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rs371898076

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1PM5PP2PP3_ModeratePP5_Very_Strong

The NM_000257.4(MYH7):c.1988G>A(p.Arg663His) variant causes a missense change. The variant allele was found at a frequency of 0.00000992 in 1,613,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R663C) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.000040 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

MYH7
NM_000257.4 missense

Scores

11
5
4

Clinical Significance

Pathogenic reviewed by expert panel P:30

Conservation

PhyloP100: 5.94
Variant links:
Genes affected
MYH7 (HGNC:7577): (myosin heavy chain 7) Muscle myosin is a hexameric protein containing 2 heavy chain subunits, 2 alkali light chain subunits, and 2 regulatory light chain subunits. This gene encodes the beta (or slow) heavy chain subunit of cardiac myosin. It is expressed predominantly in normal human ventricle. It is also expressed in skeletal muscle tissues rich in slow-twitch type I muscle fibers. Changes in the relative abundance of this protein and the alpha (or fast) heavy subunit of cardiac myosin correlate with the contractile velocity of cardiac muscle. Its expression is also altered during thyroid hormone depletion and hemodynamic overloading. Mutations in this gene are associated with familial hypertrophic cardiomyopathy, myosin storage myopathy, dilated cardiomyopathy, and Laing distal myopathy. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 15 ACMG points.

PM1
In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 12 uncertain in NM_000257.4
PM5
Other missense variant is known to change same aminoacid residue: Variant chr14-23426834-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 42874.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
PP2
Missense variant where missense usually causes diseases, MYH7
PP3
MetaRNN computational evidence supports a deleterious effect, 0.91
PP5
Variant 14-23426833-C-T is Pathogenic according to our data. Variant chr14-23426833-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 42875.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr14-23426833-C-T is described in Lovd as [Pathogenic]. Variant chr14-23426833-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYH7NM_000257.4 linkuse as main transcriptc.1988G>A p.Arg663His missense_variant 18/40 ENST00000355349.4
MYH7NM_001407004.1 linkuse as main transcriptc.1988G>A p.Arg663His missense_variant 17/39

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYH7ENST00000355349.4 linkuse as main transcriptc.1988G>A p.Arg663His missense_variant 18/401 NM_000257.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0000395
AC:
6
AN:
151758
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000656
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000795
AC:
2
AN:
251480
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135920
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000176
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000684
AC:
10
AN:
1461868
Hom.:
0
Cov.:
32
AF XY:
0.00000688
AC XY:
5
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.00000629
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000395
AC:
6
AN:
151758
Hom.:
0
Cov.:
32
AF XY:
0.0000405
AC XY:
3
AN XY:
74070
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000656
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000521
Hom.:
0
Bravo
AF:
0.0000416
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000165
AC:
2

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:30
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not provided Pathogenic:8
Pathogenic, criteria provided, single submitterclinical testingGeneDxJun 01, 2022Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Functional studies using patient derived cells demonstrated p.(R663H) is strongly implicated in the dysregulation of calcium ion cycling, causing elevation of calcium ions which can induce both cellular hypertrophy and contractile arrhythmia (Lan et al., 2013); This variant is associated with the following publications: (PMID: 23283745, 25637381, 23299917, 15563892, 27247418, 23396983, 11133230, 16199542, 28718902, 28573431, 15358028, 17125710, 15858117, 20800588, 23233322, 30984009, 24566549, 20087448, 24093860, 22857948, 18403758, 21959974, 19150014, 23054336, 23711808, 26936621, 12820698, 10750581, 28166811, 26914223, 21310275, 27532257, 25132132, 23690394, 17560888, 27600940, 27639548, 18533079, 29300372, 29121657, 29907873, 30217213, 12707239, 22112859, 31006259, 30685992, 30324321, 31931472, 31513939, 31737537, 32284968, 31447099, 33673806, 33586461, 32746448, 33407484, 32894683, 25086479, 23290139, 34137518, 33658040, 33906374, 24704860) -
Pathogenic, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Pathogenic, criteria provided, single submitterclinical testingAiLife Diagnostics, AiLife DiagnosticsJan 20, 2022- -
Pathogenic, criteria provided, single submitterclinical testingRevvity Omics, RevvityJan 03, 2023- -
Pathogenic, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Pathogenic, no assertion criteria providedclinical testingStanford Center for Inherited Cardiovascular Disease, Stanford UniversityFeb 06, 2014Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. p.Arg663His (c.1988G>A) Based on the strong case data, absence in controls, and presence of other pathogenic variants at the same codon, we consider this variant very likely disease causing. Per their ClinVar submission LMM considers it pathogenic (SCV000059409). The variant has been seen in at least 23 unrelated cases of HCM, likely more, with very strong segregation data in one family (Greber-Platzer et al 2001 1 case, Gruver et al 1999 1 family, Richard et al 2003 2 cases, van Driest et al 2004 8 cases, Mohiddin et al 2003 3 cases, Xie et al 2004 ?, Song et al 2005 4 cases). Gruver et al (1999) reported this mutation in a large family, segregating with HCM in 16 individuals. There are likely additional published cases; we have not updated our review of the literature for a few years. In our center we have seen the variant in four patients: an African-American woman with HCM and two of her affected family members (described in Lan et al 2012); a Caucasian male diagnosed with HCM in his teens with a father who also has HCM; a woman diagnosed with HCM at 41 years of age; a Japanese woman diagnosed with HCM at 25yo who underwent heart transplant at 56yo. This third patient also carries p.Val1360Ile (we classify as a VUS) on the same allele and p. Ala26Val (we classify as a VUS) on the other allele. Her affected brother carries the allele with p.Arg663His and p.Val1360Ile but not the allele with p.Ala26Val. Her affected father, paternal uncle, paternal cousin, and paternal aunt were not available for genetic testing. Other pathogenic variants have been reported at this codon: p.Arg663Cys and p.Arg663Ser. Van Driest et al (2004) described codon 663 as a ‘hotspot’ with 9 out of 58 (15%) patients with MYH7 variants in that study having a variant involving codon 663. PolyPhen2 predicts the variant to be possibly damaging and mutationtaster predicts it to be disease causing. The variant has been seen in 1 of 6873 publicly available general population samples and published controls. This variant has been reported as absent in 100 (Richard et al 2006), 200 (van Driest et al 2004) and 120 (Song et al 2005) control individuals, for a total of 420 ethnically diverse controls. The variant was recently reported online in 1 of 4250 Caucasian individuals and 0 of 2203 African-American individuals in the NHLBI Exome Sequencing Project dataset (as of May 24th, 2013). The phenotype of that individuals is not publicly available, however the cohorts that were merged to create this dataset were all either general population samples or samples recruited for common cardiovascular disease such as hypertension. Note that other very likely disease causing sarcomere variants have been seen in published controls (Pan et al 2012). -
Pathogenic, criteria provided, single submitterclinical testingInstitute of Medical Genetics and Applied Genomics, University Hospital TübingenOct 23, 2020- -
Pathogenic, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesJan 07, 2022The MYH7 c.1988G>A; p.Arg663His variant (rs371898076) was initially reported in a large hypertrophic cardiomyopathy (HC) pedigree (Gruver 1999) and has since been reported in a large number of HC patients from ethnically diverse populations (Bales 2016, Bashyam 2012, Brito 2012, Chiou 2015, Garcia-Castro 2009, Greber-Platzer 2001, Ingles 2005, Liu 2013, Marsiglia 2013, Miller 2013, Mohiddin 2003, Richard 2003, Song 2005, van Driest 2004, van Rijsingen 2009, Wang 2014, Zou 2013). Other variants affecting the same codon and other nearby codons have also been reported to be pathogenic, suggesting this is a mutational hot-spot (e.g. Curila 2012, Richard 2003, Song 2005, van Driest 2004). Structural studies indicate that this amino acid is located at the myosin-actin interface (Bashyam 2012), and functional cell-based studies demonstrate that the presence of this variant results in calcium dysregulation and elevated intracellular calcium levels (Lan 2013). This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.001% (4/282,842 alleles) and is categorized in ClinVar as pathogenic/likely pathogenic (Variation ID: 42875). Based on the available information, this variant is classified as pathogenic. References: Bales ND et al. Comprehensive Versus Targeted Genetic Testing in Children with Hypertrophic Cardiomyopathy. Pediatr Cardiol. 2016 Jun;37(5):845-51. Bashyam MD et al. A low prevalence of MYH7/MYBPC3 mutations among familial hypertrophic cardiomyopathy patients in India. Mol Cell Biochem. 2012 Jan;360(1-2):373-82. Brito D et al. Sarcomeric hypertrophic cardiomyopathy: genetic profile in a Portuguese population. Rev Port Cardiol. 2012 Sep;31(9):577-87. Doi: 10.1016/j.repc.2011.12.020. Chiou KR et al. Detection of mutations in symptomatic patients with hypertrophic cardiomyopathy in Taiwan. J Cardiol. 2015 Mar;65(3):250-6. Curila K et al. Spectrum and clinical manifestations of mutations in genes responsible for hypertrophic cardiomyopathy. Acta Cardiol. 2012 Feb;67(1):23-9. Garcia-Castro M et al. Mutations in sarcomeric genes MYH7, MYBPC3, TNNT2, TNNI3, and TPM1 in patients with hypertrophic cardiomyopathy. Rev Esp Cardiol. 2009 Jan;62(1):48-56. Greber-Platzer S et al. Beta-myosin heavy chain gene mutations and hypertrophic cardiomyopathy in Austrian children. J Mol Cell Cardiol. 2001 Jan;33(1):141-8. Gruver EJ et al. Familial hypertrophic cardiomyopathy and atrial fibrillation caused by Arg663His beta-cardiac myosin heavy chain mutation. Am J Cardiol. 1999 Jun 17;83(12A):13H-18H. Ingles J et al. Compound and double mutations in patients with hypertrophic cardiomyopathy: implications for genetic testing and counselling. J Med Genet. 2005 Oct;42(10):e59. Lan F et al. Abnormal calcium handling properties underlie familial hypertrophic cardiomyopathy pathology in patient-specific induced pluripotent stem cells. Cell Stem Cell. 2013 Jan 3;12(1):101-13. Liu W et al. Mutation spectrum in a large cohort of unrelated Chinese patients with hypertrophic cardiomyopathy. Am J Cardiol. 2013 Aug 15;112(4):585-9. Marsiglia JD et al. Screening of MYH7, MYBPC3, and TNNT2 genes in Brazilian patients with hypertrophic cardiomyopathy. Am Heart J. 2013 Oct;166(4):775-82. Miller EM et al. Uptake of cardiac screening and genetic testing among hypertrophic and dilated cardiomyopathy families. J Genet Couns. 2013 Apr;22(2):258-67. Mohiddin SA et al. Utility of genetic screening in hypertrophic cardiomyopathy: prevalence and significance of novel and double (homozygous and heterozygous) beta-myosin mutations. Genet Test. 2003 Spring;7(1):21-7. Richard P et al. Hypertrophic cardiomyopathy: distribution of disease genes, spectrum of mutations, and implications for a molecular diagnosis strategy. Circulation. 2003 May 6;107(17):2227-32. Song L et al. Mutations profile in Chinese patients with hypertrophic cardiomyopathy. Clin Chim Acta. 2005 Jan;351(1-2):209-16. van Driest SL et al. Comprehensive analysis of -
Hypertrophic cardiomyopathy Pathogenic:6
Pathogenic, criteria provided, single submitterclinical testingCenter for Human Genetics, University of LeuvenOct 31, 2018- -
Pathogenic, criteria provided, single submitterclinical testingInvitaeJan 25, 2024This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 663 of the MYH7 protein (p.Arg663His). This variant is present in population databases (rs371898076, gnomAD 0.003%). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 10750581, 11133230, 12707239, 12820698, 15358028, 15563892, 16199542, 23283745, 23290139, 23396983, 26914223). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 42875). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt MYH7 protein function with a positive predictive value of 95%. This variant disrupts the p.Arg663 amino acid residue in MYH7. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15358028, 15563892, 15858117, 18383048, 20800588, 22112859, 23233322, 23283745, 23690394). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 14, 2014The p.Arg663His variant in MYH7 has previously been reported in >40 individuals with HCM and was shown to segregate with disease in >25 affected relatives (Gruv er 1999, Greber-Platzer 2001, Mohiddin 2003, Richard 2003, Van Driest 2004, Song 2005, Ingles 2005, Zou 2013, Lan 2013, LMM unpublished data). This variant has been identified in 0.01% (1/8600) of European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS). Functional studies showed that this variant impacts protein function (Lan 2013); however, this in vitro assay may not accurately represent biological function. This variant meets our criteria to be classified as pathogenic (http://www.partners.org/personaliz edmedicine/LMM) based upon frequency in cases relative to the general population and extensive segregation with disease. -
Pathogenic, criteria provided, single submitterclinical testingKnight Diagnostic Laboratories, Oregon Health and Sciences UniversityJun 17, 2016- -
Pathogenic, reviewed by expert panelcurationClinGen Cardiomyopathy Variant Curation Expert PanelDec 15, 2016The c.1988G>A (p.Arg663His) variant in MYH7 has been reported in >30 individuals with hypertrophic cardiomyopathy (PS4; PMID:27532257; PMID:10750581; PMID:11133230; PMID:12707239; PMID:15563892; PMID:16199542; PMID:15358028; AGCMC Sydney ClinVar SCV000212629.1; Invitae ClinVar SCV000219103.7; Partners LMM ClinVar SCV000059409.5; SHaRe consortium, PMID: 30297972). This variant segregated with disease in >15 affected individuals (PP1_Strong; PMID:10750581; Partners LMM ClinVar SCV000059409.5; SHaRe consortium, PMID: 30297972). This variant was identified in 2/66718 European chromosomes (PM2; http://exac.broadinstitute.org). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; PMID:27532257). In summary, this variant meets criteria to be classified as pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PP1_ Strong; PM1; PM2 -
Likely pathogenic, criteria provided, single submitterresearchGenetics and Genomics Program, Sidra Medicine-- -
Hypertrophic cardiomyopathy 1 Pathogenic:6
Pathogenic, criteria provided, single submitterclinical testingCenter of Genomic medicine, Geneva, University Hospital of GenevaJul 17, 2017This heterozygous missense variant in the MYH7 gene was identified in a patient with hypertrophic cardiomyopathy -
Pathogenic, criteria provided, single submitterclinical testingHuman Genome Sequencing Center Clinical Lab, Baylor College of MedicineOct 10, 2018This c.1988G>A (p.Arg663His) variant in the MYH7 gene has been reported in multiple unrelated individiuals affected with hypertrophic cardiomyopathy (PMID 10750581, 11133230, 15358028, 15563892, 21959974, 22112859, 23233322, 23290139) and segregates with disease in two families (PMID 10750581, 23290139). This variant is absent in the general population. This variant is located in myosin head domain of the MYH7 gene where multiple pathogenic variants have been identified. Therefore, this c.1988G>A (p.Arg663His) variant in the MYH7 gene is classified as pathogenic. -
Likely pathogenic, criteria provided, single submitterclinical testingLaboratory of Genetics and Molecular Cardiology, University of São Paulo-- -
Pathogenic, criteria provided, single submitterclinical testingClinical Genetics Laboratory, Region OstergotlandSep 07, 2020PS4, PM1, PM5, PP5, PS3 -
Pathogenic, criteria provided, single submitterresearchAgnes Ginges Centre for Molecular Cardiology, Centenary Institute-This MYH7 Arg663His variant is a well described HCM causing mutation. Genetic screening in HCM cohorts from various ethnic populations have identified this mutation in multiple unrelated probands (see references). Haplotype analysis has shown that this mutation is not a founder mutation, but rather, this position is a mutational hotspot (Van Driest SL, et al., 2004; Song L, et al., 2005). Mutations at this position which result in different amino acid substitutions have also been detected in HCM patients (Richard P, et al., 2003; Van Driest SL, et al., 2004; Song L, et al., 2005). Familial analysis has shown co-segregation of the variant with disease, however, disease penetrance is incomplete and the phenotype can be variable (Gruver EJ, et al., 1999; Keller DI, et al., 2009). Studies in pediatric HCM cohorts have identified this mutation to be a shared genetic cause of early-onset and adult-onset cardiomyopathy (Morita H, et al., 2008). Functional studies by Lan F, et al. (2013) using patient specific iPSC cardiomyocytes from carriers of this mutation recapitulate disease characteristics including hypertrophy and arrhythmia. To date, we have identified this mutation in 3 index cases with HCM and one possible case of HCM. Based on segregation analysis and the available literature, we classify this variant as "pathogenic". -
Pathogenic, criteria provided, single submitterclinical testing3billionJan 03, 2022The variant was co-segregated with Cardiomyopathy, hypertrophic, 1 in multiple affected family members with additional meioses (PMID: 30297972, 10750581) (PP1_S). The variant has been observed in multiple (>3) similarly affected unrelated individuals(PMID: 11133230, 15358028, 27532257, 16199542, 12707239, 30297972, 10750581, 15563892, PS4_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.742, 3CNET: 0.976, PP3_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000014, PM2_M). The variant is located in a well-established functional domain or exonic hotspot, where pathogenic variants have frequently reported (PM1_M). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000042874, PMID:12707239,15358028, PM5_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Primary familial hypertrophic cardiomyopathy Pathogenic:3
Pathogenic, criteria provided, single submitterclinical testingMolecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart InstituteFeb 15, 2017- -
Pathogenic, criteria provided, single submitterclinical testingBlueprint GeneticsNov 04, 2015- -
Likely pathogenic, no assertion criteria providedresearchCSER _CC_NCGL, University of WashingtonJun 01, 2014- -
Cardiovascular phenotype Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsMar 08, 2022The p.R663H pathogenic mutation (also known as c.1988G>A), located in coding exon 16 of the MYH7 gene, results from a G to A substitution at nucleotide position 1988. The arginine at codon 663 is replaced by histidine, an amino acid with highly similar properties. This alteration has been reported in multiple unrelated individuals with hypertrophic cardiomyopathy (HCM) and co-segregated with disease in multiple families (Gruver EJ et al. Am J Cardiol. 1999;83(12A):13H-18H; Greber-Platzer S et al. J Mol Cell Cardiol. 2001;33(1):141-8; Ingles J et al. J Med Genet. 2005;42(10):e59; Keller DI et al. Int J Cardiol. 2009;134(3):e87-93; Bos JM et al. Mayo Clin Proc. 2014;89(6):727-37; Bales ND et al. Pediatr Cardiol, 2016 Jun;37:845-51). A study of induced pluripotent stem cell cardiomyocytes derived from individuals with this alteration reported that disease characteristics and abnormal calcium handling were demonstrated at the cellular-level (Lan F et al. Cell Stem Cell. 2013;12(1):101-13). In addition, two other alterations at the same codon, p.R633S (c.1987C>A) and p.R663C (c.1987C>T), have also been reported in association with HCM (Richard P et al. Circulation. 2003;107(17):2227-32; Van Driest SL et al. J Am Coll Cardiol. 2004;44(3):602-10; Song L et al. Clin Chim Acta. 2005;351(1-2):209-16). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJun 08, 2016Variant summary: The MYH7 c.1988G>A (p.Arg663His) variant involves the alteration of a conserved nucleotide. 5/5 in silico tools predict a damaging outcome for this variant, and several functional assays indicate that this variant is functionally defective (Lan_CSC_2013). This variant was found in 2/121338 control chromosomes at a frequency of 0.0000165, which does not exceed the estimated maximal expected allele frequency of a pathogenic MYH7 variant (0.0010005). It has been identified in numerous HCM patients in the literature, and has been shown to co-segregate with disease (Gruver_AJC_1999). Additionally, multiple clinical labs have classified the variant as pathogenic. Taken together, this variant is classified as pathogenic. -
not specified Pathogenic:1
Pathogenic, no assertion criteria providedclinical testingClinical Molecular Genetics Laboratory, Johns Hopkins All Children's HospitalDec 28, 2016- -
Dilated cardiomyopathy 1S;C1842160:Myosin storage myopathy;C1850709:Myopathy, myosin storage, autosomal recessive;C3495498:Hypertrophic cardiomyopathy 1;C4552004:MYH7-related skeletal myopathy Pathogenic:1
Pathogenic, no assertion criteria providedresearchDivision of Human Genetics, Children's Hospital of PhiladelphiaMar 24, 2016- -
Cardiomyopathy Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingCHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern OntarioDec 02, 2022- -
MYH7-related condition Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 24, 2023The MYH7 c.1988G>A variant is predicted to result in the amino acid substitution p.Arg663His. This variant has been reported in multiple unrelated individuals with hypertrophic cardiomyopathy (HCM) and has been observed to segregate with HCM in multiple families (Gruver et al. 1999. PubMed ID: 10750581; Richard et al. 2003. PubMed ID: 12707239; Van Driest et al. 2004. PubMed ID: 15358028; Lan et al. 2013. PubMed ID: 23290139). This variant is reported in 0.0031% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/14-23896042-C-T). The ClinGen Cardiomyopathy Variant Curation Expert Panel interprets this variant as pathogenic (https://preview.ncbi.nlm.nih.gov/clinvar/variation/42875/). Alternate nucleotide changes affecting the same amino acid (p.Arg663Ser and p.Arg663Cys) have also been reported to be associated with HCM (Human Gene Mutation Database, HGMD). The c.1988G>A (p.ArgHis) variant is interpreted as pathogenic. -
Congenital myopathy with fiber type disproportion;C1834481:Dilated cardiomyopathy 1S;C1842160:Myosin storage myopathy;C1850709:Myopathy, myosin storage, autosomal recessive;C3495498:Hypertrophic cardiomyopathy 1;C4552004:MYH7-related skeletal myopathy Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsOct 30, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
CardioboostCm
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.31
D
BayesDel_noAF
Pathogenic
0.22
Cadd
Pathogenic
32
Dann
Pathogenic
1.0
DEOGEN2
Pathogenic
0.86
D
Eigen
Uncertain
0.46
Eigen_PC
Uncertain
0.45
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.96
D
M_CAP
Pathogenic
0.83
D
MetaRNN
Pathogenic
0.91
D
MetaSVM
Uncertain
0.49
D
MutationAssessor
Benign
1.2
L
MutationTaster
Benign
1.0
D
PrimateAI
Pathogenic
0.84
D
PROVEAN
Uncertain
-3.5
D
REVEL
Pathogenic
0.74
Sift
Pathogenic
0.0
D
Sift4G
Benign
0.11
T
Polyphen
0.84
P
Vest4
0.74
MVP
0.96
MPC
2.3
ClinPred
0.94
D
GERP RS
4.0
Varity_R
0.29
gMVP
0.92

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs371898076; hg19: chr14-23896042; COSMIC: COSV62515957; API