbi.nlm.nih.gov/clinvar/variation/42838/
gnomAD: Not in gnomAD
CaseMYH7-10: N/A
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 3 other probands share this genotype
CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.
Variant: NM_000257.3:c.2779G>A (p.Glu927Lys)
ClinVar: 42932 https://www.ncbi.nlm.nih.gov/clinvar/variation/42932/
gnomAD: Not in gnomAD
CaseMYH7-21: N/A
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 5 other probands share this genotype
CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.
Variant: NM_000257.3:c.2722C>G (p.Leu908Val)
ClinVar: 14097 https://www.ncbi.nlm.nih.gov/clinvar/variation/14097/
gnomAD: European (Non-Finnish) 6.482e-5, Overall 3.185e-5 https://gnomad.broadinstitute.org/variant/14-23893316-G-C
CaseMYH7-4: N/A
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.
Variant: NM_000257.3:c.2156G>A (p.Arg719Gln)
ClinVar: 140107 https://www.ncbi.nlm.nih.gov/clinvar/variation/14107/
gnomAD: Not in gnomAD
CaseMYH7-19: N/A
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 2 other probands share this genotype
CaseGenotypingMethod: Testing for all 8 sarcomeric genes, plus GLA, LAMP2, and PRKAG2 was initiated in all probands. After the direct sequencing, the variants were filtered for pathogenicity and classified.
Variant: NM_000257.3:c.4066G>A (p.Glu1356Lys)
ClinVar: 164294 https://www.ncbi.nlm.nih.gov/clinvar/variation/164294/
gnomAD: Not in gnomAD
Case#: Consequence 29 Table 1 in Data Supplement (1 cases)
DiseaseAssertion: HCM
FamilyInfo: N/A
CasePresentingHPOs: N/A
CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3
CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing
Variant: NM_000257.4(MYH7):c.2782G>A (p.Asp928Asn)
ClinVar: 164313 https://www.ncbi.nlm.nih.gov/clinvar/variation/164313/
CAID: n/a
gnomAD: absent
Supplementary Data Table S3
Case: 349
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.4472C>G (p.Ser1491Cys)
ClinVar: 43020 https://www.ncbi.nlm.nih.gov/clinvar/variation/43020/
gnomAD: 0.01265, https://gnomad.broadinstitute.org/variant/14-23886409-G-C
MultipleGeneVariants:
(1) MYH6 Variant
Variant: NM_002471.3(MYH6):c.1763A>C (p.Asp588Ala)
ClinVar: 155811 https://www.ncbi.nlm.nih.gov/clinvar/variation/155811/
gnomAD: 0.003074, https://gnomad.broadinstitute.org/variant/14-23868065-T-G
(2) MYH6 Variant
Variant: NM_002471.3(MYH6):c.5491G>A (p.Glu1831Lys)
ClinVar: 196975 https://www.ncbi.nlm.nih.gov/clinvar/variation/196975/
gnomAD: 0.0003008, https://gnomad.broadinstitute.org/variant/14-23853725-C-T
(3) RBM20 Variant
Variant: NM_001134363.3(RBM20):c.1958C>T (p.Thr653Ile)
ClinVar: 180045 https://www.ncbi.nlm.nih.gov/clinvar/variation/180045/
gnomAD: 0.0007430, https://gnomad.broadinstitute.org/variant/10-112572113-C-T
(4) TMPO Variant
Variant: NM_003276.2(TMPO):c.821G>A (p.Arg274Lys)
ClinVar: 44673 https://www.ncbi.nlm.nih.gov/clinvar/variation/44673/
gnomAD: 0.005407, https://gnomad.broadinstitute.org/variant/12-98926856-G-A
Supplementary Data Table S3
Case: 18
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.2770G>A (p.Glu924Lys)
ClinVar: 14092, https://www.ncbi.nlm.nih.gov/clinvar/variation/14092/
gnomAD: absent
MultipleGeneVariants:
(1) LMNA Variant
Variant: NM_170707.4(LMNA):c.357C>T (p.Arg119=)
ClinVar: 48062, https://www.ncbi.nlm.nih.gov/clinvar/variation/48062/
gnomAD: 0.00424
(2) SDHA Variant
Variant: NM_004168.4(SDHA):c.1886A>T (p.Tyr629Phe)
ClinVar: 224949, https://www.ncbi.nlm.nih.gov/clinvar/variation/224949/
gnomAD: 0.1547, https://gnomad.broadinstitute.org/variant/5-254599-A-T
(2) TTN Variant
Variant: NM_001267550.2(TTN):c.74597_74599CAA[1] (p.Thr24867del)
ClinVar: 165840, https://www.ncbi.nlm.nih.gov/clinvar/variation/165840/
gnomAD: 0.001152, https://gnomad.broadinstitute.org/variant/2-179436256-ATTG-A
Supplementary Data Table S3
Case: 8
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)
ClinVar: 155814, https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/
gnomAD: 0.00006010, https://gnomad.broadinstitute.org/variant/14-23891476-C-T
MultipleGeneVariants
(1) LAMA4 Variant
Variant: NM_001105206.3(LAMA4):c.2614C>G (p.Pro872Ala)
ClinVar: 180391, https://www.ncbi.nlm.nih.gov/clinvar/variation/180391/
gnomAD: 0.0004032, https://gnomad.broadinstitute.org/variant/6-112463374-G-C
Supplementary Data Table S3
Case: 110
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant1: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)
ClinVar: 155814 https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/
gnomAD: 0.0006368, https://gnomad.broadinstitute.org/variant/14-23891476-C-T
Variant2: NM_000257.4(MYH7):c.4472C>G (p.Ser1491Cys)
ClinVar: 43020 https://www.ncbi.nlm.nih.gov/clinvar/variation/43020/
gnomAD: 0.01265, https://gnomad.broadinstitute.org/variant/14-23886409-G-C
MultipleGeneVariants:
(1) CRYAB Variant
Variant as listed does not exist on any transcript
Variant: c.331G>A (p.Gly111Ser)
ClinVar: N/A
gnomAD: N/A
(2) DSP Variant
Variant: NM_004415.4(DSP):c.4588G>T (p.Val1530Phe)
ClinVar: 137171 https://www.ncbi.nlm.nih.gov/clinvar/variation/137171/
gnomAD: 0.01477, https://gnomad.broadinstitute.org/variant/6-7581011-G-T
(3) SDHA Variant
Variant: NM_004168.4(SDHA):c.1886A>T (p.Tyr629Phe)
ClinVar: 224949 https://www.ncbi.nlm.nih.gov/clinvar/variation/224949/
gnomAD: 0.5249, https://gnomad.broadinstitute.org/variant/5-254599-A-T
(4) TMPO Variant
Variant: NM_001032283.2(TMPO):c.859G>C (p.Ala287Pro)
ClinVar: 43693 https://www.ncbi.nlm.nih.gov/clinvar/variation/43693/
gnomAD: 0.04732, https://gnomad.broadinstitute.org/variant/12-98938295-G-C
(5) TTN Variant
Variant: NM_001267550.2(TTN):c.74597_74599CAA[1] (p.Thr24867del)
ClinVar: 165840 https://www.ncbi.nlm.nih.gov/clinvar/variation/165840/
gnomAD: 0.003324, https://gnomad.broadinstitute.org/variant/2-179436256-ATTG-A
Supplementary Data Table S3
Case: 21
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)
ClinVar: 155814, https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/
gnomAD: 0.00006010, https://gnomad.broadinstitute.org/variant/14-23891476-C-T
MultipleGeneVariants:
(1) LDB3 Variant
Variant: NM_007078.3(LDB3):c.295C>T (p.Pro99Ser)
ClinVar: 178059, https://www.ncbi.nlm.nih.gov/clinvar/variation/178059/
gnomAD: 0.0009830, https://gnomad.broadinstitute.org/variant/10-88439888-C-T
Supplementary Data Table S3
Case: 216
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant1: NM_000257.4(MYH7):c.1816G>A (p.Val606Met)
ClinVar: 14091 https://www.ncbi.nlm.nih.gov/clinvar/variation/14091/
gnomAD: 0.00001548, https://gnomad.broadinstitute.org/variant/14-23896866-C-T
Variant2: NM_000257.4(MYH7):c.3853+7C>T
ClinVar: 42977 https://www.ncbi.nlm.nih.gov/clinvar/variation/42977/
gnomAD: 0.003956, https://gnomad.broadinstitute.org/variant/14-23888685-G-A
Supplementary Data Table S3
Case: 2
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)
ClinVar: 155814, https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/
gnomAD: 0.00006010, https://gnomad.broadinstitute.org/variant/14-23891476-C-T
MultipleGeneVariants:
(1) MYBPC3 Variant
Variant: NM_000256.3(MYBPC3):c.440C>T (p.Pro147Leu)
ClinVar: 181035, https://www.ncbi.nlm.nih.gov/clinvar/variation/181035/
gnomAD: 0.0005896, https://gnomad.broadinstitute.org/variant/11-47371630-G-A
(2) MYOZ2 Variant
Variant: NM_016599.4(MYOZ2):c.738A>G (p.Ile246Met)
ClinVar: 30509, https://www.ncbi.nlm.nih.gov/clinvar/variation/30509/
gnomAD: 0.002300, https://gnomad.broadinstitute.org/variant/4-120107298-A-G
(3) PSEN2 Variant
Variant: NM_000447.3(PSEN2):c.211C>T (p.Arg71Trp)
ClinVar: 192130, https://www.ncbi.nlm.nih.gov/clinvar/variation/192130/
gnomAD: 0.003711, https://gnomad.broadinstitute.org/variant/1-227071475-C-T
(4) SCN5A Variant
Variant: NM_000335.4(SCN5A):c.1715C>A (p.Ala572Asp)
ClinVar: 67683, https://www.ncbi.nlm.nih.gov/clinvar/variation/67683/
gnomAD: 0.005175, https://gnomad.broadinstitute.org/variant/3-38645378-G-T
Supplementary Data Table S3
Case: 231
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.4472C>G (p.Ser1491Cys)
ClinVar: 43020 https://www.ncbi.nlm.nih.gov/clinvar/variation/43020/
gnomAD: 0.01265, https://gnomad.broadinstitute.org/variant/14-23886409-G-C
MultipleGeneVariants:
(1) LDB3 Variant
Variant: NM_007078.3(LDB3):c.295C>T (p.Pro99Ser)
ClinVar: 178059 https://www.ncbi.nlm.nih.gov/clinvar/variation/178059/
gnomAD: 0.009200, https://gnomad.broadinstitute.org/variant/10-88439888-C-T
Supplementary Data Table S3
Case: 129
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.1987C>T (p.Arg663Cys)
ClinVar: 42874 https://www.ncbi.nlm.nih.gov/clinvar/variation/42874/
gnomAD: Not in gnomAD
MultipleGeneVariants:
(1) LAMA4 Variant
Variant: NM_001105206.3(LAMA4):c.3239G>A (p.Arg1080Gln)
ClinVar: 44374 https://www.ncbi.nlm.nih.gov/clinvar/variation/44374/
gnomAD: 0.02400, https://gnomad.broadinstitute.org/variant/6-112460365-C-T
Supplementary Data Table S3
Case: 152
DiseaseEntity: HCM
HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm
InheritancePattern: n/a
CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)
CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing
Variant: NM_000257.4(MYH7):c.3158G>A (p.Arg1053Gln)
ClinVar: 155814 https://www.ncbi.nlm.nih.gov/clinvar/variation/155814/
gnomAD: 0.0006368, https://gnomad.broadinstitute.org/variant/14-23891476-C-T
MultipleGeneVariants:
(1) CRYAB Variant
Variant as listed does not exist on any transcript
Variant: c.331G>A (p.Gly111Ser)
ClinVar: N/A
gnomAD: N/A
(2) DSP Variant
Variant: NM_004415.4(DSP):c.4372C>G (p.Arg1458Gly)
ClinVar: 44906 https://www.ncbi.nlm.nih.gov/clinvar/variation/44906/
gnomAD: 0.003556, https://gnomad.broadinstitute.org/variant/6-7580795-C-G
HCM16.1
CaseHCM16.1: Mixed ancestry
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: HP:0000819 (Diabetes mellitus)
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: See Table 1
CaseGenotypingMethod: DNA was extracted from the probands' blood, followed by sequencing of the coding regions and exon/intron boundaries of 15 genes associated with HCM. From there, they were amplified by PCR ampliication and variants were filtered by pathogenicity. Every unclassified variant was confirmed by Sanger sequencing afterwards.
Variant: NM_000257.3:c.746G>A (p.Arg249Gln)
ClinVar: 14088 https://www.ncbi.nlm.nih.gov/clinvar/variation/14088/
gnomAD: Not in gnomAD
CaseMYH7-16: Australia
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 3 other probands have the same genotype
CasePreviousTesting: See Table 1
CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.
Variant: NM_000257.3:c.2681A>G (p.Glu894Gly)
ClinVar: 42922 https://www.ncbi.nlm.nih.gov/clinvar/variation/42922/
gnomAD: Not in gnomAD
CaseMYH7-20: Australia
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: See Table 1
CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.
Variant: NM_000257.3:c.2420G>A (p.Arg807His)
ClinVar: 391904 https://www.ncbi.nlm.nih.gov/clinvar/variation/391904/
gnomAD: Latino 5.644e-5, Overall 1.414e-5 https://gnomad.broadinstitute.org/variant/14-23894494-C-T
CaseMYH7-9: Australia
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: See Table 1
CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.
Variant: NM_000257.3:c.4066G>A (p.Glu1356Lys)
ClinVar: 164294 https://www.ncbi.nlm.nih.gov/clinvar/variation/164294/
gnomAD: Not in gnomAD
CaseMYH7-33: Australia
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: See Table 1
CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.
Variant: NM_000257.3:c.1727A>G (p.His576Arg)
ClinVar: 177625 https://www.ncbi.nlm.nih.gov/clinvar/variation/177625/
gnomAD: African 4.008e-5, Overall 1.768e-5 https://gnomad.broadinstitute.org/variant/14-23896955-T-C
CaseMYH7-27: Australia
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: N/A
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: See Table 1
CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.
Variant: NM_000257.3:c.2156G>A (p.Arg719Gln)
ClinVar: 14107 https://www.ncbi.nlm.nih.gov/clinvar/variation/14107/
gnomAD: Not in gnomAD
II-3
CaseBII-3: Female, 64 years diagnosis, Italy, Caucasian
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: See Figure 1
CasePresentingHPOs: HP:0001639, HP:0002094 (Hypertrophic cardiomyopathy, Dyspnea)
HPOsFreeText: Max Left ventricular wall thickness of 19 mm, Left atrium diameter of 42 mm, Left ventricular ejection fraction of 64%
CaseNotHPOs: HP:0003115, HP:0011675 (Abnormal ECG, Arrhythmia)
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: The ACM proband from Family B was genotyped for PKP2, DSP, DSC2, DSG2, JUP and CTNNA3; the HCM patient from Family B was genotyped for MYBPC3, MYH7, TNNI3 and TNNT2.
CaseGenotypingMethod: All patients in Family B were directly sequenced according to the found variants in CTNNA3 and MYH7. These variants were filtered for pathogenicity and prevalence and classified accordingly.
Variant: NM_000257.3:c.2631G>T (p.Met877Ile)
ClinVar: 417718 https://www.ncbi.nlm.nih.gov/clinvar/variation/417718/
gnomAD: Not in gnomAD
Supplementary Material 4
Case M-12: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.1988G>A (p.Arg663His)
ClinVar: 42875, https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/
gnomAD: 0.00001414, https://gnomad.broadinstitute.org/variant/14-23896042-C-T
Supplementary Material 4
Case M-11: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.1988G>A (p.Arg663His)
ClinVar: 42875, https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/
gnomAD: 0.00001414, https://gnomad.broadinstitute.org/variant/14-23896042-C-T
Supplementary Material 4
Case M-27: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.2770G>A (p.Glu924Lys)
ClinVar: 14092, https://www.ncbi.nlm.nih.gov/clinvar/variation/14092/
gnomAD: n/a
Supplementary Material 4
Case M-3: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.746G>A (p.Arg249Gln)
ClinVar: 14088, https://www.ncbi.nlm.nih.gov/clinvar/variation/14088/
gnomAD: n/a
Supplementary Material 4
Case M-5: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.1012G>A (p.Val338Met)
Clinvar: 164381, https://www.ncbi.nlm.nih.gov/clinvar/variation/164381/
gnomAD: n/a
Supplementary Material 4
Case M-17: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.2207T>C (p.Ile736Thr)
ClinVar: 164342, https://www.ncbi.nlm.nih.gov/clinvar/variation/164342/
gnomAD: n/a
Supplementary Material 4
Case M-13: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.2011C>T (p.Arg671Cys)
ClinVar: 164350, https://www.ncbi.nlm.nih.gov/clinvar/variation/164350/
gnomAD: n/a
Supplementary Material 4
Case M-7: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant 2: NM_000257.3(MYH7):c.1357C>T (p.Arg453Cys)
ClinVar: 14089, https://www.ncbi.nlm.nih.gov/clinvar/variation/14089/
gnomAD: n/a
Supplementary Material 4
Case M-24: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.2546T>C (p.Met849Thr)
ClinVar: 42914, https://www.ncbi.nlm.nih.gov/clinvar/variation/42914/
gnomAD: n/a
Supplementary Material 4
Case M-4: Japanese
DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)
CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)
CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing
Variant: NM_000257.3(MYH7):c.746G>A (p.Arg249Gln)
ClinVar: 14088, https://www.ncbi.nlm.nih.gov/clinvar/variation/14088/
gnomAD: n/a
Table V
Case 898: Italian, 1yo at onset
DiseaseAssertion: HCM
FamilyInfo: family history of HCM
CasePresentingHPOs: HP:0001712 (left ventricular hypertrophy)
CaseHPOFreeText: LVWT = 11mm, LV ejection fraction = 70%
CasePreviousTesting: echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1), additional testing: (GLA, LAMP2, PRKAG2), additional genes added with NGS: (TNNC1, MYH6, MYOM1, MYOZ2, ANKRD1, VCL, CALR3, CAV3)
CaseGenotypingMethod: Genomic DNA extracted from peripheral leukocytes, Sanger sequencing (73 samples), Next-gen sequencing (19 samples)
Variant: NM_000257.3(MYH7):c.5302G>A (p.Glu1768Lys)
ClinVar: 43059, https://www.ncbi.nlm.nih.gov/clinvar/variation/43059/
gnomAD: n/a
father
Case#: father, diagnosis as child,
DiseaseAssertion: HCM
FamilyInfo: daughter and 2 sons also diagnosed, G6P2 30 yr mother had normal pregnancy
CasePresentingHPOs: N/A
CaseHPOFreeText: heart transplantation at 33 yr
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: N/A
Variant: NM_000257.4(MYH7):c.1969A>C (p.Lys657Gln)
ClinVar: 164351 https://www.ncbi.nlm.nih.gov/clinvar/variation/164351/
CAID: N/A
gnomAD: N/A
Table 1 and 4
Case A13: Male, 10yo, proband (III-2)
DiseaseAssertion: malignant HCM
FamilyInfo: positive family history (fig 1), grandfather died at 42yo from heart disease, father died at 40yo due to sudden cardiac death, mother (A11, II-1) had no clinical symptoms, sister (A12, III-1) diagnosed at 21yo with severe HCM
CasePresentingHPOs: HP:0100749, HP:0001279 (chest pain, syncope)
CaseHPOFreeText: interventricular septum thickness = 21.0mm, left ventricular posterior wall thickness = 12.0mm, left atrium = 40.0mm, left ventricular ejection fraction = 48%, septal asymmetry, decreased left ventricular systolic and diastolic function
CasePreviousTesting: 12-lead ECG, echocardiography, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing (LMNA, PRKAG2, SCN5A, MYH6)
CaseGenotypingMethod: genomic DNA collected from peripheral whole blood samples, PCR, high-throughput sequencing using PGM Sequencing 400 kit, variants verified via Sanger Sequencing
Variant: NM_000257.3(MYH7):c.2155C>T (p.Arg719Trp)
ClinVar: 14104, https://www.ncbi.nlm.nih.gov/clinvar/variation/14104/
gnomAD: 0.00003185, https://gnomad.broadinstitute.org/variant/14-23895180-G-A
MultipleGeneVariants:
(1) PRKAG2 Variant:
Variant: NM_016203.3(PRKAG2):c.298G>A (p.Gly100Ser)
ClinVar: 36697, https://www.ncbi.nlm.nih.gov/clinvar/variation/36697/
gnomAD: 0.006770, https://gnomad.broadinstitute.org/variant/7-151478406-C-T
KMP 22
Case KMP 22: Eastern Slovakia, Male, 21yo
DiseaseAssertion: hypertrophic cardiomyopathy
FamilyInfo: negative family history
CaseHPOFreeText: left ventricular ejection fraction = 60%, implantable cardioverter defibrillator
CaseNotHPOFreeText: left ventricular outflow tract obstruction
CasePreviousTesting: 12-lead ECG, echocardiography, partial testing (MYBPC3, MYH7, NEBL, SCN5A, TNNI3, TNNT2)
CaseGenotypingMethod: genomic DNA collected from peripheral blood leukocytes, Sanger sequencing
Variant: NM_000257.3(MYH7):c.2845G>A (p.Glu949Lys)
ClinVar: 14093, https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/
gnomAD: n/a
KMP 8
Case KMP 8: Eastern Slovakia, Male, 62yo
DiseaseAssertion: hypertrophic cardiomyopathy
FamilyInfo: no family history
CaseHPOFreeText: left ventricular outflow tract obstruction, left ventricular ejection fraction = 60%
CasePreviousTesting: 12-lead ECG, echocardiography, partial testing (MYBPC3, MYH7, NEBL, SCN5A, TNNI3, TNNT2)
CaseGenotypingMethod: genomic DNA collected from peripheral blood leukocytes, Sanger sequencing
Variant: NM_000257.3(MYH7):c.2845G>A (p.Glu949Lys)
ClinVar: 14093, https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/
gnomAD: n/a
N16
Case N16: Tunisia, Female, 72yo at onset, 76yo at study
DiseaseAssertion: hypertrophic cardiomyopathy
CasePresentingHPOs: HP:0100749 (chest pain)
CaseHPOFreeText: left ventricular septum (LVS) ≥15 mm, septum size = 18mm
FamilyInfo: family history sudden cardiac death
CasePreviousTesting: Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (FLNC, TNNC1), electrocardiogram, echocardiography
CaseGenotypingMethod: PCR, Next-generation sequencing, identified variants confirmed via Sanger Sequencing
Variant: NM_000257.3(MYH7):c.4909G>A (p.Ala1637Thr)
ClinVar: 43044, https://www.ncbi.nlm.nih.gov/clinvar/variation/43044/
gnomAD: 0.00008840, https://gnomad.broadinstitute.org/variant/14-23885257-C-T
8
Case8: Female, 58 years report, China, Asian
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: No family history
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: Interventricular septal thickness at 17.3 mm, Left ventricular posterior wall thickness at 15.9 mm, Left ventricular end-diastolic diameter at 60.7 mm, Left ventricular septal thickness at 45.3 mm, Left ventricular ejection fraction at 50%
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: See list of sequenced genes
CaseGenotypingMethod: Genomic DNA was isolated from whole blood of all patients and controls. Whole coding exons and exon-intron boundaries of the 19 HCM-related genes listed above were amplified and sequenced on Ion Torrent PGM. These variants were then filtered for pathogenicity and compared to the controls. Any mutations found were confirmed by conventional dideoxy sequencing and Sanger sequencing.
Variant: NM_000257.3:c.730T>C (p.Phe244Leu)
ClinVar: 181319 https://www.ncbi.nlm.nih.gov/clinvar/variation/181319/
gnomAD: Not in gnomAD
CaseMYH7-4: Japan, Asian
CasePresentingHPOs: HP:0001639, HP:0006685 (Hypertrophic cardiomyopathy, Endomyocardial fibrosis)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo:
CaseGenotypingMethod: Genomic DNA was extracted from whole blood from each proband. They each had 95 genes associated with DCM, HCM, and other inherited cardiovascular diseases sequenced with a panel, including both the exons and spicing regions. Variants were then filtered for rarity and pathogenicity.
Variant: NM_000257.3:c.2221G>C (p.Gly741Arg)
ClinVar: 14098 https://www.ncbi.nlm.nih.gov/clinvar/variation/14098/
gnomAD: Not in gnomAD
A feline orthologue of the human MYH7 c.5647G>A (p.(Glu1883Lys)) variant causes hypertrophic cardiomyopathy in a Domestic Shorthair cat
PMID: 31164718
Gene: MYH7
AnimalModel: detection of feline orthologue of NM_000257.2(MYH7):c.5647G>A (p.Glu1883Lys) (ClinVarID: 14121), which was determined to cause HCM in domestic short hair cat
ClinVar: 14121, https://www.ncbi.nlm.nih.gov/clinvar/variation/14121/
gnomAD: 0.00003185, https://gnomad.broadinstitute.org/variant/14-23883224-C-T
Case14: Male, 59 years diagnosis, China, Asian
DiseaseAssertion: Hypertrophic Cardiomyopathy
FamilyInfo: One sibling had recurrent syncope and HCM with ICD implantation
CasePresentingHPOs: HP:0001639, HP:0001962, HP:0000822 (Hypertrophic cardiomyopathy, Palpitations, Hypertension)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: Probands were only genotyped for MYH7 and MYBPC3 in that order, stopping once a positive finding was detected.
CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood. Each gene's coding exons and flanking introns were subject to PCR amplification and sequencing. From there, any variants found were filtered for pathogenicity and low frequencies.
Variant: NM_000257.3:c.1987C>T (p.Arg663Cys)
ClinVar: 42874 https://www.ncbi.nlm.nih.gov/clinvar/variation/42874/
gnomAD: Not in gnomAD
Case Report
Case: Male, born at 38 weeks gestation
DiseaseAssertion: Hypertrophic Cardiomyopathy
CasePresentingHPOs: HP:0030718, HP:0001667, HP:0002092, HP:0001670, HP:0200128 (enlarged right atrium, right ventricular hypertrophy, pulmonary hypertension, asymmetric septal hypertrophy, biventricular hypertrophy)
CaseHPOFreeText: birth weight = 3.283kg, apgar scores = 8,9, asymmetric septal hypertrophy of atrioventricular septum without outflow tract obstruction or myocardial scarring, confirmed diagnosis of HCM at 6mo
CaseNotHPOs: HP:0011611, HP:0001653, HP:0004308, HP:0005115 (aortic obstruction, mitral valve insufficiency, ventricular arrhythmia, supraventricular arrhythmia)
FamilyInfo: Both parents and only sibling underwent genetic testing, the father and brother harbored the same variant as the patient (p.Ala1328Thr), this variant was absent in the mother. Father (36yo) and brother (5yo) had normal echocardiograms.
CasePreviousTesting: fetal echocardiography at 32wks, postnatal echocardiography, routine cardiac follow-up at 6mo, cardiac MRI, 24hr Holter monitor, Full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (CAV3, MTTG, MTTI, MTTK, MTTQ, TNNC1, TTR, PKRAG2, LAMP2, GLA)
CaseGenotypingMethod: blood and buccal cell samples collected from patient, coding regions and splice junctions of 18 genes were enriched with a proprietary targeted capture system by GeneDx, these then underwent NextGen sequencing, capillary sequencing used to confirm potentially pathogenic variants
Variant: NM_000257.3(MYH7):c.3982G>A (p.Ala1328Thr)
ClinVar: 42985, https://www.ncbi.nlm.nih.gov/clinvar/variation/42985/
gnomAD: 0.00002154, https://gnomad.broadinstitute.org/variant/14-23887606-C-T
InheritancePattern: autosomal dominant
30
Case#: 30
DiseaseAssertion: LVNC
FamilyInfo: N/A
CasePresentingHPOs: N/A
CaseHPOFreeText: 3.31 fathom, 0.002 sift, 0.997 polyphen, 0 GVGD, mutation taster 1, -2.08 provean, -4.22 CADD
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: physical examination, ECG, variant screening and classification, genic collapsing test, group statistical analysis
Variant: NM_000257.4(MYH7):c.67C>T (p.Arg23Trp)
ClinVar: 181295 https://www.ncbi.nlm.nih.gov/clinvar/variation/181295/
CAID: N/A
gnomAD: 0.00007961 European/Finnish https://gnomad.broadinstitute.org/variant/14-23902875-G-A
Pedigree 1
Case: Pedigree 1 proband, male, 11yo at diagnosis, Iraqi‐Jewish
CasePresentingHPOs: HP:0001639, HP:0004756, HP:0005110, HP:0002094, HP:0001712 (hypertrophic cardiomyopathy, ventricular tachycardia, atrial fibrillation, dyspnea, left ventricular hypertrophy)
HPOsFreeText: clinical severity: moderate to asymptomatic, systolic murmur, NYHA Class II, maximal wall thickness at the anterior septum = 30 mm, resting LVOT gradient of 35 mmHg, increasing to 48 mmHg, normal LV systolic function, estimated ejection fraction (EF) of 65%, Grade II (moderate) LV diastolic dysfunction, ECH showed sinus rhythm, LV strain, inverted T waves, eptal wall thickness of 31 mm, extensive late gadolinium enhancement involving 45% of the left ventricle
CaseNotHPOs: HP:0001279 (syncope)
NotHPOsFreeText: skeletal involvement
CasePreviousTesting: exact genes sequenced not specified
CaseGenotypingMethod: Fifty‐six genes known to cause HCM were sequenced in parallel
Variant: NM_000257.3(MYH7):c.427C>T (p.Arg143Trp)
ClinVar: 164401, https://www.ncbi.nlm.nih.gov/clinvar/variation/164401/
gnomAD: 0.00002784, https://gnomad.broadinstitute.org/variant/14-23901923-G-A
FamilyInfo: mother was heterozygous for variant, she was asymptomatic, had mild nonobstructive hypertrophy, hypertension, and anterior septal thickness of 13 mm
DCM-12
Case#: DCM-12, female, Yunnan, China
DiseaseAssertion: DCM
FamilyInfo: n/a
CasePresentingHPOs: n/a
CaseHPOFreeText: n/a
CaseNotHPOs: n/a
CaseNotHPOFreeText: n/a
CasePreviousTesting: physical exam, invasive examination, ECG,
CaseGenotypingMethod: NGS and Sanger Sequencing
Variant: NM_000257.4(MYH7):c.77C>T (p.Ala26Val)
ClinVar: 37375 https://www.ncbi.nlm.nih.gov/clinvar/variation/37375/
CAID: n/a
gnomAD: absent
Table 5
Case EO32: Italian
DiseaseAssertion: HCM (early-onset)
CasePreviousTesting: echocardiography, Full testing (MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1), additional testing: (GLA, LAMP2, PRKAG2, TNNC1, MYH6, CSPR3, PLN, TCAP, CAV3), electrocardiography
CaseGenotypingMethod: Genomic DNA extracted from periphera whole blood, emulsion PCR, 17 HCM genes sequenced using Personal Genome Machine (PGM) IonTorrent sequencer, variants confirmed via Sanger sequencing
Variant1: NM_000257.3(MYH7):c.1988G>A (p.Arg663His)
ClinVar: 42875, https://www.ncbi.nlm.nih.gov/clinvar/variation/42875/
gnomAD: 0.00001414, https://gnomad.broadinstitute.org/variant/14-23896042-C-T
MultipleGeneVariants:
(1) MYPBC3 Variant:
Variant: NM_000256.3(MYBPC3):c.3192dupC (p.Lys1065Glnfs)
ClinVar: 42693, https://www.ncbi.nlm.nih.gov/clinvar/variation/42693/
gnomAD: n/a
CaseCM1856: Male, 15 years diagnosis, Japan, Asian
CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)
HPOsFreeText: N/A
CaseNotHPOs: HP:0001939 (Abnormality of metabolism/homeostasis)
NotHPOsFreeText: Neuromuscular disease, Malformation syndromes
CaseAddInfo: Positive family history of cardiomyopathy or sudden death, Proband found in Supplementary Table 2, Mother with an ECG abnormality and 2 brothers with HCM tested positive for this variant, Father with no phenotypes tested negative for this variant
CasePreviousTesting: 8 patients with HCM and one with RCM were analyzed by NGS for the eight sarcomere-encoding genes and MYP.
CaseGenotypingMethod: Probands were subject to PCR amplification and direct sequencing of 64 cardiomyopathy-associated genes, including the eight sarcomere-encoding genes. The variants were then filtered for rarity and tested for pathogenicity.
Variant: NM_000257.3:c.2155C>T (p.Arg719Trp)
ClinVar: 14104 https://www.ncbi.nlm.nih.gov/clinvar/variation/14104/
gnomAD: European (Non-Finnish) 6.481e-5, Overall 3.185e-5 https://gnomad.broadinstitute.org/variant/14-23895180-G-A
Supplementary Data: Table S3
Case 64:
DiseaseAssertion: left ventricular noncompaction
CasePresentingHPOs: HP:0030682 (left ventricular noncompaction)
CaseHPOFreeText: >7yo, able to hold breath, non compacted segment = distinct 2-layered appearance of trabeculated and compacted myocardium, NC/C ratio > 2.3:1
CasePreviousTesting: Cardiac MRI using 17-segment model of LV segmentation, ECG, transthoracic echocardiography, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), additional testing listed in supplementary data tables S1 and S2.
CaseGenotypingMethod: WES, variant enrichment analysis
Variant: NM_000257.3(MYH7):c.3337-3dupC written in paper as g.23889445insG
ClinVar: 42956, https://www.ncbi.nlm.nih.gov/clinvar/variation/42956/
gnomAD: 0.02126, https://gnomad.broadinstitute.org/variant/14-23889445-T-TG
MultipleGeneVariants:
(1) - TTN Variant:
Variant: g.179407388delC no ClinVar or CAID
D15
Case#: D15, male, 43 years
DiseaseAssertion: FDCM
FamilyInfo: N/A
CasePresentingHPOs: N/A
CaseHPOFreeText: N/A
CaseNotHPOs: N/A
CaseNotHPOFreeText: N/A
CasePreviousTesting: DNA extraction, whole exome sequencing, pyrosequencing, RNA extraction, q-RT-PCR, SDS-PAGE electrophoresis, western blotting and immunofluorescence microscopy
CaseGenotypingMethod: N/A
Variant: NM_000257.4(MYH7):c.4276G>A (p.Glu1426Lys)
ClinVar: 43005 https://www.ncbi.nlm.nih.gov/clinvar/variation/43005/
CAID: N/A
gnomAD: absent
For GAA (Pompe disease) screening
CaseP4-GAA: female, ethnicity = European, country origin = Italy
CasePresentingHPOs:
HPOsFreeText: enzyme activity = 2.22
CaseNotHPOs: HP:0010899, HP:0010916, HP:0003236
CaseAddInfo: homozygous
CasePreviousTesting: initial and confirmatory DBS, biochemical tests
CaseGenotypingMethod: mutation analyses
Variant: NM_000152.4(GAA):c.533G>A (p.Arg178His)
ClinVar: 554969; https://www.ncbi.nlm.nih.gov/clinvar/variation/554969/
gnomAD: 2.646e-05, http://exac.broadinstitute.org/variant/17-78078918-G-A
PD23
Patient23: Male, Southern China
CasePresentingHPOs:
HPOsFreeText: IOPD
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo:
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000152.4(GAA):c.1411_1414delGAGA (p.Glu471Profs)
ClinVar: 188874, https://www.ncbi.nlm.nih.gov/clinvar/variation/188874/
gnomAD: 1.688e-05, http://exac.broadinstitute.org/variant/17-78083827-CGAGA-C
Variant2: NM_000152.4(GAA):c.2024_2026delACA (p.Asn675del)
ClinVar: 189006, https://www.ncbi.nlm.nih.gov/clinvar/variation/189006/
gnomAD: 2.105e-05, http://exac.broadinstitute.org/variant/17-78086806-CACA-C
PD10
Patient10: Male, Southern China
CasePresentingHPOs:
HPOsFreeText: IOPD
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo:
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000152.4(GAA):c.2105G>A (p.Arg702His)
ClinVar: 426278, https://www.ncbi.nlm.nih.gov/clinvar/variation/426278/
gnomAD: 6.695e-05, http://exac.broadinstitute.org/variant/17-78087081-G-A
Variant2: NM_000152.4(GAA):c.2297A>C (p.Tyr766Ser)
ClinVar: 420102, https://www.ncbi.nlm.nih.gov/clinvar/variation/420102/
gnomAD: 8.35e-06, http://exac.broadinstitute.org/variant/17-78090874-A-C
PD11
Patient11: Male, Southern China
CasePresentingHPOs:
HPOsFreeText: IOPD, survived beyond 2yo, left ventricular mass index and left ventricular posterior wall thickness decreased during ERT. Able to raise head, sit without support, stand, walk alone
CaseNotHPOs: no significant respiratory problems during ERT
NotHPOsFreeText:
CaseAddInfo: homozygous, only patient to receive ERT treatment (rhGAA) every 2wks beginning at 5mo of age. ERT lasted for 90wks.
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: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A
PD17
Patient17: Female, Southern China
CasePresentingHPOs:
HPOsFreeText: IOPD
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo:
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)
ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/
gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A
Variant2: NM_000152.4(GAA):c.2815_2816delGT (p.Val939Leufs)
ClinVar: 371481, https://www.ncbi.nlm.nih.gov/clinvar/variation/371481/
gnomAD: 1.653e-05, http://exac.broadinstitute.org/variant/17-78093082-CTG-C
5
Patient5: male, Romanian
CasePresentingHPOs: HP:0003677, HP:0003236, HP:0003325, HP:0003418, HP:0008997
HPOsFreeText: CK > 10x increase, CK = 1500 U/L, reduced alpha-glucosidase activity
CaseNotHPOs: HP:0002093
CaseAddInfo: onset in middle age, enzyme activity also reduced in daughter
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000152.4(GAA):c.2066_2070dupAGCCG (p.Ala691Serfs)
ClinVar: 92471, https://www.ncbi.nlm.nih.gov/clinvar/variation/92471/
gnomAD: n/a
Variant2: 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
18
Patient18: female, White British
CasePresentingHPOs: HP:0003677, HP:0003236, HP:0003325, HP:0003701, HP:0003458, HP:0003715, HP:0030231
HPOsFreeText: CK > 10x increase, CK = 599 U/L. Vacuolated, degenerated, and atrophic fibers. Vacuole periphery showed abnormal immunoreactivity for desmin and p62. Z-band streaming of fibers, granular material accumulation. Treated with ERT. Normal to low alpha-glucosidase activity.
CaseNotHPOs: HP:0002093
NotHPOsFreeText: no evidence of glycogenosis
CaseAddInfo: onset after 50yo
CasePreviousTesting: same as group, muscle biopsy, NADH-tetrazolim reductase staining
CaseGenotypingMethod: same as group
Variant1: NM_000152.4(GAA):c.525delT (p.Glu176Argfs)
ClinVar: 4033, https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/
gnomAD: 7.041e-05, http://exac.broadinstitute.org/variant/17-78078909-CT-C
Variant2: 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
21
Patient21: 68yo
CasePresentingHPOs: HP:0003325, HP:0002093, HP:0003141, HP:0001513, HP:0020038
HPOsFreeText: GAA = 30%, BMI = 30.3, nucleo-capsular and subcortical white matter lacunes
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: 30yr disease duration
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant: 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
8
Patient8: 47yo
CasePresentingHPOs: HP:0003325, HP:0001513
HPOsFreeText: GAA = 5%, BMI = 30.8, Normal CTA and CT
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: 2yr disease duration, variants in cis
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant: 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.1551+1G>C
ClinVar: 554983, https://www.ncbi.nlm.nih.gov/clinvar/variation/554983/
gnomAD: n/a
2
Patient2: 76yo
CasePresentingHPOs: HP:0003325, HP:0002093, HP:0002315, HP:0004887, HP:0000822, HP:0002870, HP:0020038
HPOsFreeText: morning headaches, GAA = 13%, BMI = 23.6, right vertebral artery dominant, nucleo-capsular lacunes
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: 33yr disease duration
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant: 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
9
Patient9: 54yo
CasePresentingHPOs: HP:0003325, HP:0002093, HP:0002315, HP:0004887, HP:0003141, HP:0002870
HPOsFreeText: morning headache, GAA = 7%, smoker, BMI = 23.3, normal CTA, nucleo-capsular and subcortical white matter lacunes
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: 29yr disease duration, variants in cis
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant: 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.1551+1G>C
ClinVar: 554983, https://www.ncbi.nlm.nih.gov/clinvar/variation/554983/
gnomAD: n/a
c.2560C > T(p.Arg845*)
Case14
HPOsFreeText: See Group Phenotypes
CasePreviousTesting: Sanger sequencing
CaseMethod1: Sanger sequencing and PCR Amplification
CaseMethod2: Whole Exome Sequencing (WES)
CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.
Variant: NM_000152.4:c.2560C>T (p.Arg854*)
ClinVar: 4034 https://www.ncbi.nlm.nih.gov/clinvar/variation/4034/
gnomAD: African 1.891e-3, Overall 2.090e-4 http://gnomad.broadinstitute.org/variant/17-78092070-C-T
CaseAddInfo: Infantile Onset Pompe Disease, Patient is homozygous for this variant, 6 more patients have the same genotype
c.2481+102_2646+31del (p.Gly828_Asn882del)
Case72
HPOsFreeText: See Group Phenotypes
CasePreviousTesting: Sanger sequencing
CaseMethod1: Sanger sequencing and PCR Amplification
CaseMethod2: Whole Exome Sequencing (WES)
CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.
Variant1: NM_000152.4:c.2481+102_2646+31del (p.Gly828_Asn882del) (exon 18 del)
ClinVar: 4031 https://www.ncbi.nlm.nih.gov/clinvar/variation/4031/
gnomAD: Not in gnomAD
Variant2: 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
CaseAddInfo: Adult Late Onset Pompe Disease, 4 other patients have the same genotype
c.877G > A(p.Gly293Arg)
Case89
HPOsFreeText: See Group Phenotypes
CasePreviousTesting: Sanger sequencing
CaseMethod1: Sanger sequencing and PCR Amplification
CaseMethod2: Whole Exome Sequencing (WES)
CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.
Variant1: NM_000152.4:c.877G>A (p.Gly293Arg)
ClinVar: 4036 https://www.ncbi.nlm.nih.gov/clinvar/variation/4036/
gnomAD: Latino 5.704e-5, Overall 1.807e-5 http://gnomad.broadinstitute.org/variant/17-78081617-G-A
Variant2: 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
CaseAddInfo: Adult Late Onset Pompe Disease
Supplement Table 1)
Patient10: 6yo
CasePresentingHPOs: HP:0001638
HPOsFreeText: rhGAA dosage = 40 EOW, independent walker
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: homozygous variants, 34day old at ERT
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: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A
Supplement Table 1)
Patient14: 3yo
CasePresentingHPOs: HP:0001638
HPOsFreeText: rhGAA dosage = 20 QW, independent walker
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: homozygous variants, 14days old at ERT start
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)
ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/
gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A
CaseLP2-4: Female, Taiwan, Birth diagnosis
HPOsFreeText: GAA (MS/MS) enzyme activity at 0.10 umol/hr/L, Serum CK at 66 U/L
GenotypingMethod: GAA Gene Sequencing and PCR Amplification
Variant1: NM_000152.4:c.752C>T (p.Ser251Leu)
ClinVar: 325781 https://www.ncbi.nlm.nih.gov/clinvar/variation/325781/
gnomAD: East Asian 2.760e-3, Overall 3.540e-4 http://gnomad.broadinstitute.org/variant/17-78081415-C-T
Variant2: NM_000152.4:c.761C>T (p.Ser254Leu)
ClinVar: 325782 https://www.ncbi.nlm.nih.gov/clinvar/variation/325782/
gnomAD: East Asian 2.759e-3, Overall 1.947e-4 http://gnomad.broadinstitute.org/variant/17-78081424-C-T
CaseAddInfo: Late Onset Pompe Disease, Nomenclature indicates Variants 1 and 2 are in cis and patient is homozygous for this allele, 1 other patient has the same genotype
CaseOPOPD-12: Female, Taiwan, Birth diagnosis
HPOsFreeText: GAA (MS/MS) enzyme activity at 0.68 umol/hr/L
GenotypingMethod: GAA Gene Sequencing and PCR Amplification
Variant1: NM_000152.4:c.752C>T (p.Ser251Leu)
ClinVar: 325781 https://www.ncbi.nlm.nih.gov/clinvar/variation/325781/
gnomAD: East Asian 2.760e-3, Overall 3.540e-4 http://gnomad.broadinstitute.org/variant/17-78081415-C-T
Variant2: NM_000152.4:c.761C>T (p.Ser254Leu)
ClinVar: 325782 https://www.ncbi.nlm.nih.gov/clinvar/variation/325782/
gnomAD: East Asian 2.759e-3, Overall 1.947e-4 http://gnomad.broadinstitute.org/variant/17-78081424-C-T
Variant3: 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: One Pompe Mutation allele and One Pseudodeficency Mutation allele, Nomenclature shows that Variants 1 and 2 are in cis, 25 other patients share the same genotype
CaseIP2-10: Male, Taiwan, Birth diagnosis
HPOsFreeText: GAA (MS/MS) enzyme activity at 0.09 umol/hr/L, Serum CK at 483 U/L
GenotypingMethod: GAA Gene Sequencing and PCR Amplification
Variant: NM_000152.4:c.1935C>A (p.Asp645Glu)
ClinVar: 4029 https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/
gnomAD: East Asian 1.729e-3, Overall 1.240e-4 http://gnomad.broadinstitute.org/variant/17-78086721-C-A
CaseAddInfo: Infantile Onset Pompe Disease, Patient is homozygous for this variant
CaseOPTPD-77: Male, Taiwan, Birth diagnosis
HPOsFreeText: GAA (MS/MS) enzyme activity at 0.61 umol/hr/L
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
Variant2: NM_000152.4:c.2014C>T (p.Arg672Trp)
ClinVar: 188773 https://www.ncbi.nlm.nih.gov/clinvar/variation/188773/
gnomAD: South Asian 3.355e-5, Overall 8.290e-6 http://gnomad.broadinstitute.org/variant/17-78086800-C-T
CaseAddInfo: One Pompe Mutation allele and Two Pseudodeficency Mutation alleles, Nomenclature indicates patient is homozygous for Variant 1 and Variant 2 is in cis with one copy
17
Case17: Female, 30 years onset, 39 years diagnosis, Italy
HPOsFreeText: See Group Phenotypes, ERT started at 41
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
Paper does not specify what kind of mutation this is. Mentions only that it is a "Loss of transcript" mutation
Variant2: NM_000152.4:c.2331+1
ClinVar: N/A
gnomAD: N/A
CaseAddInfo: Late Onset Pompe Disease
12
Case12: Female, 48 years onset, 58 years diagnosis, Italy
HPOsFreeText: See Group Phenotypes, ERT started at 59, GAA Activity at ~17 pmol/min/mg before ERT and ~19 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.1561G>A (p.Glu521Lys)
ClinVar: 4022 https://www.ncbi.nlm.nih.gov/clinvar/variation/4022/
gnomAD: South Asian 3.266e-5, Overall 3.980e-6 http://gnomad.broadinstitute.org/variant/17-78084749-G-A
CaseAddInfo: Late Onset Pompe Disease
3.1 Description of the study population
Patient6: IOPD Group, 13days old
CasePresentingHPOs:
HPOsFreeText: LDH = 767 U/L, CK = 709 U/L, ALT = 30 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
9
Case#: Patient 9, male
CasePresentingHPOs: HP:0003236, HP:0003325
CaseAddInfo: 48yo at onset, 52yo at diagnosis
Variant: 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
LOPD-13
CaseLOPD-13: 2 weeks diagnosis
HPOsFreeText: GAA activity 2.6 (nmol · h−1 · mg−1), Mean percentage of normal 3.7%
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
Variant2: NM_000152.4:c.2051C>T (p.Pro684Leu)
ClinVar: 285821 https://www.ncbi.nlm.nih.gov/clinvar/variation/285821/
gnomAD: European (Non-Finnish) 1.631e-4, Overall 8.195e-5 http://gnomad.broadinstitute.org/variant/17-78087027-C-T
CaseAddInfo: Late Onset Pompe Disease
LOPD-2
CaseLOPD-2: 2 weeks diagnosis
HPOsFreeText: GAA activity 3.2 (nmol · h−1 · mg−1), Mean percentage of normal 4.5%
GenotypingMethod: Newborn Screening Panels
Variant: 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
CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant
LOPD-6
CaseLOPD-6: 32 years diagnosis
HPOsFreeText: GAA activity 3.6 (nmol · h−1 · mg−1), Mean percentage of normal 5.1%
CaseNotHPOs: HP:0003236 (Increased serum CK)
GenotypingMethod: Newborn Screening Panels
Variant: 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
CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant
PD/Pathogenic-5
CasePD/Pathogenic-5: 4 weeks diagnosis
HPOsFreeText: GAA activity 6.5 (nmol · h−1 · mg−1), Mean percentage of normal 9.1%
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
Variant3: 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
CaseAddInfo: Patient has one pseudodeficency allele and one pathogenic allele, Nomenclature claims Variant 1 and 2 are in cis
LOPD-5
CaseLOPD-5: 2 weeks diagnosis
HPOsFreeText: GAA activity 3.1 (nmol · h−1 · mg−1), Mean percentage of normal 4.4%
GenotypingMethod: Newborn Screening Panels
Variant: 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
CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant
LOPD-1
CaseLOPD-1: 3 weeks diagnosis
HPOsFreeText: GAA activity 3.2 (nmol · h−1 · mg−1), Mean percentage of normal 4.5%
GenotypingMethod: Newborn Screening Panels
Variant: 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
CaseAddInfo: Late Onset Pompe Disease, Patient is homozygous for the above variant
IOPD-4
CaseIOPD-4: 3 min diagnosis
CasePresentingHPOs: HP:0003236, HP:0001638 (Increased serum CK, Cardiomyopathy)
HPOsFreeText: GAA activity 0.6 (nmol · h−1 · mg−1), Mean percentage of normal 0.9%
GenotypingMethod: Newborn Screening Panels
Variant1: NM_000152.4:c.271G>A (p.Asp91Asn)
ClinVar: 4020 https://www.ncbi.nlm.nih.gov/clinvar/variation/4020/
gnomAD: European (Non-Finnish) 0.03291, Overall 0.02049 http://gnomad.broadinstitute.org/variant/17-78078656-G-A
Variant2: NM_000152.4:c.307T>G (p.Cys103Gly)
ClinVar: 92483 https://www.ncbi.nlm.nih.gov/clinvar/variation/92483/
gnomAD: European (non-Finnish) 7.874e-6, Overall 3.578e-6 http://gnomad.broadinstitute.org/variant/17-78078692-T-G
Variant3: NM_000152.4:c.1000G>T (p.Gly334Cys)
ClinVar: 284864 https://www.ncbi.nlm.nih.gov/clinvar/variation/284864/
gnomAD: Not in gnomAD
CaseAddInfo: Infantile Onset Pompe Disease, Nomenclature claims Variant 1 and 2 are in cis
III-10
Subject III-10: female
CasePresentingHPOs:
HPOsFreeText: DBS neutral/acid = 38.1
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: asymptomatic, asserted carrier status
CasePMIDs:
CasePreviousTesting: DBS
CaseGenotypingMethod: GAA genotyping
Variant: NM_000152.4(GAA):c.2560C>T (p.Arg854Ter)
ClinVar: 4034, https://www.ncbi.nlm.nih.gov/clinvar/variation/4034/
gnomAD: 0.0002090, http://gnomad.broadinstitute.org/variant/17-78092070-C-T
20 mg/kg (N = 16)
Case7HPOsFreeText: 20 mg/kg GAA treatment, GAA activity at 14 pmol/punch/hr, GAA activity at 58.3% 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
Variant2: NM_000152.4:c.525delT (p.Glu176Argfs)
ClinVar: 4033 https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/
gnomAD: European (Non-Finnish) 1.880e-4, Overall 9.959e-5 https://gnomad.broadinstitute.org/variant/17-78078909-CT-C
CaseAddInfo:
20 mg/kg (N = 16)
Case13HPOsFreeText: 20 mg/kg GAA treatment, GAA activity at 0.5 mU/U hexosaminid, GAA activity at 17.5% 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
Variant2: NM_000152.4:c.2482_2646del165 (p.Gly828_Asn882del) (Exon 18 del)
ClinVar: 4031 https://www.ncbi.nlm.nih.gov/clinvar/variation/4031/
gnomAD: Not in gnomAD
CaseAddInfo: Patient is heterozygous for these variants
(Supplementary Table S3 shows details, IgG trajectories, and outcomes)
Patient 12 - LOPD - homozygous
Variant: 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
P6a
Patient6: Female, 53yo
CasePresentingHPOs: HP:0000822, HP:0003077, HP:0001513,
HPOsFreeText: LOPD, smoker
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo: 5yr follow-up MRI, 17yr disease duration, ERT lasted for 99mo
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: NM_000152.4(GAA):c.1655T>C (p.Leu552Pro)
ClinVar: 279811, https://www.ncbi.nlm.nih.gov/clinvar/variation/279811/
gnomAD: n/a
c.-32-1G>C
Variant: NM_000152.4:c.-32-1G>C
ClinVar: 557429 https://www.ncbi.nlm.nih.gov/clinvar/variation/557429/
gnomAD: Not in gnomAD
VariantAddInfo: This variant was declared as novel and found in a patient, but no further information was given.
Case6: Male, 65 years report
HPOsFreeText: 8 years of ERT completed, 6 Minute Walking Test at 95 meters, Forced Vital Capacity at 36%
GenotypingMethod: GAA Gene Sequencing
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
Variant2: NM_000152.4:c.2481+102_2646+31del (p.Gly828_Asn882del) (exon 18 del)
ClinVar: 4031 https://www.ncbi.nlm.nih.gov/clinvar/variation/4031/
gnomAD: Not in gnomAD
CaseAddInfo: Late Onset Pompe Disease
PD18
Patient18: Male, Northern China
CasePresentingHPOs:
HPOsFreeText: IOPD
CaseNotHPOs:
NotHPOsFreeText:
CaseAddInfo:
CasePMIDs:
CasePreviousTesting: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000152.4(GAA):c.1935C>A (p.Asp645Glu)
ClinVar: 4029, https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/
gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A
Variant2: NM_000152.4(GAA):c.796C>T (p.Pro266Ser)
ClinVar: 556117, https://www.ncbi.nlm.nih.gov/clinvar/variation/556117/
gnomAD: n/a
NM_002203:c.780-11A>T
Unable to identify variant for following reasons: 1) NM_002203 is for ITGA2 not ITGA2B -- though ITGA2 is listed as the gene for this one so maybe that was intentional 2) c.780 is not at an exon boundary in ITGA2B Mane transcript
C
Case6 14yo diagnosis, Anglo-Celtic
CasePresentingHPOs HP:0001256, HP:0000098
(Mild intellectual disability, Tall stature)
HPOsFreeText Diagnosis was based on tall height and mild intellectual disability. 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:0001083
(Lens dislocation)
NotHPOsFreeText no other seqeulae
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. IVS8+1G>A, compound heterozygous
ClinVar 1. 120, 2. n/a
CAID 2. need more info
gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. n/a
CaseAddInfo n/a
CasePMIDs n/a
28
FamilyLabel Family 28
Family28PresentingHPOs n/a
HPOsFreeText Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Affected individuals were not responsive to the treatment, plasma homocysteine levels went unchanged. Patients were given additional oral betaine(3g twice per day) with a low protein diet.
FamilyNotHPOs n/a
NotHPOsFreeText no further sequelae
CountryOrigin n/a
Ethnicity Lebanese
Race n/a
Family28PreviousTesting 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 34
Variant NM_000071.2(CBS):c.19dupC (p.Gln7Profs), homozygous
ClinVar 371345
gnomAD MAF=0.00005473, no homozygotes
FamilyAddInfo n/a
FamilyPMIDs n/a
1622ins
the Asn541 from allele registry and mutalyzer confused me.
However, there cannot be an Asn542 as there is no Asn542 in the refseq. Asn542 is created when you insert TGAA, that is true, but the HGVS tracks the most immediate change on the refeq which is actually the Asn541.
It was also weird that mutalyzer and allele registry didn't take insTGAA, but only used insA. I wrote out the refseq, the refseq with TGAA inserted and the refseq with just A inserted. Sure enough, Asn541 is the most immediate change and the frameshift is the same "...LRGRP...stop" whether you insert TGAA or just A. Not too surprising since you are still in-frame after adding 3 bases, but cool to check.
interesting!
5
FamilyLabel Family 5
Family5PresentingHPOs 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
Family5PreviousTesting 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 7
Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. IVS1+insC, compound heterozygous
ClinVar 1. 120, 2. n/a
CAID 2. need more info
gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. n/a
FamilyAddInfo n/a
FamilyPMIDs n/a
OS-127 II-1
CaseOS-127_II-1: Male, Birth onset, Germany
CasePresentingHPOs: HP:0001992, HP:0410145 (Organic aciduria, Decreased biotinidase activity)
HPOsFreeText: N/A
CaseNotHPOs: HP:0001263 (Global developmental delay)
NotHPOsFreeText: N/A
CaseAddInfo: Parents are non-consanguineous and healthy; Proband is confirmed homozygous via parental testing
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; Biotinidase deficiency treated via 5 mg biotin/d
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.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
K1
CaseK1 Female, 12yr report, Bosnian
CasePresentingHPOs HP:0001557, HP:0025116, HP:0001941, HP:0002098, HP:0003270, HP:0002013, HP:0001290, HP:0000750, HP:0011344, HP:0002069, HP:0002305, HP:0001290, HP:0002059, HP:0004881
(Abnormal intrauterine movements, Fetal distress, Acidosis, Respiratory distress, Abdominal distension, Vomiting, Hypotonia, Speech delay, Severe GDD, Grand mal seizures, Athetosis, Hypotonia, Cerebral atrophy, Episodic hypoventilation)
HPOsFreeText born at 42wk gestation. (neonatal, pre-treatment:) apgar score at 1min:7, 5min:8, 10min:8, acidosis, respiratory distress, abdominal distension, vomiting, onset of fits at 2d, resistant to ACD's. (18mo:) introduced to pyridoxine therapy, trial dose/route of 60mg oral, complete cessation of seizures, no apnoea or hypotonia/sleepiness, initial maintenance dose of 800mg. (infancy/childhood:) recurrence of seizures with febrile illness, hypotonia, speech delay/difficulties, severe IQ delay. 1wk after withdrawal from pyridoxine trial at 7y, grand mal seizures recurred(definite PDE).
CaseNotHPOs HP:0000486
(Squint)
NotHPOsFreeText (infancy/childhood:) squint
CasePreviousTesting Administration of pyridoxine relieved patient's seizures. plasma pipecolic acid: 12(nv<2.5μM), plasma AASA: 1.5(nv<0.2μM), urine AASA: 7.5(nv<1 mmol/mol creatinine). Blood lactate: 5.4mM and CSF lactate: 4.4mM (nv <2.5mM). (PMID:17068770:)post treatment testing: Pipecolic acid in plasma 6.7(nv 0.7-2.6mmol/liter), AASA in plasma 0.9(nv<0.2mmol/liter), urine AASA 19(nv<1mmol/molcreatinine).
Variant NM_001182.4(ALDH7A1):c.328C>T (p.Arg110Ter), homozygous
ClinVar 17995
gnomAD MAF=0.0001385(Other), no homozygotes
CaseAddInfo parental consanguinity
CasePMIDs 10894227 (Patient 3...), 17068770 (Patient 8)
family S
FamilyLabel Family S
FamilySPresentingHPOs HP:0002098, HP:0010818, HP:0002280
(Respiratory distress, Generalized tonic seizures, Mega cisterna magna)
HPOsFreeText (neonatal, pre-treatment:) respiratory distress, generalised tonic seizures. (infancy/childhood:) mega cisterna magna
FamilyNotHPOs n/a
CountryOrigin n/a
Ethnicity Arabic
Race n/a
FamilySPreviousTesting Cessation of seizures during pyridoxine therapy
ProbandLabel S1, Female, 15yr report
Variant NM_001182.4(ALDH7A1):c.312+2T>A, homozygous
ClinVar 17997
gnomAD not in gnomAD
FamilyAddInfo parental consanguinity
FamilyPMIDs n/a
Patient KM03
Case#: KM03, F, neonatal (onset), Japanese
CasePresentingHPOs: HP:0001254, HP:0002179, HP:0001276, HP:0001263 (Lethargy, Opisthotonus, Hypertonia, Global developmental delay)
HPOsFreeText: Diagnosed at the time of newborn screening. Originally presented as classical form, but later determined to be the intermittent form.
CaseNotHPOs:
CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity: 0.12 nmol/h per mg of protein (~9% of control). The authors previously showed by immunoblot analysis that the level of E2 protein was significantly reduced (PMID 3417306).
CaseMethod1: PCR
CaseMethod2: Sequencing
CaseGenotypingMethod: Total RNA and genomic DNA prepared from lymphoblastoid cells or peripheral leukocytes. RT-PCR was performed with primers in exons 8 and 9 identified an insertion. Gnomic DNA was isolated and sequenced. Confirmed by restriction enzyme digestion.
Variant: NM_001918.3:c.1018-550A>G (homozygous)
ClinVar: 11946
gnomAD: Not in gnomAD
VariantEvidence: The predicted mRNA encoded a truncated protein with 282 amino acids, including 4 novel amino acids at the carboxyl terminus. 265bp fragment that included the 126 bp intronic region was subcloned into an exon trapping vector and transfected into COS-1 cells to confirm the splicing defect.
CaseAddInfo: Consanguineous, parents were heterozygous.
CasePMIDs: 3417306
Case Report
CaseAD: Male, 5 yrs onset
CasePresentingHPOs: HP:0000750, HP:0002572, HP:0012537, HP:0001944, HP:0001649, HP:0002789, HP:0001252, HP:0001942, HP:0001987, HP:0002919, HP:0012120 (Delayed speech and language development, Episodic vomiting, Food intolerance, Dehydration, Tachycardia, Tachypnea, Muscular hypotonia, Metabolic acidosis, Hyperammonemia, Ketonuria, Methylmalonic aciduria)
HPOsFreeText: Frequent catabolism episodes with vomiting were noticed without decompensation
CaseNotHPOs: HP:0001270, HP:0001919, HP:0011015 (Motor delay, Acute kidney injury, Abnormal blood glucose concentration)
NotHPOsFreeText: Propionyl-CoA carboxylase activity was within normal ranges in fibroblasts
CaseAddInfo: Parents are non-consanguineous with no family history, Dietary restriction and supplementation showed amelioration of symptoms
CasePreviousTesting: Normal ECG and MRI results; Metabolic acidosis (pH = 7.08, bicarbonates = 7.3 mmol/L, normal lactic acid, PCO2 = 25 mmHg) and hyperammmoniemia (100 µmol/L) present; Large increase in plasmatic propionylcarnitine (17.5 µmol/L; N < 0.75), undetectable methylmalonylcarnitine, and high urinary excretion of 3-hydroxypropionate and methylcitrate
CaseGenotypingMethod: Next-generation sequencing in the proband revealed a homozygous nonsense founder variant in the MCEE gene.
Variant: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)
ClinVar: 2343, http://www.ncbi.nlm.nih.gov/clinvar/variation/2343
gnomAD: 0.0004884, https://gnomad.broadinstitute.org/variant/2-71351575-G-A
1
Case# Pat1, M, Chinese, 3day onset
CasePresentingHPOs HP:0008344, HP:0008872, HP:0001250, HP:0001276, HP:0001279, HP:0001263
CaseNotHPOs HP:0002013
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.853+1delG ?
Case 2
Case#: 2, female 4 days (onset), 4 y 3 mo (current), Chinese
CasePresentingHPOs: HP: 0008344, HP: 0012088, HP: 0011968, HP: 0001276, HP: 0001941, HP: 0002543, HP: 0011342 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, hypertonia, acidosis, abnormal globus pallidus MRI signals, mild global developmental delay)
HPOsFreeText: Poor response to light and sound, abnormal MRI signals in frontal lobes, Blood ammonia: 95 uM, Hemoglobin: 117 g/L, Leucin: 745.01 uM, Valine: 526.40 uM, Isoleucine: 181.06 uM, Alloisoleucine: 69.45 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo:
CasePreviousTesting: n/a
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000709.3(BCKDHA): c.659C>T (p.Ala220Val)
ClinVar: 93367
CAID: n/a (because this doesn't need to be included if it is in ClinVar right?)
gnomAD: not in gnomAD
Results
NonPatientCell: E-Coli (DH5α)
GeneFunction: GO:0006559
GeneAlteration: PAH cDNA was cloned into a pMAL-c2E expression vector encoding an N-terminal MBP tag and an enterokinase cleavage site. PAH mutants were constructed using site-directed mutagenesis and confirmed using DNA sequencing. Both the wild-type and the 10 mutant vectors were transformed into E. coli DH5α via overexpresion of fusion proteins at midexponential phase. The proteins were purified and concentration was determined.
FunctionalEvidence: Expression of the 10 mutant proteins compared to the wild-type demonstrated that several of these mutants induce protein destabilization and subsequent loss of function. Upon deconvolution analysis, five variants showed significanly distrubed oligomerization and a preponderance to misfold and form high-molecular-weight protein aggregates. Enzyme kinetic parameter analysis demonstrated moderate reduction in PAH activity and severely affected allostery in all but one mutation, indicating the strong possibility of global confirmational changes. Protein confirmation was tested by limited proteolysis with proteinase K with six out of eight tested mutants decreasing the half-life of the protein by >50% and decreased stability in five out of eight. Thermal protein denaturation was analyzed by fluorescence and demonstrated that all of the mutations led to substantial distortion of the protein's confirmation and/or loss of structural integrity compared to the wild-type, especially those in the regulatory domain. Finally, amino acid replacements were shown to disrupt local networks of amino acid interactions and alter the normal oligomeric state and therfore the function of the protein.
FAVariant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)
ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/
FAVariant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)
ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/
FAVariant3: NM_000277.3(PAH):c.165T>G (p.Phe55Leu)
ClinVar: 92734 https://www.ncbi.nlm.nih.gov/clinvar/variation/92734/
FAVariant4: NM_000277.3(PAH):c.1249T>C (p.Tyr417His)
ClinVar: 102579 https://www.ncbi.nlm.nih.gov/clinvar/variation/102579/
FAVariant5: NM_000277.3(PAH):c.940C>T (p.Pro314Ser)
ClinVar: 102905 https://www.ncbi.nlm.nih.gov/clinvar/variation/102905/
43
Case40 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 84(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 312(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 R161Q variant destroys an AciI restriction site. Thus, while the patient's DNA fragments would not be cleaved, control fragments would be cleaved. The 848del variant creates a MspI site. This would lead to cleaved patient fragments and uncleaved control fragments.
Variant 1. NM_000159.3(GCDH):c.482G>A (p.Arg161Gln), 2. NM_000159.3(GCDH):c.848delT (p.Leu283Argfs), compound heterozygous
gnomAD 1. MAF=0.0001384(Other), no homozygotes, 2. MAF= 0.0003331(Other), no homozygotes
CaseAddInfo n/a
CasePMIDs n/a
6, 7
Case6 unknown sex, Spain
CasePresentingHPOs HP:0000707
(Neurological abnormality)
HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. 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 500(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 461(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.
Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous
ClinVar 2083
gnomAD MAF= 0.0004013(African), no homozygotes
CaseAddInfo Sibling (Case 7) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 3200mmol/mol creatinine and 3-OH-glutarate was 843mmol/mol creatinine.
CasePMIDs n/a
4, 5
Case4 sex unknown, Spain
CasePresentingHPOs HP:0001332
(Dystonia)
HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.
CaseNotHPOs HP:0002540
(Non-ambulatory)
NotHPOsFreeText n/a
CasePreviousTesting GC-MS measured glutarate of 4135(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 752(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 5) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 2166mmol/mol creatinine and 3-OH-glutarate was 420mmol/mol creatinine.
CasePMIDs see note on previous studies
20
Case20 sex unknown, Spain
CasePresentingHPOs HP:0001332
(Dystonia)
HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.
CaseNotHPOs HP:0002540
(Non-ambulatory)
NotHPOsFreeText n/a
CasePreviousTesting GC-MS measured glutarate of 3571(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 232(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 R132Q variant destroys an AciI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.
Variant 1. NM_000159.3(GCDH):c.395G>A (p.Arg132Gln), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous
gnomAD 1. not in gnomAD, 2. MAF= 0.00005646(Latino), no homozygotes
CaseAddInfo n/a
CasePMIDs n/a
32
Case32 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 69(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 429(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 3.
CaseMethod1 SSCP
CaseMethod2 Sanger
CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.
Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous
gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes
CaseAddInfo n/a
CasePMIDs n/a
5
Case5 Female, 24yo report, USA, Lumbee
CasePresentingHPOs HP:0001344, HP:0002540, HP:0003150
(Nonverbal, Non-ambulatory, Glutaricaciduria)
HPOsFreeText Urine glutaric acid was highly elevated and 3-hydroxyglutaric acid was elevated. Patient presented with acute metabolic decompensation at 2yo and feeds by mouth. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.
CaseNotHPOs n/a
NotHPOsFreeText n/a
CasePreviousTesting n/a
CaseMethod1 PCR
CaseMethod2 Sanger
CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.
Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous
ClinVar 167133
gnomAD MAF=0.0002017(African), no homozygotes
CaseAddInfo nonconsanguineous
CasePMIDs n/a
Case#: Patient 5, Japanese, 8 years old (report) CaseHPOs: Hyperornithinemia
CaseHPOsFreeText: (From Hayasaka et al. 1981; PMID 7260021, Patient 2). First noted visual problems at age 5 years, glasses prescribed for myopia. Evaluation for night blindness at age 8. Best corrected visual acuity was RE 04 with correction of myopia (-8 D), LE 04 with correction of myopia (-10 D). Typical chorioretinal atrophy with scallop margins at the peripheral fundus and an abnormal reflex in the macular area. Concentric constriction of visual fields. Dark adaptation curve was monophasic. ERG was subnormal, and the electro-oculogram was flat. The ciliary processes were normal by cycloscopy. Not responsive to Vitamin B6.
CaseNotHPOsFreeText: Normal lens
CasePreviousTesting: Serum ornithine 12.95 mg/dl (normal 0-36-1-56). OAT activity was not detectable in cell extracts from skin fibroblasts. CaseAddInfo: No consanguinity reported CaseMethod1: PCR
CaseMethod2: Sequence analysis
CaseGenotypingMethod: DGGE and sequence analysis of genomic DNA was carried out to identify the variant on the other allele. Variant: NM_000274.3(OAT):c.1276C>T (p.Arg426Ter)
ClinVar: 177
gnomAD: Maximum population minor allele frequency = 0.00002893 (Latino); no homozygotes in any population.
ee
CaseKLC2: Male, 32 yrs death, Japan, Asian
CasePresentingHPOs: HP:0001249, HP:0002078, HP:0000651, HP:0008353, HP:0000992 (Intellectual disability, Truncal ataxia, Diplopia, Neutral hyperaminoaciduria, Cutaneous photosensitivity)
HPOsFreeText: Monoamino-monocarboxylic aciduria
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Parents are first-cousin consanguineous, Max LOD score is 2.1 for family
CasePreviousTesting: Defects in the intestinal absorption of monoamino-monocarboxylic acids determined by oral loading; Urine analyses confirmed the absence of hyperaminoaciduria in the mother (III-4), father (III-5) and the younger brother (IV-3), Brother of proband
CaseGenotypingMethod: DNA was isolated from peripheral blood samples and from liver samples collected at autopsy. A genome-wide screen with 343 different markers was carried out and linkage analysis performed using homozygosity mapping. Both SLC6A18 and SLC6A19 were investigated for possible pathogenicity, with SLC6A19's pattern of expression supporting it as a primary candidate. Intronic primers were used to bidirectionally sequence each exon and flanking intronic regions, locating a homozygous frameshift mutation that perfectly segregated with the phenotype.
CasePMIDs: 2582682, 11394870
Variant: NM_001003841.3(SLC6A19):c.882_883TG1
ClinVar: 2018 https://ww.ncbi.nlm.nih.gov/clinvar/variation/2018/
gnomAD: 0.000008900, https://gnomad.broadinstitute.org/variant/5-1214174-CTG-C?dataset=gnomad_r2_1
Patient 4
Case4 sex unknown, Netherlands, Dutch
CasePresentingHPOs HP:0001250, HP:0002194
(Seizures, Delayed motor skills)
HPOsFreeText Seizures ceased upon administration of pyridoxine. (PMID:16159904:) 1st seizure at 8do, first administered pyridoxine(and age at trial) 2mo, initial dose:100mg, maintenance dose:100mg/day, mildly affected motor skills. (PMID:17088338:) Definite="recurrent (two or more) seizures of any type that cease within seven days of the administration of oral pyridoxine (usual dose, 30 mg/ kg/day; minimum dose, 15 mg/kg/day; maximum dose, 1000 mg/kg/day) or within 30 minutes of intravenous pyridoxine (usual dose, 100 mg; minimum dose, 50 mg), that recur when pyridoxine supplementation is withdrawn, and that cease again when pyridoxine is given as above"
CaseNotHPOs n/a
NotHPOsFreeText intrauterine seizures
CasePreviousTesting PDS confirmed metabolically: α‐AASA urine 4.0(nv <1mmol/mol cr), α‐AASA plasma 1.1(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 7.0(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk)
Variant NM_001182.4(ALDH7A1):c.834G>A (p.Val278=)
ClinVar 18002
gnomAD not in gnomAD(C and not G at that position?)
CaseAddInfo Metabolic testing of sibling(Patient 6, heterozygous for the p.Val278= variant): α‐AASA urine 0.2(nv <1mmol/mol cr), α‐AASA plasma <0.2(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 2.2(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk), but was not metabolically confirmed for PDS, development was also normal
CasePMIDs 17088338 , 16159904
The variant p.Y403N is located in the turn region adjacent to the alpha helix where hydrogen bond formations are more favourable (Fig. 4). The absence of this variant in 200 normal chromosomes, the clinically severe phenotypes in the two patients, the abnormal biochemical and organic acid profiles (Table 1), and the computational prediction (Figs 3 and 4 and Table 3) suggest a potential genotype–phenotype correlation for this variant.
Variant 1: NM_002225.3:c.1207T>A
Variant 2: NM_002225.4(IVD):c.863C>T
VariantEvidence: This variant is located in the turn region next to the alpha helix where hydrogen bonding is favorable, this location along with the presentation of severe phenotypes and biochemical profiles in the patients harboring these variants suggests a genotype-phenotype correlation (fig. 4)
Table 2
Case11a: Male, Sweden
CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0002804 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Arthrogryposis)
HPOsFreeText: N/A
CaseNotHPOs: HP:0001627 (Cardiac abnormality)
NotHPOsFreeText: N/A
CaseAddInfo: Severe congenital myopathy, Deceased in 5 months
CasePreviousTesting: N/A
CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.
Variant: NM_198271.4:c.1069G>T (p.Glu357Ter)
ClinVar: 162219 https://www.ncbi.nlm.nih.gov/clinvar/variation/162219/
gnomAD: Not in gnomAD
P17
FamilyPY: White, United Kingdom
FamilyPresentingHPOs: HP:0002131, HP:0001260, HP:0008003, HP:0030453 (Episodic ataxia, Dysarthria, Jerky ocular pursuit movements, Abnormal visual electrophysiology)
HPOsFreeText: N/A
FamilyNotHPOs: HP:0000640, HP:0000648, HP:0003390, HP:0011402, HP:0001272, HP:0002283 (Gaze-evoked nystagmus, Optic atrophy, Sensory axonal neuropathy, Demyelinating sensory neuropathy, Cerebellar atrophy, Global brain atrophy)
NotHPOsFreeText: N/A
FamilyGenotypingMethod: Blood genomic DNA was enriched and whole exome sequenced. Alightment to hg19 and variant filtering was performed with putative pathogenic variants being confirmed via Sanger sequencing.
FamilyPreviousTesting: Underwent brain MRI and CSF examination with oligoclonal band analysis; Negative genetic testing for SCA1, 2, 3, 6, 7, 17 (now known as ATXN1, ATXN2, CACNA1A, ATXN7, and TBP, respectively), DRPLA (now known as ATN1), FA (now known as FXN) and FMR1
FamilyAddInfo: N/A
Variant: NM_004172.5(SLC1A3):c.1496G>A (p.Arg499Gln)
ClinVar: 242994, https://www.ncbi.nlm.nih.gov/clinvar/variation/242994/
gnomAD: 0.0001471, https://gnomad.broadinstitute.org/variant/5-36686238-G-A
Affected: 3
Segregations: 2
AddSegregationInfo: Pedigree in Sup Data, Not enough info provided
Subject C
CaseGuC: Male, 5 days onset
CasePresentingHPOs: HP:0200134, HP:0011153, HP:0010850, HP:0011199, HP:0001252, HP:0003487, HP:0003423, HP:0010864, HP:0011344, HP:0002188, HP:0002059 (Epileptic encephalopathy, Focal motor seizure, EEG with spike-wave complexes, EEG with generalized sharp slow waves, Muscular hypotonia, Babinski sign, Thoracolumbar kyphoscoliosis, Severe intellectual disability, Severe global developmental delay, Delayed CNS myelination, Cerebral atrophy)
HPOsFreeText: Multiple seizure types, Bilateral T2 prolongation in caudate heads and putamina
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Variant is confirmed heterozygous de novo
CasePreviousTesting: Investigations include electroencephalography (EEG), head MRI, neurometabolic testing, and chromosome microarray; Individuals with self-limiting benign electroclinical syndromes, such as childhood absence epilepsy (onset > 4 years), were excluded; Head circumference was 44 cm at 4 months (91st percentile); Partial response to ketogenic diet and phenytoin, no response to other antiseizure medications;
CaseGenotypingMethod: Variants within co-expressed candidate genes in Table S1 were extracted from exome sequencing data. Variants were annotated and were verified with Sanger sequencing of the proband and parents.
Variant: NM_004171.4(SLC1A2):c.866C>G (p.Pro289Arg)
ClinVar: 438737, https://www.ncbi.nlm.nih.gov/clinvar/variation/438737/
gnomAD: Not in gnomAD
III4/F
Case# FIII.4, F, 19 day old diagnosis, Cyprus (Greek Cypriot)
CasePresentingHPOs HP:0010910, HP:0010911, HP:0010913, HP:0001254, HP:0011968, HP:0001290, HP:0001276, HP:0002789, HP:0002353,
HPOcont: Hypervalinemia, Hyperleucinemia, Hyperisoleucinemia, Lethargy, Poor feeding, Hypotonia, Hypertonia, Tachypnea, Abnormal EEG
HPOfreetext: Reduced alloisoleucine and grunting
CasePreviousTesting Tested blood BCAA (AIleu: 0, Ileu: 220 (NR: 26–100), Leu: 3270 (NR: 65–220), Val: 459 (NR: 90–300), urine organic acids (Increased:lactate, 2-keto-glutarate, 2-keto-isocaproic, 2-OH-isovaleric, 2-keto-isovaleric, 2-keto-3-methylvaleric, 4-OH-phenylacetate, 4-OH-phenylpyruvate and BCKD activity (0.03(NR: 0.4–3.4) (Fibroblasts))
CaseMethod1 PCR
CaseMethod2 Direct Sequencing
CaseGenotypingMethod Direct sequencing repeated on proband and father for deletion varaint
Variant (1) NM_000709.3(BCKDHA):c.632C>T (p.Thr211Met) (2) NM_000709.3:c.718delG
ClinVar (1) 93365
CAID (2) register link if I put that in correctly
gnomAD (1) 0.0001163(East Asian), 0.00002043 (Overall)
CaseAddInfo nonconsanguineous
Individual 1
Case1: Female
CasePresentingHPOs: HP:0011343, HP:0012072, HP:0007018 (Moderate global developmental delay, Aciduria, Attention deficit hyperactivity disorder)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Parents are non-consanguineous, Unremarkable family history, Variants are parentally confirmed with c.2185 G>A apparently de novo
CasePreviousTesting: At 2 yrs had elevated 2-oxoadipate (range = 10–120 mmol/mol creatinine) and 2-hydroxyadipate (range = 5–40 mmol/mol creatinine) in urine (Reference 0 mmol/mol creatinine); Elevated 2-aminoadipate (120 μmol/l); Moderate protein restriction did not influence disease course and was discontinued, Serial cranial magnetic-resonance-imaging studies showed no morphological abnormalities; Neuropsychological testing at 8 years revealed an IQ of 117; Symptoms improved after implementation of methylphenidate and at 14 is clinically normal; No mutation detected in ODC
CaseGenotypingMethod: Whole exome sequencing was performed to identify mutations responsible for the biochemical abnormality. Exonic sequences were enriched and sequenced with data analysis being used to filter according to inheritance and low allele frequencies in controls. This narrowed down to eight different genes (ADAMTS10, AIRE, C8orf38, DHTKD1, OVOS2, CAMTA2, LPPR3, and RADIL) of which three had been associated with unrelated phenotypes and only one other had predicted pathogenic variants, DHTKD1.
Variant1: NM_018706.7(DHTKD1):c.1A>G (p.Met1Val)
ClinVar: 39563 https://www.ncbi.nlm.nih.gov/clinvar/variation/39563/
gnomAD: Not in gnomAD
Variant2: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)
ClinVar: 39564 https://www.ncbi.nlm.nih.gov/clinvar/variation/39564/
gnomAD: 0.002748, https://gnomad.broadinstitute.org/variant/10-12154929-G-A
3.1.1. Patient 1
CaseFI1: Female, Tunisia, 18 months report
CasePresentingHPOs: HP:0001511, HP:0001508, HP:0001263, HP:0001249, HP:0001337, HP:0000325, HP:0000272, HP:0000303, HP:0000411, HP:0007495, HP:0000518, HP:0000963, HP:0000973, HP:0100678, HP:0012785, HP:0004220, HP:0009162, HP:0010107, HP:0002827, HP:0002808, HP:0001252, HP:0008619, HP:0001629, HP:0001684, HP:0001643, HP:0005301, HP:0003572, HP:0005961, HP:0025082, HP:0030774 (Intrauterine growth retardation, Failure to thrive, Global developmental delay, Intellectual disability, Tremor, Triangular face, Malar flattening, Mandibular prognathia, Protruding ear, Prematurely aged appearance, Cataract, Thin skin, Cutis laxa, Premature skin wrinkling, Flexion contracture of finger, Short middle phalanx of the 5th finger, Absent middle phalanx of 5th finger, Short proximal phalanx of hallux, Hip dislocation, Kyphosis, Muscular hypotonia, Bilateral sensorineural hearing impairment, Ventricular septal defect, Secundum atrial septal defect, Patent ductus arteriosus, Persistent left superior vena cava, Low plasma citrulline, Hypoargininemia, Abnormal cutaneous elastic fiber morphology, Mitochondrial swelling)
HPOsFreeText: Weight: 1770 g (< 3rd percentile); length: 39 cm (< 3rd percentile); OFC: 31 cm (< 3rd percentile); Hand and foot malformations; First metacarpal was bowed bilaterally; Serum Ornithine at 23 μmol/l (ref 21–77), Serum Citrulline at 3 μmol/l (ref 27–43), Serum Arginine at 39 μmol/l (ref 49-129), Serum Proline at 105 μmol/l (ref 71-303), Serum Glutamate at 61 μmol/l (ref 8-64), Serum Aspartate at 8 μmol/l (ref <14)
CaseNotHPOs: HP:0002305, HP:0012443, HP:0009832 (Athetosis, Abnormality of brain morphology, Abnormal distal phalanx morphology of finger)
NotHPOsFreeText: Urinary organic acids, oligosaccharides, purines and pyrimidines were normal
CaseAddInfo: Parents are first-degree cousins, Deletion leads to a frameshift and a premature termination codon
CasePreviousTesting: A skin biopsy was taken and amino acid profiles were analyzed from plasma according to standard procedures
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 no result for Exon 15. To confirm if a deletion was responsible, copy number analysis by qPRC was performed with Exon 15 showing a dramatic decrease in signal compared to the others in the affected individual suggesting a homozygous deletion. The parents showed a 50% reduction suggesting a heterozygous phase for the deletion. Different primer combinations allowed for confirmation of the breakpoints with a microdeletion of exon 15 and flanking intronic sequence (1522 bp) with a guanosine insertion.
Variant: NM_002860.4(ALDH18A1):c.1802-2_1924-901del
ClinVar: 156547 https://www.ncbi.nlm.nih.gov/clinvar/variation/156547/
gnomAD: Not in gnomAD
ID no. 817
Case817: Female, 7 years report, Spain
CasePresentingHPOs: HP:0003153, HP:0002345, HP:0002174 (Cystathioninuria, Action tremor, Postural tremor)
HPOsFreeText: Elevated urine cystathionine (1916 umol/g creatine; reference <46), Normal plasma tHcys (3.5 umol/l; reference <7.5), Post treatment normal urine cystathionine (24 umol/g creatine)
CaseNotHPOs: HP:0003345, HP:0001249 (Glutathione synthetase deficiency, Mental retardation)
NotHPOsFreeText: N/A
CaseAddInfo: Patient is homozygous for this variant
CasePreviousTesting: Karyotype, magnetic resonance imaging, specific genetic tests for neurogenetic diseases and screening for inborn errors of metabolism (lactate, pyruvate, ammonium, uric acid, amino acids, organic acids, glycosaminoglycanes, creatine and guanidinoacetate, purines and pyrimidines, and isoelectric focusing pattern of transferrin), as well as folate, pyridoxine and cobalamine deficiencies, neural tumors and genetically determined homocystinurias, were all ruled out.
CaseGenotypingMethod: All twelve exons of the CTH gene and the intronic flanking sequences of the subjects and their parents was PCR amplified and directly sequenced.
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
F-22
CaseF-22 male, 5do onset, Ethinicity: North Indian, Muslim
CasePresentingHPOs HP:0006846, HP:0001254, HP:0011968, HP:0001250, HP:0001987, HP:0001946, HP:0045045, HP:0003571
(Acute encephalopathy, Lethargy, Poor feeding, Seizures, Hyperammonemia, Ketosis, Elevated acylcarnitines, Propionicacidemia)
HPOsFreeText Serum ammonia 700micromolar
CaseNotHPOs n/a
CasePreviousTesting Also screened for variants in PCCA
Variant NM_000532.4(PCCB):c.183+5G>A
ClinVar 217896
gnomAD MAF= 0.00003328(South Asian), no homozygotes
CaseAddInfo consanguineous, no abnormality in family history noted
CasePMIDs n/a
The retrieved soluble fraction of mutated GNMT lacked measurable enzymatic activity
VariantEvidence: Expression of recombinant GMT was performed in E. coli. Firstly, the wild-type protein showed high solubility compared to the mutant of which only a minor fraction was soluble. Furthermore, enzyme activity was measured and the mutant GMNT lacked any activity while the wild-type exibits activity of >200 pmol/min/ug.
Variant: NM_018960.4:c.296G>A (p.Arg99His)
Proband II.1
CaseII-2: Female, Turkey
CasePresentingHPOs: HP:0001558, HP:0000337, HP:0045075, HP:0000463, HP:0000343, HP:0000278, HP:0000470, HP:0000767, HP:0002375, HP:0002033, HP:0006829 (Decreased fetal movement, Wide forehead, Sparse eyebrow, Anteverted nares, Long philtrum, Retrognathia, Short neck, Pectus excavatum, Decreased spontaneous movement, Poor suck, Severe muscular hypotonia)
HPOsFreeText: Birth weight was 2050 g and length was 43 cm, Absent Moro reflex, Required ventilator support from birth
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Born with fractures of the right humerus and left femur
CasePreviousTesting: N/A
CaseGenotypingMethod: Whole blood smaples were obtained from the parents and the probands and DNA was extracted. WES was performed on II-2, with the results being sequenced and filtered for pathogenicity. Once the LMOD3 variant was detected, PCR amplification and Sanger sequencing was used to amplify exon 1 and confirm the results.
Variant: NM_198271.4:c.138dup (p.Ser47Glnfs*13)
ClinVar: 162215 https://www.ncbi.nlm.nih.gov/clinvar/variation/162215/
gnomAD: European (Non-Finnish) 8.879e-6, Overall 8.049e-6 https://gnomad.broadinstitute.org/variant/3-69171399-T-TG
six
CaseSA6P: Male, 7 months onset, European
CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001250, HP:0001987 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Seizures, Hyperammonemia)
HPOsFreeText: N/A
CaseNotHPOs: N/A
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
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FamilyST-VII: Iran
FamilyPresentingHPOs: HP:0002197, HP:0000316, HP:0001889 (Generalized-onset seizure, Hypertelorism, Megaloblastic anemia)
HPOsFreeText: N/A
FamilyNotHPOs: HP:0002904, HP:0001410, HP:0001943, HP:0001257, HP:0001347, HP:0001251, HP:0001276 (Hyperbilirubinemia, Decreased liver function, Hypoglycemia, Spasticity, Hyperreflexia, Ataxia, Hypertonia)
NotHPOsFreeText: N/A
FamilyGenotypingMethod: See Group
FamilyPreviousTesting: See Supp Info for methionine/transaminase values; Normal height, weight and head circumference at birth
FamilyAddInfo: Family is consanguineous, Family is homozygous for this variant
Variant: NM_006721.4(ADK):c.1022A>G (p.His341Arg)
ClinVar: 265772, https://www.ncbi.nlm.nih.gov/clinvar/variation/265772/
gnomAD: Not in gnomAD
Affected: 2
Unaffected: 0
Segregations: 1
AddSegregationInfo: Not enough info
PD
Case#: PD, 44 years, female
CasePresentingHPOsFreeText: apo-B plasma levels <5% of normal; total cholesterol 2.57 (normal range 4-6.5 mmol/l), triglyceride 0.59 (normal range 0.3-1.8 mmol/l), apoB 17 (normal range 60-140 mg/dl).
CasePreviousTesting: On Western blot a truncated species of apo-B was found in the VLDL/chylomicron fraction (fig. 3), predicted based on size to be at the 5’ end of exon 26. The protein was absent from the HDL or infranate fractions.
CaseGenotypingMethod: Genomic DNA was digested with a panel of restriction enzymes and Southern blotted. Based on truncated apoB size (detected on Western blot), the variant was predicted to be at the end of exon 26. Approximately 1.7 kb of genomic DNA including exon 26 was amplified by the polymerase chain reaction (PCR), cloned into M13, and sequenced.
Variant: NM_000384.3(APOB):c.5463del (p.His1822fs), heterozygous
ClinVar: 17882
gnomAD: 0.000008797 (European non-Finnish)
Figure 5.
RescueModel Mus Musculus
GeneAlteration knock-in strain was generated by homologous recombination of the targeting vector with 129Sv/J embryonic stem cells genome. A 450-bp DNA segment encompassing 5′ UTR and exon 1 of the CASQ2 was used to screen RPCI-21 PAC mouse genomic library. Positive clones were sequenced to define the structure of an 8.5-Kb region encompassing promoter, exon 1, and part of intron 1 of mouse CASQ2. This region was cloned in 3 parts and assembled into the targeting vector pFlrt (supplemental Figure I). The linearized targeting vector was electroporated into 129Sv/J embryonic stem cells. The clone selected with G418 and gancyclovir was injected into C57BL/6NCrL blastocyts and transferred to pseudopregnant CD-1 females. Genotype was determined by sequencing of DNA extracted from tail biopsy specimens (DNasy Tissue Kit, Qiagen).
RescueVariant murine cardiac CASQ2 , WT?
RescuePhenotype HP:0004756
RescueMethod The AAV recombinant virus (AAV9-CASQ2) and the empty virus (AAV9-GFP) were produced by the AAV Vector Core of the Telethon Institute of Genetics and Medicine (Napoli, Italy) according to a previously published protocol.18 The viral titer was 2.6×1012 genome copies per milliliter for AAV9-CASQ2 and 4.3×1012 genome copies per milliliter for AAV9-GFP. The infection was performed by intraperitoneal injection in pups on postnatal day 3 (100 μL), which recovered until euthanasia was performed at 6, 9, or 12 months. Three-month-old mice were anesthetized with Avertin (0.025 mg/kg), and viral particles (200 μL) were injected into the tail vein and studied 2 months later. ECG recordings in mice of either sex were performed with implantable loop recorders (Data Sciences International).
RescueEvidence (Fig.5&8) Epinephrine/Isoprenol administration had lead to diminished incidence of VT in CASQ infected mice vs R33Q mice.
ModelVariant NM_001232.3(CASQ2):c.97C>T (p.Arg33Ter), ClinVar: 41043
Pedigrees
FamilyLabel UM Family 2
FamilyUM2PresentingHPOs HP:0012125 (Prostate Cancer)
FamilyNotHPOs n/a
CountryOrigin n/a
Ethnicity n/a
Race n/a
FamilyUM2PreviousTesting Screened nonsense and missense variants in 202 candidate genes comprising ~15.5Mb. Established evidence of linkage of 17q21-22.
Affected 3
Unaffected 1
Segregations n/a
PublishedLOD n/a
eLOD n/a
AddSegregationInfo One female typed negative(cannot have prostate cancer)
ProbandLabel UM2 III-1, Male, 40
Variant NM_006361.5(HOXB13):c.251G>A (p.Gly84Glu)
ClinVar 128031
CAID n/a
gnomAD MAF=0.007574(European(Finnish)), 2 homozygotes
FamilyAddInfo ages rounded to nearest 5 year interval
FamilyPMIDs 17120048
JHU Family 1
FamilyLabel JHU Family 1
FamilyJHUPresentingHPOs n/a
FamilyNotHPOs n/a
CountryOrigin n/a
Ethnicity n/a
Race n/a
FamilyJHUPreviousTesting Screened nonsense and missense variants in 202 candidate genes comprising ~15.5Mb. Established evidence of linkage of 17q21-22.
Affected 5
Unaffected 1
Segregations n/a
PublishedLOD n/a
eLOD n/a
AddSegregationInfo n/a
ProbandLabel JHU III-14, Male, 50
CasePresentingHPOs HP:0012125 (Prostate Cancer)
Variant NM_006361.5(HOXB13):c.251G>A (p.Gly84Glu)
ClinVar 128031
CAID n/a
gnomAD MAF=0.007574(European(Finnish)), 2 homozygotes
FamilyAddInfo ages rounded to nearest 5 year interval
FamilyPMIDs 17120048
FSIP2_3
CaseFSIP2_3 male, 45yo report, Tunisian
CasePresentingHPOs HP:0003251, HP:0012207, HP:0012868
(male infertility, asthenospermia, sperm tail anomaly)
HPOsFreeText Sperm volume: 3.4mL, sperm concentration: 0.66 million/mL, total motility: 0h, vitality: 30%, normal spermatozoa: 0%, absent flagella: 6%, short flagella: 78%, coiled flagella: 6%, flagella of irregular caliber: 6%
CaseNotHPOs n/a
CasePreviousTesting Previous genetic analysis of DNAH1, CFAP43, and CFAP44 did not end in diagnosis. "Normal somatic karyotypes 46,XY and were negative for Y chromosome microdeletions."
Variant NM_173651.3(FSIP2):c.1607_1616delAAAGATTGCAinsTGT (p.Lys536Metfs)
ClinVar 586970
gnomAD not in gnomAD
CaseAddInfo Consanguineous parents
CasePMIDs 29449551
c.7051C→T
Case# Kolehmainen_Proband 2
CasePresentingHPOs HP:0001263, HP:0001875, HP:0001135, HP:0011504, HP:0000252, HP:0001290, HP:0001999
CaseNotHPOs
CasePreviousTesting None
CaseMethod1 Sanger sequencing
CaseMethod2
CaseGenotypingMethod Sanger sequencing of COH1
Variant NM_017890.4(VPS13B):c.7051C>T (p.Arg2351Ter)
ClinVar 2820
CAID
gnomAD 0.00003249 in South Asians
VariantEvidence This variant is a nonsense mutation, introducing a termination of the protein product, and is awarded default points. The variant reported is found in gnomAD with a frequency of 0.00003249 in South Asians. It is not reported in Finnish or non-Finnish European populations.
CaseAddInfo This individual is also reported by Fryns et al, who provide the clinical features observed in this individual.
CasePMIDs 8832131
Patient 1
Case1: Male, United States, Birth onset
CasePresentingHPOs: HP:0001558, HP:0003552, HP:0002804, HP:0001762, HP:0001188, HP:0000023, HP:0001385, HP:0006380, HP:0004482, HP:0004322, HP:0003782, HP:0011220, HP:0000160, HP:0000470, HP:0000301, HP:0002751, HP:0003306, HP:0001270, HP:0003808, HP:0003044, HP:0012453, HP:0001193, HP:0012785, HP:0003273, HP:0012894, HP:0002174, HP:0004370, HP:0002362, HP:0002942, HP:0012418, HP:0002789, HP:0002205, HP:0002870, HP:0003458, HP:0040129, HP:0003236, HP:0003388, HP:0002015, HP:0003557, HP:0003803, HP:0003715, HP:0012240, HP:0100295 (Decreased fetal movement, Muscle stiffness, Arthrogryposis multiplex congenita, Talipes equinovarus, Hand clenching, Inguinal hernia, Hip dysplasia, Knee flexion contracture, Relative macrocephaly, Short stature, Eunuchoid habitus, Prominent forehead, Small mouth, Short neck, Abnormality of facial musculature, Kyphoscoliosis, Spinal rigidity, Motor delay, Abnormal muscle tone, Shoulder flexion contracture, Bilateral wrist flexion contracture, Ulnar deviation of the hand or of fingers of the hand, Flexion contracture of finger, Hip contracture, Paraspinal muscle hypertrophy, Postural tremor, Abnormality of temperature regulation, Shuffling gait, Thoracic kyphosis, Hypoxemia, Tachypnea, Recurrent respiratory infections, Obstructive sleep apnea, EMG: myopathic abnormalities, Abnormal nerve conduction velocity, Elevated serum creatine phosphokinase, Easy fatigability, Dysphagia, Increased variability in muscle fiber diameter, Type 1 muscle fiber predominance, Myofibrillar changes, Increased intramyocellular lipid droplets, Muscle fiber atrophy)
HPOsFreeText: Jaw contracture, Heel contracture, Strong bilateral grasp, Occasional grunting, Supplemental oxygen required, Ultrastructural evidence of accumulation of mitochondria, Focal Z-line streaming and broadening
CaseNotHPOs: HP:0100543, HP:0001315, HP:0001324, HP:0002486, HP:0100288, HP:0002353, HP:0002363, HP:0003116, HP:0003798 (Cognitive impairment, Reduced/absent deep tendon reflexes, Muscle weakness, Myotonia, EMG: myokymic discharges, EEG abnormality, Abnormality of brainstem morphology, Abnormal echocardiogram, Nemaline bodies)
NotHPOsFreeText: N/A
CaseAddInfo: Case is de novo and confirmed via parental testing
CasePreviousTesting: Negative Results from WES: ACTA1, MYH3, TPM2, HSPG2, TNNT3, TNNI2, FKRP, CRYAB, and microarray.
CaseGenotypingMethod: DNA was obtained from blood and WES was performed on the samples using Illumina technology. Mutations were analyzed and filtered.
Variant: NM_152263.4(TPM3):c.670_672GAA[1] (p.Glu225del)
ClinVar: 235143 https://www.ncbi.nlm.nih.gov/clinvar/variation/235143/
gnomAD: Not in gnomAD
For the non-Newfoundland patient with the p.S358L mutation, the parents were also sequenced and paternity confirmed.
Case# NonNew, male, 40yr
CasePresentingHPOs HP:0002119, HP:0002375 , HP:0031317
CaseNotHPOs Annotate with the HPOs that were noted not to manifest within the proband of interest.
CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).
CaseMethod1 PCR
CaseMethod2 as mentioned
CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.
Variant NM_024334.2(TMEM43):c.1073C>T (p.Ser358Leu)
ClinVar 734
VariantEvidence ?????Surely the presenting relevant phenotypes is not enough, neither are the in silico programs they are running forpathogenicity prediction. There seems to be nothing else provided????
CaseAddInfo De Novo, Maternity/Paternity confirmed
only one variant was segregating with the disease. It revealed a homozygous premature stop mutation in NKX6-2: c.121A>T; p.Lys41∗ (NM_177400.2) in families 1 and 2. There were no other variants that segregated with the disease in these two families. Although these families are not known to be related, we found that the same homozygous truncating variant in NKX6-2 fully segregated with the disease in each family
Families 1 and 2
Same single variant (NKX6-2: c.121A>T; p.Lys41∗ (NM_177400.2)) segregated in both Families 1 and 2. No relation between the families.
Haplotype analysis performed on each individual in both families which located four areas of homozygosity between each individual.
These shared regions include 1.4M region on chromosome 10 and a haplotype block around NKX6-2 (founder effect support).
Family 1
FamilyName: Family 1
FamilyPresentingHPOS: HP:0001257, HP:0000639, HP:0001251
FamilyNotHPOs:
CountryOrigin: India
Ethnicity: n/a
Race: n/a
FamilyPreviousTesting: MRI showed brain hypomyelination.
FamilyGenotypingMethod: combination of homozygosity mapping and WES, haplotype analysis
Affected: 3
Unaffected:
Segregations:
PublishedLOD:
eLOD:
AddSegregationInfo:
ProbandLabel: III-1, Female, 27 yo
Variant: NM_177400.2(NKX6-2):c.121A>T (p.Lys41Ter)
ClinVar: 430622, https://www.ncbi.nlm.nih.gov/clinvar/variation/430622/
gnomAD: n/a
FamilyAddInfo:
FamilyPMIDs:
Only one homozygous variant remained after application of these filters: NKX6-2 (NM_177400.2; c.487C>G; p.Leu163Val), and it fully segregated with the disease in the family under a fully penetrant autosomal-recessive model (Figure 2E). This variant was only present once in the heterozygous state in our database and is absent in ExAC
Family 3
Variant (NM_177400.2; c.487C>G; p.Leu163Val) fully segregated with disease, absent from ExAC, only present as heterozygous state in this study's data set.
Autozygosity mapping and exome sequencing identified the homozygous mutations within PLAA, which segregated in an autosomal-recessive manner in all four families (combined LOD score of 4.52 for families A–C, Figure S1). Although families A–C are not knowingly related, we inferred that the c.68G>T (p.Gly23Val) mutation was derived from a distant common ancestor, as it was inherited on the same haplotype (Table S2).
FamilyName: Families A,B,C Founder, Pakistani
FamilyPresentingHPOs: HP:0002033,
FamilyNotHPOs:
CountryOrigin: Pakistani
Ethnicity:
Race: Asian
FamilyPreviousTesting: n/a
FamilyMethod1: same as group
FamilyMethod2: same as group
FamilyGenotypingMethod: Identified region of homozygosity on Chromosome 9, that also encoded for the genes CER1, FREM1, IFN4A, IFNA10, TEK, and IFNK. Potentially deleterious mutations were found in FREM1 and IFNA10 were noted in supplement, but when the refseq was cross referenced to gnomAD, the variants were present in a substantial number homozygotes. For a lethal conditions, this would indicate benign variation.
Affected: 7
Unaffected:
Segregations:
PublishedLOD: 4.52
eLOD: n/a
AddSegregationInfo: All families from Pakistani origin. Family A and C were Pakistani. Family B was from Kashmir, on the Pakistani border.
ProbandLabel: Family A-IV:6/ CaseA IV:6, male, Pakistani, died as 12 days old
Homozygous
Variant: NM_001031689.2(PLAA):c.68G>T (p.Gly23Val)
ClinVar or CAID: 427941
gnomAD: n/a
FamilyAddInfo:
FamilyPMIDs:
CasePresentingHPOs: HP:0025116, HP:0001561, HP:0008872, HP:0008936, HP:0002509, HP:0002033, HP:0002015, HP:0001007, HP:0003196, HP:0000343, HP:0000218, HP:0000369, HP:0007598, HP:0100259, HP:0010576, HP:0007633, HP:0031605, HP:0000851, HP:0011968, HP:0100022, HP:0002871, HP:0001522
CaseNOTHPOs:HP:0001507
AddCaseInfo:
VariantEvidence: PLAA G23V homozygous mice were generated by Crispr/Cas9 genome editing. Examination of PLAA protein levels in the cerebellum of the homozygous G23V mutant mice vs the wildtype littermates (Figure 3A) revealed significantly reduced protein expression, indicating the G23V variation effects protein stability, and indicates a loss of function mechanism for the variant.
Score: Default for homozygous missense.
Note: Will score the phenotypes associated with the G23V mouse as experimental evidence seperately.
proband with p.K3394N
Case# B16, female, 30
CasePresentingHPOs HP:0003124 Hypercholesterolemia
CasePreviousTesting The APOB domains, including amino acids 2955–3092 and amino acids 3303–3492, were analysed in the 600 molecularly undefined ADH cases by direct Sanger sequencing
CaseMethod1 as mentioned
CaseMethod2 as mentioned
CaseGenotypingMethod Exome sequencing
Variant NM_000384.2(APOB):c.10182G>T (p.Lys3394Asn)
ClinVar 438310
gnomAD n/a
VariantEvidence Deficient LDL uptake (fig. 2).
Family UW-AP
Family#PresentingHPOs HP:0001251, HP:0001272
FamilyNotHPOs HP:0001875, HP:0001873, HP:0001903, HP:0005518
Family#PreviousTesting Haplotype analysis by evaluation of STRP markers flanking disease causeing genes such as SCA1-19, AT, TERC, etc. (Table S1).
CountryofOrigin Germany, Ireland, North America
Family#Method1 PCR
Family#GenotypingMethod Allele-specific PCR amplification of the SAMD9L c.2640C>A variant was performed, (SNP)-based genome-wide linkage analysis
Affected 7
Unaffected 4
Segregations 6
eLOD 1.8
ProbandLabel UW-AP:IV-1, M, 18yo onset
CasePreviousTesting MVC(44[0/1]), WBC(87[0/1]), platelets(8.1[0/1])
CaseGenotypingMethod WES then confirmed with Sanger
Variant NM_152703.4(SAMD9L):c.2640C>A (p.His880Gln)
ClinVar 242372
Haplotype analyses using exon-specific primers (Table S3) on families 1, 4, and 5 showed they carried the allele on a common founder haplotype and suggested that the c.713C>T (p.Ser238Leu) change is a founder variant
Family Name: Family 4
FamilyPresentingHPOs: HP:0000705
FamilyNotHPOs:
CountryOrigin: Turkey
Ethnicity: Turkish
Race: n/a
FamilyPreviousTesting: candidate gene sequencing, array comparative genomic hybridization, or exome sequencing
FamilyGenotypingMethod: WES, haplotype analysis
Affected: 2
Unaffected: 2
Segregations: 1
PublishedLOD: n/a
eLOD: 0.85
AddSegregationInfo: non-consanguineous family
ProbandLabel: Family 4: III:1, female, 10 yo
Variant: NM_033068.2(ACP4):c.713C>T (p.Ser238Leu)
ClinVar or CAID: 374862, https://www.ncbi.nlm.nih.gov/clinvar/variation/374862/
genomAD: 8.127e-6, http://gnomad.broadinstitute.org/variant/19-51297008-C-T
FamilyAddInfo: parents unaffectd
CasePresentingHPOs: HP:0006297, HP:0011073, HP:0006316
CasePresentingHPOTerm: hypoplasia of dental enamel, black staining of cervical teeth, large dental spacing due to thin enamel
CaseNotHPOs: HP:0010299
AddCaseInfo:
VariantEvidence:
Individual F5-II1
Case# F5-II1, female, 7mo death, Portuguese
CasePresentingHPOs HP:0006579, HP:0001433, HP:0001508, HP:0001582, HP:0001290, HP:0001943, HP:0001987, HP:0002611, HP:0001399, HP:0001903, HP:0012115, HP:0001298, HP:0012358, HP:0012347, HP:0003155, HP:0003141, HP:0001394 (Neonatal jaundice, Hepatosplenomegaly, Failure to thrive, Redundant skin, Hypotonia, Hypoglycemia, Hyperammonemia, Cholestatic liver disease, Liver failure, anemia, Hepatitis, Encephalopathy, O-glycosylation, N-glycosylation, Elevated alkaline phosphatase, High cholesterol, Increased LDL cholesterol, Cirrhosis)
HPOsFreeText persisting jaundice, hepatosplenomegaly, FTT, redundant skin, poor muscle volume, generalized hypotonia(5mo) abnormal coagulation factors, perinuclear iron deposition, severe cholestatic hepatitis, multi-organ failure, elevated aminotransferases, on bone marrow biopsy: dyserythropoiesis, lipidic histiocytes and erythrophagocytosis
CaseNotHPOs n/a
CasePreviousTesting type 2 CDG, metabolic work up: AST 207–972 U/l[normal range, 0–50 U/l], ALT 48–153 U/l[normal range, 0–50 U/l], ALP 850–1,031 U/l[normal range, < 360 U/l], cholesterol 431 mg/dl[normal range, 120–200 mg/dl], LDL cholesterol 314 mg/dl[normal range, 50–130 mg/dl], low FVII and high FVIII, INR 0.79–3.0, HB 7 g/dl
CaseMethod1 WES
CaseMethod2 n/a
CaseGenotypingMethod WES on proband, Sanger on parents. Variants with frequency of >0.2%, synonymous variants, deep intronic variants, and variants in UTRs were excluded.
Variant (1) NM_032357.3(CCDC115):c.92T>C (p.Leu31Ser), (2)NM_032357.3(CCDC115):c.(?-258) (∗1245_?) del(p.0?), compound heterozygous
ClinVar (1) 218967(2) n/a
gnomAD (1) 0.00002384(European (Non-Finnish)), 0.00001086(Total)-3 heterozygotes
VariantEvidence n/a
CaseAddInfo n/a
CasePMIDs 29759592
Case 17
Case17 Female, Finland
CasePresentingHPOs HP:0000347, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0002126, HP:0007260, HP:0007165
(Micrognathia, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Polymicrogyria, Type II lissencephaly, Periventricular neuronal heterotopia)
HPOsFreeText Crown-heel body length 48cm, body weight 2695g, brain weight 249g, abnormal larynx/trachea, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occipitoschisis/keyhole, leptomeningeal heterotopia, neuroepithelial rosettes, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus, (Fig6:) cervical spinal cord shows a polypoid bulge from the posterior part of the cord and a slit-like central canal
CaseNotHPOs HP:0000202, HP:0001161, HP:0001829, HP:0001627, HP:0000157
(Oral cleft, Hand polydactyly, Foot polydactyly, Congenital heart defect, Tongue abnormality)
NotHPOsFreeText Uterus duplex, hydranencephaly/anencephaly, true alobar or semilobar holoprosencephaly
CasePreviousTesting n/a
Variant NM_145014.2(HYLS1):c.632A>G (p.Asp211Gly), homozygous
ClinVar 1143
gnomAD MAF= 0.009594(European(Finnish)), no homozygotes
CaseAddInfo died 5 hours after birth, 36+4wk gestational age
CasePMIDs n/a
4
Case4: Female, 74 yrs report
CasePresentingHPOs: HP:0002751, HP:0002540, HP:0100753, HP:0003236, HP:0003089, HP:0003798, HP:0031237, HP:0003555, HP:0012785 (Kyphoscoliosis, Inability to walk, Schizophrenia, Elevated serum creatine phosphokinase, Hamstring contracture, Nemaline bodies, Internally nucleated skeletal muscle fibers, Muscle fiber splitting, Flexion contracture of finger)
HPOsFreeText: Jaw contractures, Pectoral contractures, Quad contractures, Disorganized sarccomeres, Nuclear clumps
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Mother of Case 5 and 6, Proband for Family C
CasePreviousTesting: N/A
CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.
Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)
ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/
gnomAD: Not in gnomAD