ClinVar Genomic variation as it relates to human health

The c.2845G>A (p.Glu949Lys) variant in MYH7 has been reported in 12 individuals with HCM (PS4_Moderate; Watkins 1992 PMID:1552912; Walsh 2017 PMID:27532257; Zigova 2018 PMID:28815794; CHEO pers comm.). This variant segregated with disease in 1 affected relative with HCM (Watkins 1992 PMID:1552912); however, this data is currently insufficient to establish co-segregation with disease and apply PP1. Additionally, this variant has been reported as a de novo occurence in 1 child with RCM (PM6; Kapoor 2017 http://repository.ias.ac.in/114592/1/JPractCardiovascSci33143-8313497_230534.pdf). This variant was absent from large population studies (PM2; http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (Kelly 2018 PMID:29300372): PS4_Moderate; PM6; PM2; PP3

The p.Glu949Lys variant in MYH7 has been reported in >11 individuals with hypertrophic cardiomyopathy (HCM) and as a de novo occurrence in 1 individual with restrictive cardiomyopathy (RCM) and segregated with disease in 1 affected individual from 1 family (Watkins 1992 PMID: 1552912, Kapoor 2017, Zigova 2017 PMID: 28815794, Walsh 2017 PMID: 27532257/LMM data). It was absent from large population studies. Computational prediction tools and conservation analyses suggest that this variant may impact the protein. Additionally, this variant was classified as Likely Pathogenic on March 22, 2021 by the ClinGen-approved Cardiomyopathy Variant Curation expert panel (Variation ID 14093). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PS4_Moderate, PM6, PM2_Supporting, PP3.

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 949 of the MYH7 protein (p.Glu949Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy and/or restrictive cardiomyopathy (PMID: 1552912, 27532257, 28815794; http://repository.ias.ac.in/114592/1/JPractCardiovascSci33143-8313497_230534.pdf). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 14093). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt MYH7 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

The c.2845G>A (p.Glu949Lys) variant in MYH7 gene, that encodes for myosin heavy chain 7, has been identified in at least twelve individuals affected with Hypertrophic Cardiomyopathy (HCM) (ClinGen Expert Panel review [ClinVar ID: 14093], PMID:1552912, 27532257, 28815794, 1552912). This variant has been reported as de novo status in a proband with restrictive cardiomyopathy (ClinVar ID: 14093, PMID: NA). In-silico computational prediction tools suggest that this variant may have deleterious effect on the protein function (REVEL score: 0.909). This variant is found to be absent in the general population database (gnomAD) and interpreted as likely pathogenic by the ClinGen Cardiomyopathy Variant Curation Expert Panel (ClinVar ID: 14093). Therefore, the c.2845G>A (p.Glu949Lys) variant in the MYH7 gene is classified as likely pathogenic.

This missense variant replaces glutamic acid with lysine at codon 949 in the neck and hinge domain of the MYH7 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 10 unrelated individuals affected with hypertrophic cardiomyopathy (PMID: 1552912, 25611685, 27532257, 28815794, 33495597), and in one individual affected with restrictive cardiomyopathy (doi:10.1186/1755-8166-7-S1-P34 Kapoor 2014). In one family, this variant has been reported in two affected individuals (PMID: 1552912). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.