ExperimentalAssay

Variant: NM_000257.4(MYH7):c.5134C>T (p.Arg1712Trp), homozygous

ClinVar: 14118, https://www.ncbi.nlm.nih.gov/clinvar/variation/14118/

CaseST4-91: Sweden

DiseaseAssertion: Idiopathic Dilated Cardiomyopathy

FamilyInfo: N/A

CasePresentingHPOs: HP:0001644 (Dilated cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: HP:0002140, HP:0000822, HP:0001654, HP:0030955, HP:0000819, HP:0002666, HP:0000845, HP:0000820 (Ischemic stroke, Hypertension, Valvular heart disease, Alcoholism, Diabetes mellitus, Pheochromocytoma, Acromegaly, Thyroid disease)

NotHPOsFreeText: Patients were excluded for significant systemic infection, systemic diseases, previous cancer treatment including irradiation, and tachycardia-induced cardiomyopathy or other primary cardiomyopathy.

CaseAddInfo: N/A

CasePreviousTesting: See Supplemental Table 1

CaseGenotypingMethod: Genomic DNA was extracted from the patients. 41 exons of previously-reported genes that were reported in DCM patients were amplified and directly sequenced. Afterwards, the variants were aligned and sorted for pathogenicity.

Variant: NM_000257.3:c.1113G>C (p.Glu371Asp)

CAID: CA389051328 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000257.3%3Ac.1113G%3EC

gnomAD: Not in gnomAD

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

CaseHCM14.1: 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.2167C>T (p.Arg723Cys)

ClinVar: 14095 https://www.ncbi.nlm.nih.gov/clinvar/variation/14095/

gnomAD: South Asian 3.266e-5, Overall 1.194e-5 https://gnomad.broadinstitute.org/variant/14-23895023-G-A

Case1: male fetus

DiseaseAssertion: LVNC

FamilyInfo: first two pregnancies had resulted in miscarriages due to cervical insufficiency. The third pregnancy (after cerclage) resulted in a healthy nondysmorphic female with mild Ebstein anomaly of the tricuspid valve. The father was reported to have a history of a cardiac murmur and possible “hole in the heart.” Fetal echocardiography revealed that our patient's second child (fourth pregnancy) also had mild Ebstein anomaly. Father also has Ebstein anomaly, with significant apical displacement of the tricuspid valve, moderate tricuspid valve insufficiency, and right heart enlargement

CasePresentingHPOs: HP:0010316, HP:0031195

"Ebstein anomaly of the tricuspid valve, Apical hypertrabeculation of the left ventricle"

CaseHPOFreeText: mild apical displacement of the tricuspid valve, presence of multiple trabeculations on parasternal short‐axis and apical 4‐chamber views, with deep intertrabecular recesses

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: echocardiogram, Peripheral blood samples use to test 46 genes initially (including MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

GenotypingMethod: Testing was performed by oligonucleotide‐based target capture, followed by next generation sequencing. Sanger sequencing was used to provide data in areas with insufficient coverage and confirm clinically significant and novel variants. Heterozygous.

VariantMYH7: NM_000257.4:c.3658_3660del

ClinVar: 42968

CAID: CA013921

gnomAD: not reported

**VariantTTN: c.25722_25724delAGA (p.Glu8576del)

Allele registry currently not working

CaseMYH7-13: 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.1208G>A (p.Arg403Gln)

ClinVar: 14087 https://www.ncbi.nlm.nih.gov/clinvar/variation/14087/

gnomAD: Not in gnomAD

CaseMYH7-24: 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.2221G>T (p.Gly741Trp)

ClinVar: 177665 https://www.ncbi.nlm.nih.gov/clinvar/variation/177665/

gnomAD: Not in gnomAD

CaseMYH7-6: Australia

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: N/A

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: 2 other probands have 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.4135G>A (p.Ala1379Thr)

ClinVar: 42993 https://www.ncbi.nlm.nih.gov/clinvar/variation/42993/

gnomAD: Latino 2.822e-5, Overall 3.535e-6 https://gnomad.broadinstitute.org/variant/14-23887453-C-T

CaseMYH7-37: 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.1207C>T (p.Arg403Trp)

ClinVar: 14102 https://www.ncbi.nlm.nih.gov/clinvar/variation/14102/

gnomAD: Not in gnomAD

CaseMYH7-13: 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.3064A>G (p.Lys1022Glu)

CAID: CA389045738 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000257.3%3Ac.3064A%3EG

gnomAD: Not in gnomAD

Supplementary Material 4

Case M-14: 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.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

Supplementary Material 4

Case M-22: 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.2333A>G (p.Asp778Gly)

ClinVar: 14100, https://www.ncbi.nlm.nih.gov/clinvar/variation/14100/

gnomAD: n/a

Supplementary Material 4

Case M-15: 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.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

11 Unique Variants

Variant1: c.2069T>A p.(Met690Lys)

Variant2: c.2608C>T p.(Arg870Cys)

Variant3: c.2189T>C p.(Ile730Thr)

Variant4: c.400T>C p.(Tyr134His)

Variant5: c.2608C>T p.(Arg870Cys)

Variant6: c.1350G>T p.(Lys450Asn)

Variant7: c.1988G>A p.(Arg663His)

Variant8: c.1477A>G p.(Met493Val)

Variant9: c.4130C>T p.(Thr1377Met)

Variant10: c.2972A>G p.(Lys991Arg)

Variant11: c.1350G>T p.(Lys450Asn)

Variant12: c.1426C>T p.(Leu476Phe)

Variant13 c.5560-8G>A p.(?)

(NM_000257.4:c.5560-8G>A MANE Preferred)

Case N3: Tunisia, Female, 28yo at onset, 30yo at study

DiseaseAssertion: hypertrophic cardiomyopathy

CasePresentingHPOs: HP:0100749 (chest pain)

CaseHPOFreeText: left ventricular septum (LVS) ≥15 mm, septum size = 25mm

FamilyInfo: Family history of HCM and 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:c.5639G>A

CAID: CA257807907, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA257807907

gnomAD: n/a

MultipleGeneVariants:

(1) MYBPC3 Variant:

Variant: NM_000256.3(MYBPC3):c.772G>A (p.Glu258Lys)

ClinVar: 42792, https://www.ncbi.nlm.nih.gov/clinvar/variation/42792/

gnomAD: 0.00001656, https://gnomad.broadinstitute.org/variant/11-47369975-C-T

Case N39: Tunisia, Male, 30yo at onset, 40yo at study

DiseaseAssertion: hypertrophic cardiomyopathy

CasePresentingHPOs: HP:0100749, HP:0002094 (chest pain, dyspnea)

CaseHPOFreeText: left ventricular septum (LVS) ≥15 mm, septum size = 26mm

FamilyInfo: no family history of HCM or 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:c.353C>T

CAID: CA389052998, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA389052998

gnomAD: n/a

MultipleGeneVariants:

(1) MYBPC3 Variant:

Variant: NM_000256.3:c.3296G>A

CAID: CA380314113, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA380314113

gnomAD: 0.000004667, https://gnomad.broadinstitute.org/variant/11-47354779-C-T

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.2945T>C (p.Met982Thr)

ClinVar: 42941, https://www.ncbi.nlm.nih.gov/clinvar/variation/42941/

gnomAD: 0.0008484, https://gnomad.broadinstitute.org/variant/14-23892910-A-G

Supplementary Data table 1

Variant noted to be present in 2 individuals

Variant: NM_000257.3(MYH7):c.1727A>G (p.His576Arg)

ClinVar: 177625, https://www.ncbi.nlm.nih.gov/clinvar/variation/177625/

gnomAD: 0.00001768, https://gnomad.broadinstitute.org/variant/14-23896955-T-C

Case#: II-9, female, 46 yrs

DiseaseAssertion: HCM

FamilyInfo: Yes, 2 siblings and niece have HCM

CasePresentingHPOs: chest tightness, palpitations (HP:0031352, HP:0001962)

CaseHPOFreeText: T flattened and inverted and left axis deviation (-48 degrees), 22mm MLVWT, 63% LVE F, 1.29 E/A ratio, LVOT-PG 4mm

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

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

MultipleGeneVariants:

(1) Variant: absent (MYH7- A934V)

ClinVar: N/A

CAID: CA389047003

gnomAD: absent

(2) Variant: NM_000257.4(MYH7):c.4159G>A (p.Glu1387Lys)

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

CAID: N/A

gnomAD: 0.00003266 South Asian https://gnomad.broadinstitute.org/variant/14-23887429-C-T

Supplementary Data: S2 Table

Case 160: 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, 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:c.78641C>T

CAID: CA1988519, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_133378.4%3Ac.78641C%3ET

gnomAD: 0.00001646, https://gnomad.broadinstitute.org/variant/2-179424514-G-A

Supplementary Data: S2 Table

Case 2: 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, PCR, Sanger 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 Data Table S3

Case: 355

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.2945T>C (p.Met982Thr)

ClinVar: 42941 https://www.ncbi.nlm.nih.gov/clinvar/variation/42941/

gnomAD: 0.001416, https://gnomad.broadinstitute.org/variant/14-23892910-A-G

MultipleGeneVariants:

(1) MYBPC3 Variant

Variant: NM_000256.3(MYBPC3):c.3413G>A (p.Arg1138His)

ClinVar: 177689 https://www.ncbi.nlm.nih.gov/clinvar/variation/177689/

gnomAD: 0.01063, https://gnomad.broadinstitute.org/variant/11-47354442-C-T

Supplementary Data Table S3

Case: 19

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

Supplementary Data Table S3

Case: 256

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.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

MultipleGeneVariants:

(1) PLB1 Variant

Variant: NM_153021.4:c.275A>G (p.Lys92Arg)

CAID: CA1586810 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_153021.5%3Ac.275A%3EG

gnomAD: 0.03209, https://gnomad.broadinstitute.org/variant/2-28748165-A-G

(2) RBM20 Variant

Variant: NM_001134363.3(RBM20):c.2662G>A (p.Asp888Asn)

ClinVar: 43995 https://www.ncbi.nlm.nih.gov/clinvar/variation/43995/

gnomAD: 0.02090, https://gnomad.broadinstitute.org/variant/10-112581039-G-A

Supplementary Data Table S3

Case: 353

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) EYA4 Variant

Variant: NM_004100.5(EYA4):c.979G>A (p.Asp327Asn)

ClinVar: 191664 https://www.ncbi.nlm.nih.gov/clinvar/variation/191664/

gnomAD: 0.004341, https://gnomad.broadinstitute.org/variant/6-133802609-G-A

(2) TTN Variant

Variant: NM_133378.4:c.21031G>T (p.Glu7011Ter)

CAID: CA349496727 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_133378.4%3Ac.21031G%3ET

gnomAD: Not in gnomAD

Supplementary Data Table S3

Case: 46

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) EYA4 Variant

Variant: NM_004100.5(EYA4):c.1495G>A (p.Val499Ile)

ClinVar: 534385, https://www.ncbi.nlm.nih.gov/clinvar/variation/534385/

gnomAD: 0.0002548, https://gnomad.broadinstitute.org/variant/6-133834170-G-A

(2) FKTN Variant

Variant: NM_006731.2(FKTN):c.1297A>G (p.Thr433Ala)

ClinVar: 36137, https://www.ncbi.nlm.nih.gov/clinvar/variation/36137/

gnomAD: 0.002206, https://gnomad.broadinstitute.org/variant/9-108397456-A-G

DiseaseAssertion: cardiomyopathy

Variant: NM_000257.4:c.2543A>G

ClinVar: 177758

CAID: CA012584

CaseMYH7-7: 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.1358G>A (p.Arg453His)

ClinVar: 42838 https://www.ncbi.nlm.nih.gov/clinvar/variation/42838/

gnomAD: Not in gnomAD

CaseMYH7-9: 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.1012G>A (p.Val338Met)

ClinVar: 164381 https://www.ncbi.nlm.nih.gov/clinvar/variation/164381/

gnomAD: Not in gnomAD

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:c.902T>A

CAID: CA389051788, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA389051788

gnomAD: n/a

Supplementary Data: Online Table 1a

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.732+1G>A

ClinVar: 14127, https://www.ncbi.nlm.nih.gov/clinvar/variation/14127/

gnomAD: 0.000003976, https://gnomad.broadinstitute.org/variant/14-23900793-C-T

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.1727A>G (p.His576Arg)

ClinVar: 177625, https://www.ncbi.nlm.nih.gov/clinvar/variation/177625/

gnomAD: 0.00001768, https://gnomad.broadinstitute.org/variant/14-23896955-T-C

Supplementary Data, Table 2

Variant noted to be present in 3 individuals

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

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.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

Supplementary Data, Table 2

Variant noted to be present in 7 individuals

Variant: NM_000257.3(MYH7):c.2093T>C (p.Val698Ala)

ClinVar: 42878, https://www.ncbi.nlm.nih.gov/clinvar/variation/42878/

gnomAD: n/a

Case298: Female, 6 years onset, Japan, Asian

DiseaseAssertion: Left ventricular noncompaction

CasePresentingHPOs: HP:0030682 (Left ventricular noncompaction)

HPOsFreeText: Left Ventricular Ejection Fraction at 65%, LVDD-Z score at 2.1

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.2710C>T (p.Arg904Cys)

ClinVar: 164316 https://www.ncbi.nlm.nih.gov/clinvar/variation/164316/

gnomAD: Ashkenazi Jewish 9.921e-5, Overall 3.977e-6 https://gnomad.broadinstitute.org/variant/14-23893328-G-A

CaseII2: 65 year old male

DiseaseAssertion: left ventricular non compaction cardiomyopathy

FamilyInfo: three family members presenting with the same MYH7 mutation

CasePresentingHPOs: HP:0012764, HP:0002515, HP:0003376, HP:0003307, HP:0003391, HP:0003547

"Orthopnea, Waddling gait, Steppage gait, Hyperlordosis, Gowers sign, Shoulder girdle muscle weakness"

CaseHPOFreeText: shortness of breath during exertion, foot drop, At lower limbs weakness and hypotrophy were severe in distal muscles and moderate in proximal muscles

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: molecular analysis for ACTA1 and ITGA7 was performed, resulted negative. Molecular analysis for DES, LMNA and MYH7 genes were carried out

GenotypingMethod: mutation screening, primers flanking the intron-exon junctions of each MYH7 exon, the 5′ and 3′ UTR

Variant: NM_000257.4:c.5401G>A

ClinVar: 43069

CAID: CA016087

gnomAD: not found

Case II-2: Italian, Female

DiseaseAssertion: severe obstructive hypertrophic cardiomyopathy

CasePresentingHPOs:

CaseHPOFreeText: interventricular septal and/or posterior wall thickness in end-diastole ≥15 mm, had surgical myectomy

CasePreviousTesting: M-mode-2D and color-Doppler study to analyze cardiac chamber dimensions, global systolic and diastolic function, valve and great arteries anomalies, echocardiography,

CaseGenotypingMethod: exon 23 and flanking regionals analyzed via Sanger Sequencing, Variants found via exome sequencing tested for segregation in family by Sanger sequencing on an ABI PRISM 3130 DNA sequencer

Variant: NM_000257.3:c.2795T>A

CAID: CA389047028, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA389047028

gnomAD: n/a

CaseA14: Female, 44 years report, China, Asian

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: No family history

CasePresentingHPOs: HP:0001639 (Hypertrophic cardiomyopathy)

HPOsFreeText: Interventricular septal thickness at 17.6 mm, Left ventricular posterior wall thickness at 8.8 mm, Left ventricular end-diastolic diameter at 42.7 mm, Left ventricular septal thickness at 36.6 mm, Left ventricular ejection fraction at 68%

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.161G>A (p.Arg54Gln)

ClinVar: 42856 https://www.ncbi.nlm.nih.gov/clinvar/variation/42856/

gnomAD: East Asian 2.506e-4, Overall 2.475e-5 https://gnomad.broadinstitute.org/variant/14-23902781-C-T

Case#: 24

DiseaseAssertion: LVNC

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: 5.9 Fathmm, 0 sift, 0.984 polyphen2, 0 GVGD, mutation taster 1, -4.96 provean, -6.07 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.689T>C (p.Phe230Ser)

ClinVar: 263543 https://www.ncbi.nlm.nih.gov/clinvar/variation/263543/

CAID: N/A

gnomAD: absent

Case KMP 11: Eastern Slovakia, Female, 57yo

DiseaseAssertion: hypertrophic cardiomyopathy

FamilyInfo: positive family history

CaseHPOFreeText: left ventricular ejection fraction = 60%, New York Heart Association Classification I

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

PMID: 23508784

Gene: MYH7

HGNC: 7577

Variant(1) NM_000257.4:c.1357C>T

ClinVar: 14089

CAID: CA010630

Variant(2) NM_000257.4:c.2146G>A

ClinVar: 14105

CAID: CA011770

"As shown in Table 3 and Figure 2A, 9 of the 15 mutations found in MYH7 were novel. In silico analysis of the new mis-sense mutations was performed using a suite of bioinformatic tools. Analysis in SIFT, Pmut, PolyPhen, SNAP and PhDSNP revealed that for the E1555G mutation there was a consensus between the different bioinformatic tools to classify it as pathological. But, for 6 mutations (A355S, L427M, D587H, R1382Q, N1890S, and G1931C), at least 1 program did not predict a clear effect on protein function. Moreover, 2 of these were variants, R845K and A1637T, predicted to be neutral by all 5 methods."

CaseV-4: Female, 11 years old

DiseaseAssertion: CFTD and LVNC

FamilyInfo: Multigenerational Italian family. Phenotypic data were available for 10 individuals (3 males and 7 females) ranging in age from 4 to 50 years old. All individuals were of Caucasian ancestry. DNA was available for 6 individuals (IV-10, IV-13, IV-14, V-1, V-4, V-5). Authors identified a mild LVNC phenotype in the mother (IV-14), sister (V-5) and cousin (V-1) of the proband, with hypertabeculations of the mid inferolateral wall and of the ape and without neuromuscular disorders. During the growth, there was a reduction of clinical signs in patients V-1 and V-5. No data have been collected for individual IV-9, who died at the age of 35 of unknown causes. The father (IV-13) of the proband was asymptomatic.

Proband is the first child of a family with a history of consanguinity (mother’s parents are first-degree cousins) and diabetes in the maternal line (grandmother, one great-uncle, one uncle and a first-degree cousin) without neuromuscular diseases.

LVNC segregated as a dominant mode of inheritance with high phenotypic heterogeneity and reduced penetrance. CFTD phenotype showed a recessive mode of inheritance.

CasePresentingHPOs: HP:0001290, HP:0002033, HP:0001643, HP:0001655, HP:0001374, HP:0004325, HP:0001943, HP:0001508, HP:0002515, HP:0002650, HP:0001284

"Generalized hypotonia, poor suck, Patent ductus arteriosus, Patent foramen ovale, Congenital hip dislocation, Decreased body weight (below 3rd percentile), Hypoglycemia, Failure to thrive, waddling gait, Scoliosis, Areflexia

CaseHPOFreeText: persistent crying, Persistent arterial duct and patent foramen ovale were diagnosed at birth but resolved spontaneously, as shown by echocardiography at the age of 1 month, congenital dislocation of the left hip, at 17 months of age hospitalized due to body weight below the third percentile and hypoglycemia, difficulties in chewing and swallowing, inability to stand up from a sitting position, a slight degree of weakness of the facial and masticator muscles, mild weakness of the glutei and ileo-psoas and marked bilateral quadriceps, Tendon reflexes were absent. Joints contractures had never been observed, A blood test confirmed hypoglycemia and normal levels of serum creatine kinase and isoenzymes, quadriceps muscle biopsy displayed a predominance of type 1 fibers

CaseNotHPOs:

CaseNotHPOFreeText: internal nuclei, nemaline bodies, cores were observed

CasePreviousTesting: Authors extended the clinical and instrumental (EMG, ECG, Echocardiography, muscle biopsy) evaluation to the whole family, Echocardiography showed a slight left ventricular (LV) dilatation, a moderate reduction of the LV global function (ejection fraction 40%), and a non-compacted aspect of the overall infero-lateral wall. The karyotype and FISH were normal. The serum creatine kinase (CK) was within the normal range, Dystrophin, emerin, calpain and lamin A/C were examined and found to be normal, cardiological investigation confirmed a long QTc and showed signs of left ventricular hypertrophy and repolarization abnormalities in the ECG, performed a thorough survey of all previously identified CFTD and LVNC genes to definitively exclude their involvement in the disease phenotype. Only intronic polymorphic variants were detected in TPM3, ACTA1, TPM2, MYL2, MYL3, G4.5, DTNA, ZASP, ACTC1, MYBPC3 and TMP1. Both intronic and coding polymorphic variants were detected in SEPN1, RYR1, MYH7, LMNA/C, TNNT2 and TNNI3

GenotypingMethod: Whole-exome sequencing of the proband and her cousin

VariantMYH7B: NM_020884.5:c.2668C>T

ClinVar:

CAID: CA9827409

gnomAD: https://gnomad.broadinstitute.org/variant/20-33582046-C-T

Case1: 18 year old male

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: parents and 2 siblings all phenotype negative for HCM, tested negative for the mutation

CasePresentingHPOs: HP:0001639, HP:0031992, HP:0031972, HP:0004755, HP:0004756

"Hypertrophic cardiomyopathy, Apical hypertrophic cardiomyopathy, presyncope, Supraventricular tachycardia, Ventricular tachycardia"

CasePreviousTesting: Authors simply state "on genetic testing"

Variant: NM_000257.4:c.1588A>G

ClinVar: 520309

CAID: CA028909

gnomAD: https://gnomad.broadinstitute.org/variant/14-23897094-T-C?dataset=gnomad_r2_1

Total Allele Frequency 0.000003980 South Asian 0.00003266

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 probands

Variant: NM_000257.4(MYH7):c.1207C>T (p.Arg403Trp)

ClinVarID: 14102 https://www.ncbi.nlm.nih.gov/clinvar/variation/14102/

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 HCM probands

Variant: NM_000257.4(MYH7):c.746G>A (p.Arg249Gln)

ClinVar: 14088 https://www.ncbi.nlm.nih.gov/clinvar/variation/14088/

gnomAD: Not in gnomAD

PMID: 24183960

Gene: MYH7

HGNC: 7577

Variant 1: NM_000257.4(MYH7):c.2167C>G (p.Arg723Gly)

ClinVar: 42885, https://www.ncbi.nlm.nih.gov/clinvar/variation/42885/

gnomAD: n/a

Variant 2: NM_000257.4:c.599C>T (p.Ala200Val)

CAID: CA389052449, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA389052449

gnomAD: n/a

No Case Info

PMID: 23798412

Gene: MYH7

HGNC: 7577

PMID: 23794396

Gene: MYH7

HGNC: 7577

CaseHCM051: 39 yrs report, Vietnam, Asian

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: Family history of hypertrophic cardiomyopathy, Has 2 siblings where the MYH7 and MYOZ2 mutations are solely present in the brother and sister respectively, Brother has LVH and palpitations while sister has no symptoms whatsoever

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

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.3424G>A (p.Glu1142Lys)

ClinVar: 181222 https://www.ncbi.nlm.nih.gov/clinvar/variation/181222/

gnomAD: Not in gnomAD

Multiple Gene Variants

(1) MYOZ2 Variant

Variant: NM_016599.4:c.326C>G (p.Pro109Arg)

CAID: CA104971226 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA104971226

gnomAD: Not in gnomAD

CasePT-62: 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.1370T>C (p.Ile457Thr)

ClinVar: 42840 https://www.ncbi.nlm.nih.gov/clinvar/variation/42840/

gnomAD: European (Non-Finnish) 8.790e-6, Overall 3.976e-6 https://gnomad.broadinstitute.org/variant/14-23898201-A-G

ExperimentalAssay: The authors used TALEN genome editing to introduce the orthologous mutation in MYH7 into pigs. Sanger sequencing verified successful knock-in. Most of the pigs using embryos with this mutation died prematurely, with the surviving cohort showing phenotypes of HCM similar to those in human patients. Whole genome sequencing was also performed to test for off-target mutations, but none were found.

Human Variant

Variant: NM_000257.3:c.2167C>G (p.Arg723Gly)

ClinVar: 42885 https://www.ncbi.nlm.nih.gov/clinvar/variation/42885/

gnomAD: Not in gnomAD

Pig Variant

Variant: NM_213855:c.2223C>G

This variant is orthologous to the above mutation in humans.