Case KMP 15: Eastern Slovakia, Female, 82yo

DiseaseAssertion: hypertrophic cardiomyopathy

FamilyInfo: positive family history

CaseHPOFreeText: left ventricular outflow tract obstruction, left ventricular ejection fraction = 60%, New York Heart Association Classification = III, implantable cardioverter defibrillator

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.2734A>G (p.Lys912Glu)

ClinVar: 520267, https://www.ncbi.nlm.nih.gov/clinvar/variation/520267/

gnomAD: n/a

CaseMYH7-8: 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.2539A>G (p.Lys847Glu)

ClinVar: 177757 https://www.ncbi.nlm.nih.gov/clinvar/variation/177757/

gnomAD: Not in gnomAD

CaseMYH7-27: 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.505A>G (p.Arg169Gly)

ClinVar: 177664 https://www.ncbi.nlm.nih.gov/clinvar/variation/177664/

gnomAD: Not in gnomAD

CaseMYH7-5: 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.2198G>T (p.Gly733Val)

ClinVar: 181177 https://www.ncbi.nlm.nih.gov/clinvar/variation/181177/

gnomAD: Not in gnomAD

CasePT-41: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo:

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.3749G>C (p.Arg1250Pro)

ClinVar: 181232 https://www.ncbi.nlm.nih.gov/clinvar/variation/181232/

gnomAD: East Asian 5.437e-5, Overall 7.958e-6 https://gnomad.broadinstitute.org/variant/14-23888796-C-G

CasePT-110: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo:

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.5326A>G (p.Ser1776Gly)

ClinVar: 177629 https://www.ncbi.nlm.nih.gov/clinvar/variation/177629/

gnomAD: East Asian 3.007e-4, Overall 4.595e-5 https://gnomad.broadinstitute.org/variant/14-23884437-T-C

Multiple Gene Variants:

MYBPC3 Variant:

Variant is reported as below, but the nucleotide sequence is incorrect. Unable to register

Variant: NM_000256.3:c.76A>G (p.Ser236Gly)

CasePT-99: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo:

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.4199C>G (p.Ala1400Gly)

ClinVar: 181248 https://www.ncbi.nlm.nih.gov/clinvar/variation/181248/

gnomAD: Not in gnomAD

CasePT-42: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo: 2 other siblings share the same genotype

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.5317C>A (p.Gln1773Lys)

ClinVar: 181277 https://www.ncbi.nlm.nih.gov/clinvar/variation/181277/

gnomAD: Not in gnomAD

CasePT-33: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo: PT-34 is the proband's sibling in Family 17 with the same genotype

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.1615A>G (p.Met539Val)

ClinVar: 181409 https://www.ncbi.nlm.nih.gov/clinvar/variation/181409/

gnomAD: Not in gnomAD

CasePT-30: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo:

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.2606G>A (p.Arg869His)

ClinVar: 177667 https://www.ncbi.nlm.nih.gov/clinvar/variation/177667/

gnomAD: African 1.230e-4, Overall 2.386e-5 https://gnomad.broadinstitute.org/variant/14-23894051-C-T

CasePT-76: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo:

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.2334C>G (p.Asp778Glu)

ClinVar: 265252 https://www.ncbi.nlm.nih.gov/clinvar/variation/265252/

gnomAD: Not in gnomAD

CasePT-97: United States

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001650, HP:0001658 (Aortic valve stenosis, Myocardial infarction)

NotHPOsFreeText: N/A

CaseAddInfo:

CaseGenotypingMethod: DNA was collected from the participants using blood samples. 18 genes suspected on contributing to HCM were targeted and sequenced. The variants were then located and filtered for pathogenicity.

Variant: NM_000257.3:c.4159G>A (p.Glu1387Lys)

ClinVar: 181244 https://www.ncbi.nlm.nih.gov/clinvar/variation/181244/

gnomAD: South Asian 3.266e-5, Overall 3.977e-6 https://gnomad.broadinstitute.org/variant/14-23887429-C-T

Table 5

Case EO5: 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.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

Variant2: NM_000257.3(MYH7):c.676G>A (p.Ala226Thr)

ClinVar: 372429, https://www.ncbi.nlm.nih.gov/clinvar/variation/372429/

gnomAD: n/a

Table 5

Case LO1: Italian

DiseaseAssertion: HCM (late-onset)

FamilyInfo: positive family history

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

Variant: NM_000257.3(MYH7):c.3133C>T (p.Arg1045Cys)

ClinVar: 177753, https://www.ncbi.nlm.nih.gov/clinvar/variation/177753/

gnomAD: 0.00002828, https://gnomad.broadinstitute.org/variant/14-23891501-G-A

CaseHCM041: 50 yrs report, Vietnam, Asian

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: N/A

CasePresentingHPOs: HP:0001712, HP:0100749, HP:0002875, HP:0011103, HP:0031295 (Left ventricular hypertrophy, Chest pain, Exertional dyspnea, Abnormality of the left ventricular outflow tract, Left atrial enlargement)

HPOsFreeText: Maximal LV thickness 30 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.1324C>T (p.Arg442Cys)

ClinVar: 177897 https://www.ncbi.nlm.nih.gov/clinvar/variation/177897/

gnomAD: 0.00005012, http://gnomad.broadinstitute.org/variant/14-23898247-G-A

CaseHCM133: 64 yrs report, Vietnam, Asian

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: Family history of sudden cardiac death

CasePresentingHPOs: HP:0100749, HP:0001712, HP:0031295 (Chest pain, Left ventricular hypertrophy, Left atrial enlargement)

HPOsFreeText: Maximal LV thickness 21 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.3551A>T (p.Gln1184Leu)

ClinVar: 181226 https://www.ncbi.nlm.nih.gov/clinvar/variation/181226/

gnomAD: 0.0006115, http://gnomad.broadinstitute.org/variant/14-23889229-T-A

Multiple Gene Variants

(1) MYH6 Variant

Variant: NM_002471.3(MYH6):c.1252G>A (p.Val418Met)

ClinVar: 44449 https://www.ncbi.nlm.nih.gov/clinvar/variation/44449/

gnomAD: 0.001954, http://gnomad.broadinstitute.org/variant/14-23870076-C-T

CaseHCM083: 53 yrs report, Vietnam, Asian

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: N/A

CasePresentingHPOs: HP:0002875, HP:0001712, HP:0001667, HP:0001705 (Exertional dyspnea, Left ventricular hypertrophy, Right ventricular hypertrophy, Right ventricular outlet obstruction)

HPOsFreeText: Maximal LV thickness 18 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.4159G>A (p.Glu1387Lys)

ClinVar: 181244 https://www.ncbi.nlm.nih.gov/clinvar/variation/181244/

gnomAD: 0.00003266, http://gnomad.broadinstitute.org/variant/14-23887429-C-T

Case: Patient 17, male, 36yo, symptom onset in childhood

CasePresentingHPOs: HP:0003327, HP:0008959, HP:0009053 (axial muscle weakness, Distal upper limb muscle weakness, Distal lower limb muscle weakness)

HPOsFreeText: normal CK levels

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.5779A>T (p.Ile1927Phe)

ClinVar: 487639, https://www.ncbi.nlm.nih.gov/clinvar/variation/487639/

gnomAD: 0.00004598, https://gnomad.broadinstitute.org/variant/14-23882979-T-A?dataset=gnomad_r2_1

Case#: 11

DiseaseAssertion: LVNC

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: -5.47 Fathmm, 0 sift, 0.988 polyphen2, GVGD C25, mutation taster 1, -4.54 provean, -4.35 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.2135G>A (p.Arg712His)

ClinVar: 575575 https://www.ncbi.nlm.nih.gov/clinvar/variation/575575/

CAID: N/A

gnomAD: absent

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.698C>T (p.Ala233Val)

ClinVar: 177858, https://www.ncbi.nlm.nih.gov/clinvar/variation/177858/

gnomAD: n/a

Supplementary Data: Online Table 2b

Case 6:

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 1: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

Variant 2: NM_000257.3(MYH7):c.1633G>A (p.Asp545Asn)

ClinVar: 264607, https://www.ncbi.nlm.nih.gov/clinvar/variation/264607/

gnomAD: 0.000007954, https://gnomad.broadinstitute.org/variant/14-23897049-C-T

variants asserted to be in cis

Supplementary Data: Online Table 2b

Case 5:

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 1: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

Variant 2: NM_000257.3(MYH7):c.1633G>A (p.Asp545Asn)

ClinVar: 264607, https://www.ncbi.nlm.nih.gov/clinvar/variation/264607/

gnomAD: 0.000007954, https://gnomad.broadinstitute.org/variant/14-23897049-C-T

variants asserted to be in cis

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.2704G>A (p.Glu902Lys)

ClinVar: 228905, https://www.ncbi.nlm.nih.gov/clinvar/variation/228905/

gnomAD: n/a

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.2678C>T (p.Ala893Val)

ClinVar: 177763, https://www.ncbi.nlm.nih.gov/clinvar/variation/177763/

gnomAD: n/a

Supplementary Data: Online Table 1a

Case:

CaseHPOFreeText: heart transplant

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.495G>A (p.Met165Ile)

ClinVar: 524948, https://www.ncbi.nlm.nih.gov/clinvar/variation/524948/

gnomAD: n/a

Supplementary Data: Online Table 2b

Case 4:

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 1: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

Variant 2: NM_000257.3(MYH7):c.1633G>A (p.Asp545Asn)

ClinVar: 264607, https://www.ncbi.nlm.nih.gov/clinvar/variation/264607/

gnomAD: 0.000007954, https://gnomad.broadinstitute.org/variant/14-23897049-C-T

variants asserted to be in cis

Supplementary Data: Online Table 2a

Case:

CasePresentingHPOs: HP:0010316 (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.847T>G (p.Tyr283Asp)

ClinVar: 66081, https://www.ncbi.nlm.nih.gov/clinvar/variation/66081/

gnomAD: n/a

Supplementary Data: Online Table 2b

Case 3:

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 1: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

Variant 2: NM_000257.3(MYH7):c.1633G>A (p.Asp545Asn)

ClinVar: 264607, https://www.ncbi.nlm.nih.gov/clinvar/variation/264607/

gnomAD: 0.000007954, https://gnomad.broadinstitute.org/variant/14-23897049-C-T

variants asserted to be in cis

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.4075C>T (p.Arg1359Cys)

ClinVar: 178082, https://www.ncbi.nlm.nih.gov/clinvar/variation/178082/

gnomAD: 0.000007954, https://gnomad.broadinstitute.org/variant/14-23887513-G-A

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.4125T>A (p.Tyr1375Ter)

ClinVar: 579879, https://www.ncbi.nlm.nih.gov/clinvar/variation/579879/

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.5534G>A (p.Arg1845Gln)

ClinVar: 181286, https://www.ncbi.nlm.nih.gov/clinvar/variation/181286/

gnomAD: 0.000004023, https://gnomad.broadinstitute.org/variant/14-23884229-C-T

CaseMYH7-12: 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.3236G>A (p.Arg1079Gln)

ClinVar: 177826 https://www.ncbi.nlm.nih.gov/clinvar/variation/177826/

gnomAD: European (Non-Finnish) 1.549e-5, Overall 7.073e-6 https://gnomad.broadinstitute.org/variant/14-23891398-C-T

CaseMYH7-8: 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.4075C>T (p.Arg1359Cys)

ClinVar: 178082 https://www.ncbi.nlm.nih.gov/clinvar/variation/178082/

gnomAD: European (Non-Finnish) 8.793e-6, Overall 7.954e-6 https://gnomad.broadinstitute.org/variant/14-23887513-G-A

CaseMYH7-22: 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.2333A>T (p.Asp778Val)

ClinVar: 454354 https://www.ncbi.nlm.nih.gov/clinvar/variation/454354/

gnomAD: Not in gnomAD

CaseMYH7-19: 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.2539A>G (p.Lys847Glu)

ClinVar: 177757 https://www.ncbi.nlm.nih.gov/clinvar/variation/177757/

gnomAD: Not in gnomAD

CaseAJV: 17 years diagnosis, Australia

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: Father (index case) died awaiting cardiac transplant (carried both variants). Two possibly affected relatives.

CasePresentingHPOs: HP:0001639, HP:0006536 (Hypertrophic cardiomyopathy, Obstructive lung disease)

HPOsFreeText: Maximum left ventricular hypertrophy at 17 mm, Sudden cardiac death event at 17 years, Maximal wall thickness at 22mm,

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.1954A>G (p.Arg652Gly)

ClinVar: 177626 https://www.ncbi.nlm.nih.gov/clinvar/variation/177626/

gnomAD: Not in gnomAD

Multiple Gene Variants:

MYBPC3 Variant

Variant: NM_000256.3:c.2980C>T (p.Leu994Phe)

ClinVar: 180992 https://www.ncbi.nlm.nih.gov/clinvar/variation/180992/

gnomAD: European (Non-Finnish) 1.624e-4, Overall 8.461e-5 https://gnomad.broadinstitute.org/variant/11-47355487-G-A

CaseMYH7-11: 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.3325A>G (p.Lys1109Glu)

ClinVar: 492984 https://www.ncbi.nlm.nih.gov/clinvar/variation/492984/

gnomAD: Not in gnomAD

CaseMYH7-10: 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.3592G>T (p.Asp1198Tyr)

ClinVar: 520451 https://www.ncbi.nlm.nih.gov/clinvar/variation/520451/

gnomAD: Not in gnomAD

CaseMYH7-31: Australia

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

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.1954A>G (p.Arg652Gly)

ClinVar: 177626 https://www.ncbi.nlm.nih.gov/clinvar/variation/177626/

gnomAD: Not in gnomAD

CaseMYH7-18: 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.2578A>G (p.Lys860Glu)

ClinVar: 192312 https://www.ncbi.nlm.nih.gov/clinvar/variation/192312/

gnomAD: Not in gnomAD

CaseMYH7-2: 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.5287G>A (p.Ala1763Thr)

ClinVar: 177846 https://www.ncbi.nlm.nih.gov/clinvar/variation/177846/

gnomAD: European (Non-Finnish) 1.238e-4, Overall 7.423e-5 https://gnomad.broadinstitute.org/variant/14-23884476-C-T

Supplementary Data, Table 2

Variant noted to be present in 3 individuals

Variant: NM_000257.3(MYH7):c.1954A>G (p.Arg652Gly)

ClinVar: 177626, https://www.ncbi.nlm.nih.gov/clinvar/variation/177626/

gnomAD: 0.000003978, https://gnomad.broadinstitute.org/variant/14-23896451-T-C

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.2539A>G (p.Lys847Glu)

ClinVar: 177757, https://www.ncbi.nlm.nih.gov/clinvar/variation/177757/

gnomAD: n/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.1324C>T (p.Arg442Cys)

ClinVar: 177897, https://www.ncbi.nlm.nih.gov/clinvar/variation/177897/

gnomAD: 0.00002121, https://gnomad.broadinstitute.org/variant/14-23898247-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.1478T>A (p.Met493Lys)

ClinVar: 192308, https://www.ncbi.nlm.nih.gov/clinvar/variation/192308/

gnomAD: n/a

Case IV-5: Male, Iranian, 30yo at diagnosis, 31yo at study, proband

DiseaseAssertion: DCM (initially); paper notes that phenotype is more consisted with hypokinetic non-dilated cardiomyopathy based on guideline from ESC working group on myocardial and pericardial diseases (PMID: 26792875)

FamilyInfo: consanguineous family, pedigree in fig. 1

CasePresentingHPOs: HP:0001712, HP:0002375, HP:000516 (left ventricular hypertrophy, hypokinesia, left ventricular dysfunction)

CaseHPOFreeText: New York Heart Association Class = II, left ventricular ejection fraction = 20-25%, left ventricular internal end-diastolic diameter = 5.7cm, left ventricular internal end-systolic diameter = 5.2cm, interventricular septum = 0.8cm, posterior wall = 0.9cm, normal ECG and normal sinus rhythm, Normal heart valve function

CaseNotHPOFreeText: Ischemic heart disease

CasePreviousTesting: ECG, Full testing (https://hyp.is/2c24ajtuEemXQ-fRmGkjTA/www.sciencedirect.com/science/article/pii/S1769721217300484)

CaseGenotypingMethod: WES, targeted exome sequence capture using SureSelectXT Human All Excon v5 kig (Agilent), co-segregation analysis via Sanger sequencing

Variant: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

MultipleGeneVariants:

(1) TNNT2 Variant:

Variant: NM_000364.3(TNNT2):c.247A>C (p.Asn83His)

ClinVar: 427814, https://www.ncbi.nlm.nih.gov/clinvar/variation/427814/

gnomAD: n/a

Case IV-8: Female, Iranian, 36yo

DiseaseAssertion: DCM

FamilyInfo: consanguineous family, pedigree in fig. 1

CasePresentingHPOs: HP:0005162 (left ventricular dysfunction)

CaseHPOFreeText: New York Heart Association Class = I, left ventricular ejection fraction = 60%, left ventricular internal end-diastolic diameter = 5.0cm, left ventricular internal end-systolic diameter = 3.1cm, interventricular septum = 0.7cm, posterior wall = 0.7cm, normal sinus rhythm, Normal heart valve function

CaseNotHPOFreeText: Ischemic heart disease

CasePreviousTesting: ECG

CaseGenotypingMethod: co-segregation analysis via Sanger sequencing

Variant: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

Case III-10: Female, Iranian, 60yo

DiseaseAssertion: DCM

FamilyInfo: consanguineous family, pedigree in fig. 1

CasePresentingHPOs: HP:0001653, HP:0011713, HP:0005162, HP:0005185, HP:0002375 (mitral regurgitation, left bundle branch block, left ventricular dysfunction, systolic dysfunction, hypokinesia)

CaseHPOFreeText: New York Heart Association Class = II, left ventricular ejection fraction = 15-20%, left ventricular internal end-diastolic diameter = 5.6cm, left ventricular internal end-systolic diameter = 4.3cm, interventricular septum = 0.7cm, posterior wall = 0.6cm, Normal heart valve function, grade II diastolic dysfunction

CaseNotHPOFreeText: Ischemic heart disease

CasePreviousTesting: ECG

CaseGenotypingMethod: co-segregation analysis via Sanger sequencing

Variant: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

MultipleGeneVariants:

(1) TNNT2 Variant:

Variant: NM_000364.3(TNNT2):c.247A>C (p.Asn83His)

ClinVar: 427814, https://www.ncbi.nlm.nih.gov/clinvar/variation/427814/

gnomAD: n/a

Case IV-6: Female, Iranian, 34yo at diagnosis, 37yo at study

DiseaseAssertion: DCM (initially); paper notes that phenotype is more consisted with hypokinetic non-dilated cardiomyopathy based on guideline from ESC working group on myocardial and pericardial diseases (PMID: 26792875)

FamilyInfo: consanguineous family, pedigree in fig. 1

CasePresentingHPOs: HP:0001653, HP:0002375 (mitral regurgitation, hypokinesia)

CaseHPOFreeText: New York Heart Association Class = II, left ventricular ejection fraction = 35%, left ventricular internal end-diastolic diameter = 5.2cm, left ventricular internal end-systolic diameter = 4.2cm, interventricular septum = 0.9cm, posterior wall = 1.0cm, normal sinus rhythm, grade I diastolic function

CaseNotHPOFreeText:

CasePreviousTesting: ECG, Full testing (https://hyp.is/2c24ajtuEemXQ-fRmGkjTA/www.sciencedirect.com/science/article/pii/S1769721217300484)

CaseGenotypingMethod: https://hyp.is/IKjfsDtxEem3Sh8RHHdYSg/www.sciencedirect.com/science/article/pii/S1769721217300484) WES, targeted exome sequence capture using SureSelectXT Human All Excon v5 kig (Agilent), co-segregation analysis via Sanger sequencing

Variant: NM_000257.3(MYH7):c.2863G>A (p.Asp955Asn)

ClinVar: 264608, https://www.ncbi.nlm.nih.gov/clinvar/variation/264608/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23893175-C-T

MultipleGeneVariants:

(1) TNNT2 Variant:

Variant: NM_000364.3(TNNT2):c.247A>C (p.Asn83His)

ClinVar: 427814, https://www.ncbi.nlm.nih.gov/clinvar/variation/427814/

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.3133C>T (p.Arg1045Cys)

ClinVar: 177753, https://www.ncbi.nlm.nih.gov/clinvar/variation/177753/

gnomAD: 0.00002828, https://gnomad.broadinstitute.org/variant/14-23891501-G-A

Supplementary Data table 1

Variant noted to be present in 2 individuals

Variant: NM_000257.3(MYH7):c.2783A>T (p.Asp928Val)

ClinVar: 181379, https://www.ncbi.nlm.nih.gov/clinvar/variation/181379/

gnomAD: n/a

Supplementary Data table 1

Variant noted to be present in 2 individuals

Variant: NM_000257.3(MYH7):c.2080C>T (p.Arg694Cys)

ClinVar: 177627, https://www.ncbi.nlm.nih.gov/clinvar/variation/177627/

gnomAD: 0.00001989, https://gnomad.broadinstitute.org/variant/14-23895255-G-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.5786C>T (p.Thr1929Met)

ClinVar: 181397, https://www.ncbi.nlm.nih.gov/clinvar/variation/181397/

gnomAD: n/a

DiseaseAssertion: Dilated Cardiomyopathy

VariantPreviousTesting: ACTC1, ACTN2, CSRP3, LAMP2, MYBPC3, MYH7, NEXN, PLN, TNNC1, TNNI3, TNNT2, TPM1, ABCC9, CTF1, DES, EMD, LDB3, LMNA, MYH6, RBM20, SGCD, TAZ, TCAP, TTN, and VCL were all tested via NGS.

VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 74 DCM 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 DCM probands and relatives

Variant: NM_000257.4(MYH7):c.5395G>A (p.Glu1799Lys)

ClinVarID: 181278 https://www.ncbi.nlm.nih.gov/clinvar/variation/181278/

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.2539A>G (p.Lys847Glu)

ClinVarID: 177757 https://www.ncbi.nlm.nih.gov/clinvar/variation/177757/

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 one proband

Variant: NM_000257.4(MYH7):c.1324C>T (p.Arg442Cys)

ClinVarID: 177897 https://www.ncbi.nlm.nih.gov/clinvar/variation/177897/

gnomAD: 0.00005012, http://gnomad.broadinstitute.org/variant/14-23898247-G-A

DiseaseAssertion: Cardiomyopathy

VariantPreviousTesting: 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 all tested in the PanCM panel.

VariantGenotypingMethod: Next-generation sequencing panels were used to sequence and read the genetic information of the 305 PanCM 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 PanCM proband

Variant: NM_000257.4(MYH7):c.3157C>T (p.Arg1053Trp)

ClinVar: 181382 https://www.ncbi.nlm.nih.gov/clinvar/variation/181382/

gnomAD: Not in gnomAD

Supplementary Data Table S3

Case: 344

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.2348G>A (p.Arg783His)

ClinVar: 180437 https://www.ncbi.nlm.nih.gov/clinvar/variation/180437/

gnomAD: 0.00004005, https://gnomad.broadinstitute.org/variant/14-23894566-C-T

MultipleGeneVariants:

(1) ABCC9 Variant

Variant: NM_005691.3(ABCC9):c.2200G>A (p.Val734Ile)

ClinVar: 35627 https://www.ncbi.nlm.nih.gov/clinvar/variation/35627/

gnomAD: 0.01123, https://gnomad.broadinstitute.org/variant/12-22017410-C-T

Supplementary Data Table S3

Case: 111

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.1193G>A (p.Gly398Glu)

ClinVar: 180434 https://www.ncbi.nlm.nih.gov/clinvar/variation/180434/

gnomAD: 0.0001946, https://gnomad.broadinstitute.org/variant/14-23898502-C-T

MultipleGeneVariants:

(1) DSP Variant

Variant: NM_004415.4(DSP):c.5498A>T (p.Glu1833Val)

ClinVar: 44929 https://www.ncbi.nlm.nih.gov/clinvar/variation/44929/

gnomAD: 0.02491, https://gnomad.broadinstitute.org/variant/6-7582993-A-T

(2) PSEN1 Variant

Variant: NM_000021.4(PSEN1):c.953A>G (p.Glu318Gly)

ClinVar: 98094 https://www.ncbi.nlm.nih.gov/clinvar/variation/98094/

gnomAD: 0.03394, https://gnomad.broadinstitute.org/variant/14-73673178-A-G

(3) 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

Supplementary Data Table S3

Case: 278

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.2348G>A (p.Arg783His)

ClinVar: 180437 https://www.ncbi.nlm.nih.gov/clinvar/variation/180437/

gnomAD: 0.00004005, https://gnomad.broadinstitute.org/variant/14-23894566-C-T

MultipleGeneVariants:

(1) 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

Supplementary Data Table S3

Case: 33

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.5656-4G>A

ClinVar: 516360, https://www.ncbi.nlm.nih.gov/clinvar/variation/516360/

gnomAD: 0.00006011, https://gnomad.broadinstitute.org/variant/14-23883106-C-T

MultipleGeneVariants:

(1) CRYAB Variant

Variant: c.331G>A (p.Gly111Ser) unregistered variant

(2) DES Variant

Variant: NM_001927.4(DES):c.638C>T (p.Ala213Val)

ClinVar: 44265, https://www.ncbi.nlm.nih.gov/clinvar/variation/44265/

gnomAD: 0.009280, https://gnomad.broadinstitute.org/variant/2-220284876-C-T

(3) FKTN Variant

Variant: NM_006731.2(FKTN):c.1336A>G (p.Asn446Asp)

ClinVar: 36138, https://www.ncbi.nlm.nih.gov/clinvar/variation/36138/

gnomAD: 0.01093, https://gnomad.broadinstitute.org/variant/9-108397495-A-G

(4) MYBPC3 Variant

Variant: NM_000256.3(MYBPC3):c.2686G>A (p.Val896Met)

ClinVar: 42652, https://www.ncbi.nlm.nih.gov/clinvar/variation/42652/

gnomAD: 0.006194, https://gnomad.broadinstitute.org/variant/11-47357479-C-T

Supplementary Data Table S3

Case: 52

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.2451C>A (p.Asn817Lys)

ClinVar: 235029, https://www.ncbi.nlm.nih.gov/clinvar/variation/235029/

gnomAD: absent

MultipleGeneVariants:

(1) 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: absent

Case1: Female, 33 yrs report

DiseaseAssertion: MYH7 Gene-Related Skeletal Myopathy

FamilyInfo: Uneventful family history

CasePresentingHPOs: HP:0002650, HP:0001324, HP:0001263, HP:0001252, HP:0006794, HP:0002652, HP:0002751, HP:0002094, HP:0003121, HP:0003044, HP:0006471, HP:0003273, HP:0008112 (Scoliosis, Muscle weakness, Global developmental delay, Muscular hypotonia, Loss of ability to walk in first decade, Skeletal dysplasia, Kyphoscoliosis, Dyspnea, Limb joint contracture, Shoulder flexion contracture, Fixed elbow flexion, Hip contracture, Plantar flexion contractures)

CaseHPOFreeText: EMG: short duration, small amplitude motor unit action potential (MUAP), and early recruitment patterns were observed in the involved proximal muscles

CaseNotHPOs: HP:0001239, HP:0012785, HP:0002127, HP:0100543 (Wrist flexion contracture, Flexion contracture of finger, Abnormal upper motor neuron morphology, Cognitive impairment)

CaseNotHPOFreeText: No significant abnormal findings during the perinatal period and at the time of birth

CasePreviousTesting: SMN 1del/dup test was performed and no specific findings were observed, Physical exam, serologic test, and neurophysiologic test, including nerve conduction study (NCS) and electromyogram (EMG), were performed, On the manual muscle test (MMT) she received a grade of 4 for wrist flexor, extensor muscle, finger flexor, and extensor muscle, and a grade of 1 for all other upper and lower limb muscles, Cobb angle was 126° at the time of measurement, NGS using a targeted gene sequencing panel analyzing 293 genes performed using 2 x 150 bp in the paired-end mode of MiSeq platform from Illumina

CaseGenotypingMethod: Chromosomal microarray was performed with no abnormal findings. A NGS study was then performed on the proband using a targeted gene sequencing panel for neuromuscular diseases. Genomic DNA was extracted and captured, with massively parallel sequencing and subsequent reading and annotating/filtering of any located variants.

Variant: NM_000257.4:c.1495_1497delGAG (p.Glu500del)

ClinVar: 525034

gnomAD: Not in gnomAD

Case#: 12th case, male, 35 years

DiseaseAssertion: SHCM

FamilyInfo: No

CasePresentingHPOs: Mycardial fibrosis (HP:0001685)

CaseHPOFreeText: 494 g heart, IVST to LVWT ratio 1.35, IVST 2.3 cm, LVWT 1.7 cm, hypertrophy of myocardial fibers, stenosis in lumens,

CaseNotHPOs: N/A

CaseNotHPOFreeText: no pathological changes found in major organs besides heart

CasePreviousTesting: N/A

CaseGenotypingMethod: physical examination, ECG, 2D and Doppler echocardiography, histological examinations, genomic DNA extraction, DNA cloning, sequence analysis

Variant: NM_000257.4(MYH7):c.1402T>C (p.Phe468Leu)

ClinVar: 177821 https://www.ncbi.nlm.nih.gov/clinvar/variation/177821/

CAID: N/A

gnomAD: absent

Case#: Case III-2, female, 74, early adulthood onset

DiseaseAssertion: Congenital Fiber Type Disproportion

FamilyInfo: Family A, late-onset weakness in her deceased mother (II-5) and maternal aunt (II-4), and lifelong weakness in her older sister (III-3)

CasePresentingHPOs: lower limb muscle weakness, gait disturbance, hearing loss, psoriasiform dermatitis, osteoarthritis, glaucoma, hypertension, muscle dystrophy, left ventricular diastolic dysfunction, hyperlordosis, genu recurvatum, proximal lower limb amyotrophy, foot dorsiflexor weakness, hip flexor weakness (HP:0007340, HP:0001288, HP:0000365, HP:0003765, HP:0002758, HP:0000501, HP:0000822, HP:0003560, HP:0025168, HP:0003307, HP:0002816, HP:0008956, HP:0009027, HP:0012515)

CaseHPOFreeText: Pes cavus and hammertor deformities, bilataeral steppage in gait,

CaseNotHPOs: N/A

CaseNotHPOFreeText: myotatic reflexes normal, ECG normal, normal NCS, no fibrillation potentials, sharp waves, or myotonic discharges

CasePreviousTesting: Analysis was negative for sequence variants affecting other congenital myopathy genes associated with CFTD pathology including ACTA1, RYR1, SEPN1, TPM2, and TPM3

CaseGenotypingMethod: neurological examination, serum creatine kinase (60 unit/L), nerve conduction studies, concentric needle electromyography (early recruitment of small polyphasic MUAP in diffuse pattern), electrocardiogram, echocardiogram, forced vital capacity (2.13% (76)), muscle biopsy, immunohistochemical analyses,

Variant: NM_000257.4(MYH7):c.484T>G (p.Tyr162Asp)

ClinVar: 525040 https://www.ncbi.nlm.nih.gov/clinvar/variation/525040/

CAID: N/A

gnomAD: absent

Case: Case report, female, 41yo

CasePresentingHPOs: HP:0001270, HP:0002094, HP:0007340, HP:0010535, HP:0002540, HP:0003323, HP:0002015, HP:0100749, HP:0001662, HP:0005952 (motor delay, dyspnea, lower limb weakness, sleep apnea, inability to walk, progressive muscle weakness, dysphagia, chest pain, bradychardia, decreased pulmonary function)

HPOsFreeText: non-smoker, onset of neuromuscular disorders in early childhood, written language delay, difficulty completing exercise, dyspnea and lower limb weakness presenting during patient's first pregnancy (33yo), required mechanical ventilation machine, symptoms of skeletal muscle disorder began after delivery of first child, unable to get up without assistance, unable to climb stairs, required use of cane, walker, then eventually a wheelchair, episodes of paralysis in lower limbs, normal tone/bulk of arm muscles but bilateral weakness in shoulders and upper limbs (MRC scale of 3/5), intact fine finger movements, down-going toes, reduced perception of vibration in lower limbs, needle EMG showed tendency of myotonic potentials, muscle biopsy of left quadricep showed features of end-stage process consistent with chronic myopathy (Fig. 2A-D), forced vital capacity = 27%, forced expiratory volume per second = 29%

CaseNotHPOs: HP:0001513, HP:0040129 (obese, abnormal nerve conduction velocity)

NotHPOsFreeText: pronator drift, sensory deficit, ocular muscle involvement

FamilyInfo: mother died at 66yo due to heart attack associated with non-compaction cardiomyopathy, daughter (11yo) has signs of muscle disorders, congenital muscular torticollis, excessive growing pains, and underdeveloped muscles in half of body

CaseGenotypingMethod: WES, variants confirmed via Sanger Sequencing

Variant: NM_000257.4(MYH7):c.1370T>G (p.Ile457Arg)

ClinVar: 560881, https://www.ncbi.nlm.nih.gov/clinvar/variation/560881/

gnomAD: absent

MultipleGeneVariants:

(1) SNCB Variant

Variant: NM_003085.5(SNCB):c.368C>A (p.Pro123His)

ClinVar: 7026, https://www.ncbi.nlm.nih.gov/clinvar/variation/7026/

gnomAD: 0.0001929, https://gnomad.broadinstitute.org/variant/5-176048219-G-T

(2) GDF6 Variant:

Variant: NM_001001557.4(GDF6):c.746C>A (p.Ala249Glu)

ClinVar: 8371, https://www.ncbi.nlm.nih.gov/clinvar/variation/8371/

gnomAD: 0.001948, https://gnomad.broadinstitute.org/variant/8-97157413-G-T

Supplementary Data: S2 Table

Case 8: Spanish, 81yo, 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.3056C>A (p.Thr1019Asn)

ClinVar: 195720, https://www.ncbi.nlm.nih.gov/clinvar/variation/195720/

gnomAD: 0.00001591, https://gnomad.broadinstitute.org/variant/14-23892799-G-T

Supplementary Data: S2 Table

Case 4: Spanish, 67yo, 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.1324C>T (p.Arg442Cys)

ClinVar: 177897, https://www.ncbi.nlm.nih.gov/clinvar/variation/177897/

gnomAD: 0.00002121, https://gnomad.broadinstitute.org/variant/14-23898247-G-A

Supplementary Data: S2 Table

Case 12: Spanish, 83yo, 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.3236G>A (p.Arg1079Gln)

ClinVar: 177826, https://www.ncbi.nlm.nih.gov/clinvar/variation/177826/

gnomAD: 0.000007073, https://gnomad.broadinstitute.org/variant/14-23891398-C-T

Supplementary Data: S2 Table

Case 11: Spanish, 27yo, 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.5359G>C (p.Glu1787Gln)

ClinVar: 427207, https://www.ncbi.nlm.nih.gov/clinvar/variation/427207/

gnomAD: n/a

Supplementary Data: S2 Table

Case 3: Spanish, 17yo, 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.1207C>G (p.Arg403Gly)

ClinVar: 505562, https://www.ncbi.nlm.nih.gov/clinvar/variation/505562/

gnomAD: n/a

Supplementary Data: S2 Table

Case 126: Spanish, 12yo, 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.5779A>T (p.Ile1927Phe)

ClinVar: 487639, https://www.ncbi.nlm.nih.gov/clinvar/variation/487639/

gnomAD: n/a

Supplementary Data: S2 Table

Case 49: Spanish, 18yo, 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

Variant1: NM_000257.3(MYH7):c.2890G>C (p.Val964Leu)

ClinVar: 42938, https://www.ncbi.nlm.nih.gov/clinvar/variation/42938/

gnomAD: 0.0004383, https://gnomad.broadinstitute.org/variant/14-23893148-C-G

Variant2: NM_000257.3(MYH7):c.3613G>A (p.Glu1205Lys)

ClinVar: 179656, https://www.ncbi.nlm.nih.gov/clinvar/variation/179656/

gnomAD: 0.000004004, https://gnomad.broadinstitute.org/variant/14-23889167-C-T

Supplementary Data: Table S3

Case 135:

DiseaseAssertion: left ventricular noncompaction

CasePresentingHPOs: HP:0030682 (left ventricular noncompaction)

CaseHPOFreeText: suspected LVNC, >7yo, able to hold breath, non compacted segment = distinct 2-layered appearance of trabeculated and compacted myocardium

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.4010G>A (p.Arg1337Gln)

ClinVar: 181238, https://www.ncbi.nlm.nih.gov/clinvar/variation/181238/

gnomAD: 0.0001207, https://gnomad.broadinstitute.org/variant/14-23887578-C-T

Supplementary Data: Table S3

Case 90:

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.745C>T (p.Arg249Ter)

ClinVar: 407183, https://www.ncbi.nlm.nih.gov/clinvar/variation/407183/

gnomAD: 0.000003977, https://gnomad.broadinstitute.org/variant/14-23900678-G-A

MultipleGeneVariants:

(1) TPM1 Variant:

Variant: NM_001018004.1(TPM1):c.775A>G (p.Lys259Glu)

ClinVar: 43687, https://www.ncbi.nlm.nih.gov/clinvar/variation/43687/

gnomAD: 0.0008382, https://gnomad.broadinstitute.org/variant/15-63363291-A-G

(2) PRKAG2 Variant:

Variant: p.Lys133Ile no ClinVar or CAID

Supplementary Data: Table S3

Case 12:

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.5786C>T (p.Thr1929Met)

ClinVar: 181397, https://www.ncbi.nlm.nih.gov/clinvar/variation/181397/

gnomAD: 0.00005308, https://gnomad.broadinstitute.org/variant/14-23882972-G-A

Table V

Case 902: Italian, Female, 25yo at onset

DiseaseAssertion: HCM

CasePresentingHPOs: HP:0001712, HP:0000821, HP:0006682, HP:0004756 (left ventricular hypertrophy, hypothyroidism, premature ventricular contractions, ventricular tachycardia)

CaseHPOFreeText: maximum left ventricular wall thickness of ≥15 mm, LVWT = 19mm, automatic implantable cardioverter defibrillator, LV ejection fraction = 64%

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_000256.3(MYBPC3):c.2507T>C (p.Met836Thr) written in paper as p.Ile836Thr

ClinVar: 454315, https://www.ncbi.nlm.nih.gov/clinvar/variation/454315/

gnomAD: n/a

Case#: HCM516, male, 23 years,

DiseaseAssertion: HCM

FamilyInfo: Yes, father and mother has HCM

CasePresentingHPOs: syncope, chest tightness (HP:0001279, HP:0031352)

CaseHPOFreeText: inverted T-waves, ST-segment depression, 28mm MLVWT, 67% LVE F, 0.64 E/A ratio, LVOT-PG 44mm

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

CaseGenotypingMethod: sequencing, physical examination, ECG, 3D modeling, statistical analysis

MultipleGeneVariants:

(1) Variant: NM_000257.4(MYH7):c.2631G>A (p.Met877Ile)

ClinVar: 955476 https://www.ncbi.nlm.nih.gov/clinvar/variation/955476/

CAID: N/A

gnomAD: absent

(2) Variant: NM_000257.4(MYH7):c.3134G>A (p.Arg1045His)

ClinVar: 651054 https://www.ncbi.nlm.nih.gov/clinvar/variation/651054/

CAID: N/A

gnomAD: absent

Case#: 6, female, 45 yr at onset, 66 yr at diagnosis

DiseaseAssertion: Myopathy

FamilyInfo: N/A

CasePresentingHPOs: HP:0100595, HP:0003202, HP:0003715, HP:0100301 (Camptocormia, skeletal muscle atrophy, myofibrillar myopathy, muscle fiber tubular inclusions)

CaseHPOFreeText: muscle atrophy specifically paraspinal, no clinical signs of the atrophy

CaseNotHPOs: HP:0003701, HP:0000508, HP:0000602, HP:0002015 (proximal muscle weakness, ptosis, ophthalmoplegia, dysphagia)

CaseNotHPOFreeText: No ALS, MG, or Parkinson's disease

CasePreviousTesting: spinal cord imaging, EMG, deltoid muscle, repetitive nerve stimulation, intravenous Prostigmin therapeutic text, screening for anti-ancetylcholine receptor and anti-muscle specific kinase antibodies, left deltoid muscle biopsy

CaseGenotypingMethod: N/A

Variant: NM_000257.4(MYH7):c.5329G>A (p.Ala1777Thr)

ClinVar: 177697 https://www.ncbi.nlm.nih.gov/clinvar/variation/177697/

CAID: N/A

gnomAD: 0.0001316 (European/non-Finnish) https://gnomad.broadinstitute.org/variant/14-23884434-C-T

CaseHCM4.1: 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.2282C>A (p.Thr761Asn)

ClinVar: 546292 https://www.ncbi.nlm.nih.gov/clinvar/variation/546292/

gnomAD: Not in gnomAD

Case2: Male, 43 years diagnosis, China, Asian

DiseaseAssertion: Hypertrophic Cardiomyopathy

CasePresentingHPOs: HP:0001639, HP:0001667, HP:0005110 (Hypertrophic cardiomyopathy, Right ventricular hypertrophy, Atrial fibrillation)

HPOsFreeText: 0 SCD risk factors, NYHA class is II, Right ventricular wall thickness 14.9 mm

CaseNotHPOs: HP:0002092, HP:0001642, HP:0030680 (Pulmonary arterial hypertension, Pulmonary stenosis, Congenital heart disease)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CaseGenotypingMethod: Probands' genomic DNA was extracted from blood samples. WES was performed, with the resulting sequence data mapped to a reference genome and variants filtered for pathogenicity and predicted effects. All variants identified were confirmed via Sanger sequencing of the respective genes.

Variant: NM_000257.3:c.2123G>C (p.Gly708Ala)

ClinVar: 42882 https://www.ncbi.nlm.nih.gov/clinvar/variation/42882/

gnomAD: Not in gnomAD

MultipleGeneVariants:

MYBPC3 Variant:

Variant: NM_000256.3:c.1000G>A (p.Glu334Lys)

ClinVar: 177902 https://www.ncbi.nlm.nih.gov/clinvar/variation/177902/

gnomAD: East Asian 3.338e-3, Overall 2.368e-4 https://gnomad.broadinstitute.org/variant/11-47367848-C-T

**TTN Variant

Unknown Variant

Variant: TTN-E23808K

CAID: N/A

gnomAD: N/A

ACTN2 Variant

Unknown Variant

Variant: ACTN2-P32fs

CAID: N/A

gnomAD: N/A

DSC2 Variant

Unknown Variant, as 3 possible mutations can be responsible for this protein change

Variant: DSC2-S574R

CAID: N/A

gnomAD: N/A

LAMA4 Variant

Unknown Variant

Variant: LAMA4-L1040P

CAID: N/A

gnomAD: N/A

SYNEC2 Variant

Unknown Variant, as 3 possible mutations can be responsible for this protein change

Variant: SYNE2-W5861C

CAID: N/A

gnomAD: N/A

CaseARVC-02: Male, 35 year diagnosis, Caucasian, Germany

CasePresentingHPOs: HP:0011663, HP:0001635 (Right ventricular cardiomyopathy, Heart failure)

HPOsFreeText: RVEDD at 61 mm

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband treated with HTx and ICD, Father died of cardiac issues, Brother has heart disease, Patient is heterozygous for MYH7 variant

CaseGenotypingMethod: Using a Cardiomyopathy gene panel of 46 genes, the proband's DNA was screened for variants. Afterwards, the variants were classified based on pathogenicity and modeled using predictive software.

Variant: NM_000257.3:c.3715A>G (p.Ile1239Val)

ClinVar: 265831 https://www.ncbi.nlm.nih.gov/clinvar/variation/265831/

gnomAD: Not in gnomAD

CaseCM1832: Male, 0 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: No family history of cardiomyopathy or sudden death, Proband found in Supplementary Table 2, Mother is 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.2609G>T (p.Arg870Leu)

ClinVar: 235031 https://www.ncbi.nlm.nih.gov/clinvar/variation/235031/

gnomAD: Not in gnomAD

CaseCM0969: Male, 6 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, Variant is asserted as novel, Both father and sister with HCM tested positive 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.2777T>C (p.Leu926Pro)

ClinVar: 525005 https://www.ncbi.nlm.nih.gov/clinvar/variation/525005/

gnomAD: Not in gnomAD

Case#: male, 43 yrs,

DiseaseAssertion: FDCM

FamilyInfo: Family B; sister also proband; brother died of SCD; daughter and father asymptomatic

CasePresentingHPOs: HP:0012250 (ST segment depression)

CaseHPOFreeText: severe cardiac enlargement, increased LVEDD (77.8 mm), decreased LVESD (69.8 mm), decreased LVEF (21% < 50%), heart rate 78 beats/min, widened QRS complex (120 ms > 110 ms)

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: N/A

CaseGenotypingMethod: Sanger sequencing, Genome Analyzer IIx, ECG,

Variant: NM_000257.4(MYH7):c.3134G>A (p.Arg1045His)

ClinVar: 651054 https://www.ncbi.nlm.nih.gov/clinvar/variation/651054/

CAID: N/A

gnomAD: absent

Case#: female

DiseaseAssertion: FDCM

FamilyInfo: Family B; brother also proband; brother died of SCD, niece and father asymptomatic

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

CaseGenotypingMethod: Sanger sequencing, Genome Analyzer IIx, ECG,

Variant: NM_000257.4(MYH7):c.3134G>A (p.Arg1045His)

ClinVar: 651054 https://www.ncbi.nlm.nih.gov/clinvar/variation/651054/

CAID: N/A

gnomAD: absent

Case: Case 9, male, 69yo

CasePresentingHPOs: HP:0031318 (myocardial fiber disarray)

HPOsFreeText: BMI = 25.2kg/m^2, cause of death: accidental head injury, heart weight = 624g, left ventricular thickness = 1.8cm, distribution of myocyte disarray in ventricular septum, area of disarray = 7.8%, grade of fibrosis = 3

CaseNotHPOs: HP:0031296 (atrial septal hypertrophy)

CasePreviousTesting: NGS of 81 cardiovascular disorder-related genes (Supplemental Table S1)

CaseGenotypingMethod: genomic DNA extracted from whole blood, PCR, NGS of 81 cardiovascular disorder-related genes (Supplemental Table S1)

Variant: NM_000257.4(MYH7):c.2822G>A (p.Arg941His)

ClinVar: 636633, https://www.ncbi.nlm.nih.gov/clinvar/variation/636633/

gnomAD: 0.00001590, https://gnomad.broadinstitute.org/variant/14-23893216-C-T?dataset=gnomad_r2_1

Supplemental data table e-1

Case: MYH7 Case 2

InheritancePattern: autosomal recessive

DiseaseEntity: n/a

PreviouslyPublished: PMID: 16858239, PMID: 27247418

PreviousTesting: Not specified

CaseGenotypingMethod: paper notes single gene, NGS, and WES were used, but does not specify which method was used for each individual family

Variant: NM_000257.4(MYH7):c.2594A>G (p.Lys865Arg)

ClinVar: 524996, https://www.ncbi.nlm.nih.gov/clinvar/variation/524996/

gnomAD: 0.000003977, https://gnomad.broadinstitute.org/variant/14-23894063-T-C

CaseVI,1: Early adult onset, 63 years diagnosis

CasePresentingHPOs: HP:0003701, HP:0003327, HP:0002795, HP:0003388, HP:0003326 (Proximal muscle weakness, Axial muscle weakness, Abnormal respiration, Easy fatiguability, Myalgia)

HPOsFreeText: GAA activity from dried blood spot: 0.24%, Forced Vital Capacity Seated: 1520 (38%)

CaseNotHPOs: HP:0003236 (Increased serum CK)

CaseAddInfo: Late-Onset Pompe Disease

CaseVII: Adolescent onset, 33 years diagnosis

CasePresentingHPOs: HP:0003701, HP:0003236, HP:0002460, HP:0003394 (Proximal muscle weakness, Increased serum CK, Distal muscle weakness, Muscle cramps)

HPOsFreeText: GAA activity from dried blood spot: 0.20%, Forced Vital Capacity Seated: 5260 (112%), Plasma CK 2.5-5x Normal, Vacuoles in histology

CaseNotHPOs: HP:0002795 (Abnormal respiration)

CaseAddInfo: Late-Onset Pompe Disease

CaseVIII: Early adult onset, 56 years diagnosis

CasePresentingHPOs: HP:0003701, HP:0003236, HP:0003388, HP:0003326, HP:0003198 (Proximal muscle weakness, Increased serum CK, Easy fatiguability, Myalgia, Myopathy)

HPOsFreeText: GAA activity from dried blood spot: 0.13%, Forced Vital Capacity Seated: 2480 (75%), Plasma CK 2.5-5x Normal, 6-Minute Walking Test: 385 min

CaseNotHPOs: HP:0002795 (Abnormal respiration)

CaseAddInfo: Late-Onset Pompe Disease, Reduced staining for dystrophin in patient VIII suggested Becker dystrophy before LOPD diagnosis

Patient28: Male

CasePresentingHPOs: HP:0004887, HP:0011471, HP:0001270, HP:0002546, HP:0000365, HP:0001371

HPOsFreeText: CRIM positive, Anti-rh GGA antibodies maximum titer = 1:3200, infusion associated reaction, tracheostomy, heart normalization

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: variants in trans, symptom onset at 2yo, diagnosis at 4yo, ERT at 9yo

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.2237G>A (p.Trp746Ter)

ClinVar: 280063, https://www.ncbi.nlm.nih.gov/clinvar/variation/280063/

gnomAD: 0.000003988, http://gnomad.broadinstitute.org/variant/17-78090814-G-A

Variant2: NM_000152.4(GAA):c.1655T>C (p.Leu552Pro)

ClinVar: 279811, https://www.ncbi.nlm.nih.gov/clinvar/variation/279811/

gnomAD: 0.00003188, http://gnomad.broadinstitute.org/variant/17-78085800-T-C

Patient16: male

CasePresentingHPOs: HP:0004887, HP:0011471, HP:0001270, HP:0002546, HP:0001371, HP:0001025

HPOsFreeText: CRIM negative, Anti-rh GGA antibodies maximum titer = 1:102.400, immunomodulation, infusion associated reaction, tracheostomy, partial heart normalization

CaseNotHPOs: HP:0000365

CaseAddInfo: variants in trans, symptom onset at birth, diagnosis at 3 days, ERT at 4 days

CasePreviousTesting: same as group

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.2237G>A (p.Trp746Ter)

ClinVar: 280063, https://www.ncbi.nlm.nih.gov/clinvar/variation/280063/

gnomAD: 8.301e-06, http://exac.broadinstitute.org/variant/17-78090814-G-A

Patient23: Female

CasePresentingHPOs: HP:0000365

HPOsFreeText: CRIM positive, heart normalization, moderate periventricular white matter abnormalities (hypomyelination)

CaseNotHPOs: HP:0004887, HP:0025156, HP:0002355, HP:0002546, HP:0001371

Not HPOsFreeText: infusion associated reaction

CaseAddInfo: homozygous variants in trans, symptom onset at birth, diagnosis and ERT at 1yo

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.4(GAA):c.1933G>A (p.Asp645Asn)

ClinVar: 188728, https://www.ncbi.nlm.nih.gov/clinvar/variation/188728/

gnomAD: 0.000008250, http://gnomad.broadinstitute.org/variant/17-78086719-G-A

Patient11: male

CasePresentingHPOs: HP:0002546, HP:0001371

HPOsFreeText: CRIM positive, heart normalization, moderate periventricular white matter abnormalities (hypomyelination)

CaseNotHPOs: HP:0004887, HP:0025156, HP:0002355, HP:0000365

CaseAddInfo: variants in trans, symptom onset at birth, diagnosis at 12 days. Died at 78mo due to cardiorespiratory failure.

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.1942G>A (p.Gly648Ser)

ClinVar: 188902, https://www.ncbi.nlm.nih.gov/clinvar/variation/188902/

gnomAD: 0.0001018, http://exac.broadinstitute.org/variant/17-78086728-G-A

Variant2: NM_000152.4(GAA):c.2646+2T>A

ClinVar: 188924, https://www.ncbi.nlm.nih.gov/clinvar/variation/188924/

gnomAD: n/a

Patient26: Female

CasePresentingHPOs: HP:0004887, HP:0001270, HP:0001371

HPOsFreeText: CRIM positive, Anti-rh GGA antibodies maximum titer = ≤ 1:400, heart normalization

CaseNotHPOs: HP:0025156, HP:0002546, HP:0000365

NotHPOsFreeText: infusion associated reaction

CaseAddInfo: variants in trans, symptom onset at 3yo, diagnosis at 5yo, ERT at 8yo

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.1064T>C (p.Leu355Pro)

ClinVar: 284093, https://www.ncbi.nlm.nih.gov/clinvar/variation/284093/

gnomAD: 0.000007972, http://gnomad.broadinstitute.org/variant/17-78082197-T-C

Patient14: male

CasePresentingHPOs: HP:0004887, HP:0040288, HP:0002546, HP:0000365

HPOsFreeText: CRIM negative, Anti-rh GGA antibodies maximum titer = 1:204.800, immunomodulation, infusion associated reaction, able to sit independently, partial heart normalization

CaseNotHPOs: HP:0001371

CaseAddInfo: homozygous variants in trans. Symptom onset, diagnosis and ERT at 4yo.

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.4(GAA):c.236_246delCCACACAGTGC (p.Pro79Argfs)

ClinVar: 371302, https://www.ncbi.nlm.nih.gov/clinvar/variation/371302/

gnomAD: n/a

Patient17: Male

CasePresentingHPOs: HP:0004887, HP:0011471, HP:0001270, HP:0002546

HPOsFreeText: CRIM negative, tracheostomy, heart normalization

CaseNotHPOs: HP:0000365, HP:0001371

NotHPOsFreeText: infusion associated reaction

CaseAddInfo: homozygous variants in trans, symptom onset at 2yo, diagnosis and ERT at 6yo

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.4(GAA):c.1A>G (p.Met1Val)

ClinVar: 188785, https://www.ncbi.nlm.nih.gov/clinvar/variation/188785/

gnomAD: n/a

Case35: Male, 26 years report

HPOsFreeText: ERT not started, 6 Minute Walking Test at 645 meters, Forced Vital Capacity at 101%

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.655G>A (p.Gly219Arg)

ClinVar: 189065 https://www.ncbi.nlm.nih.gov/clinvar/variation/189065/

gnomAD: African 4.024e-5, Overall 1.809e-5 http://gnomad.broadinstitute.org/variant/17-78079656-G-A

CaseAddInfo: Late Onset Pompe Disease

Case12: Male, 45 years report

HPOsFreeText: 5 years of ERT completed, 6 Minute Walking Test at 301 meters, Forced Vital Capacity at 13%

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.655G>A (p.Gly219Arg)

ClinVar: 189065 https://www.ncbi.nlm.nih.gov/clinvar/variation/189065/

gnomAD: African 4.024e-5, Overall 1.809e-5 http://gnomad.broadinstitute.org/variant/17-78079656-G-A

CaseAddInfo: Late Onset Pompe Disease

Case17: Female, 49 years report

HPOsFreeText: 2 years of ERT completed, 6 Minute Walking Test at 314 meters, Forced Vital Capacity at 54%

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.1548G>A (p.Trp516Ter)

ClinVar: 189025 https://www.ncbi.nlm.nih.gov/clinvar/variation/189025/

gnomAD: European (Non-Finnish) 1.552e-5, Overall 7.079e-6 http://gnomad.broadinstitute.org/variant/17-78084636-G-A

CaseAddInfo: Late Onset Pompe Disease

Case26: Female, 65 years report

HPOsFreeText: 5 years of ERT completed, Forced Vital Capacity at 57%

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.1548G>A (p.Trp516Ter)

ClinVar: 189025 https://www.ncbi.nlm.nih.gov/clinvar/variation/189025/

gnomAD: European (Non-Finnish) 1.552e-5, Overall 7.079e-6 http://gnomad.broadinstitute.org/variant/17-78084636-G-A

CaseAddInfo: Late Onset Pompe Disease

Case27: Male, 71 years report

HPOsFreeText: 0.3 years of ERT completed, 6 Minute Walking Test at 348 meters, Forced Vital Capacity at 53%

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.2608C>T (p.Arg870Ter)

ClinVar: 189009 https://www.ncbi.nlm.nih.gov/clinvar/variation/189009/

gnomAD: European (Non-Finnish) 4.888e-5, Overall 2.662e-5 http://gnomad.broadinstitute.org/variant/17-78092118-C-T

CaseAddInfo: Late Onset Pompe Disease

Case23: Male, 77 years report

HPOsFreeText: 2 years of ERT completed, 6 Minute Walking Test at 120 meters, Forced Vital Capacity at 40%

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.925G>A (p.Gly309Arg)

ClinVar: 188797 https://www.ncbi.nlm.nih.gov/clinvar/variation/188797/

gnomAD: Ashkenazi Jewish 1.010e-4, Overall 2.860e-5 http://gnomad.broadinstitute.org/variant/17-78081665-G-A

CaseAddInfo: Late Onset Pompe Disease

Family 7 - Patient 7

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0003306, HP:0002111, HP:0040081

HPOsFreeText: muscle pathology with vacuolar myopathy with glycogen excess, myopathic muscle unit action potentials

FamilyNotHPOs: HP:0010628, HP:0002015, HP:0003691, HP:0002650

Ethnicity: Iranian

ProbandLabel:

FamilyAddInfo: male, 20yo at onset, 23yo at diagnosis, MRC sum score = 96, patient required use of NIV

FamilyPreviousTesting: Respiratory Evaluation: FVC = 20%, CK = 2,550 U/L, muscle pathology examined, DBS enzyme activity (with inhibition) = 0.1 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: 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

VariantAllele2: NM_000152.4(GAA):c.2662G>T (p.Glu888Ter)

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

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

Family 1 - Patient 1

FamilyPresentingHPOs: HP:0002355, HP:0003701, HP:0040081, HP:0100284

HPOsFreeText: myopathic muscle unit action potentials

FamilyNotHPOs HP:0010628, HP:0002015, HP:0003691, HP:0003306, HP:0002650

NotHPOsFreeText:

Ethnicity: Iranian

ProbandLabel: Patient 1, male

FamilyAddInfo: 2yo at onset, 4yo at diagnosis, MRC sum score not available, consanguineous family

FamilyPreviousTesting: Respiratory evaluation: FVC = 90%, CK = 2,960 U/L,DBS enzyme activity (with inhibition) = 0.3 μmol/L/h, no muscle pathology performed, cardiac evaluations, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

Variant: NM_000152.4(GAA):c.854C>G (p.Pro285Arg)

ClinVar: 225114, https://www.ncbi.nlm.nih.gov/clinvar/variation/225114/

gnomAD: n/a

Family 8 - Patients 8a and 8b

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0000467, HP:0003327, HP:0010628, HP:0002015, HP:0003691, HP:0002650, HP:0040081

HPOsFreeText: 8b muscle pathology with mild lysosomal vacuolar myopathy with slight glycogen excess, no metachromatic debris, myopathic muscle unit action potentials

FamilyNotHPOs: HP:0003306

Ethnicity: Iranian

ProbandLabel: 8a, female, 27yo at onset, 32yo at diagnosis

FamilyAddInfo: 8b (male) dx at 40yo, 8a MRC sum score = 82, 8b MRC sum score = 60, 8b is wheelchair bound, both patients required use of NIV

FamilyPreviousTesting: Respiratory Evaluation: 8a FVC = 102%, 8b FVC = 17%, 8a CK = 268 U/L, 8b CK = 199 U/L, muscle pathology (examined only in 8b), DBS enzyme activity (with inhibition) for 8a = 0.11 μmol/L/h, for 8b = 0.15 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: 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

VariantAllele2: NM_000152.4(GAA):c.2078dupA (p.Ala694Glyfs)

ClinVar: 180143, https://www.ncbi.nlm.nih.gov/clinvar/variation/180143/

gnomAD: n/a