ClinVar

Description

Variant summary: MYH7 c.4276G>A (p.Glu1426Lys) results in a conservative amino acid change located in the Myosin tail domain (IPR002928) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function (ACMG PP3). The variant was absent in 251934 control chromosomes (gnomAD and publication ACMG PM2). c.4276G>A has been reported in the literature in multiple individuals affected with Dilated Cardiomyopathy (Kelly_2018, Vikhorev_2017, Shipman_2011, Villard_2005). In one of these studies the variant was found to co-segregate with disease in 3 affected family members (Villard_2005). Additionally, the variant was also reported in one HCM patient as part of a large well genotyped study that included 7,855 cardiomyopathy cases although the authors classified the variant as a VUS (Walsh_2017). These data indicate that the variant is very likely to be associated with disease (ACMG PS4-moderate). Experimental evidence evaluating an impact on protein function demonstrated the variant protein to have faster relaxation kinetics and reduced passive stiffness compared to controls while the degree of cardiomyocyte apoptosis and interstitial cell apoptosis measured for the related sample was considerably increased compared to controls (Vikhorev_2017). Although, ClinGens Inherited Cardiomyopathy Expert Panel released recommendations stating that typically performed MYH7 in vitro assays were generally deemed to have relatively low positive predictive value (Kelly_2018), this publication by Vikhorev et al represents an in-vivo human tissue model representative of the pathophysiology associated with MYH7 related cardiomyopathy. The same expert panel classified c.4276G>A as a variant of uncertain significance (ClinVar, Kelly_2018). Three other ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=2) and once as likely pathogenic. The expert panel stated that ACMG PM1 was applicable mainly to variants located in the head region domain of MYH7 (amino acids 181-937) and that ACMG PP2 was deemed not applicable for variants located outside the head domain to avoid double counting in scenarios where ACMG PM1 could be applied. However, we believe that the ACMG PP2 rule for MYH7 can still apply for variants located outside the head domain where the ACMG PM1 evidence has not been engaged. Based on the evidence outlined above and utilizing ClinGens expert panels adapted criteria PM2, PP3 and PS4_Moderate (i.e. variant identified in greater than or equal to 6 probands with consistent phenotypes) in conjunction with ACMG PP2 and ACMG PS3 the variant was classified as pathogenic.