ClinVar Miner

Submissions for variant NM_000257.4(MYH7):c.4066G>A (p.Glu1356Lys) (rs727503246)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Cardiomyopathy Variant Curation Expert Panel RCV000461192 SCV000564448 likely pathogenic Hypertrophic cardiomyopathy 2016-12-15 reviewed by expert panel curation The c.4066G>A (p.Glu1356Lys) variant in MYH7 has been reported in >15 individuals with hypertrophic cardiomyopathy (PS4; PMID:24704860; PMID:23396983; PMID:19808356; PMID:22857948; PMID:15856146; PMID:27532257; AGCMC Sydney ClinVar SCV000692494.1; Partners LMM ClinVar SCV000199128.3; SHaRe consortium, PMID: 30297972). This variant segregated with disease in 5 affected individuals (PP1_Moderate; Partners LMM ClinVar SCV000199128.3; SHaRe consortium, PMID: 30297972). This variant was absent from large population studies (PM2; http://exac.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 (PMID:29300372): PS4; PM2; PP1_Moderate; PP3
GeneDx RCV000223815 SCV000208565 likely pathogenic not provided 2021-02-23 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In vivo studies suggested this variant may lead to reduced sarcomere incorporation of myosin, but adverse effects on muscle contraction were not observed (Wolny et al., 2013); In vitro functional analysis demonstrated decreased thermal stability and decreased ability to form filaments, though the filaments that did form were indistinguishable from wild-type and contraction was not significantly affected (Armel et al., 2010); This variant is associated with the following publications: (PMID: 25961035, 15856146, 15358028, 23782526, 28687478, 30297972, 25125180, 23396983, 25649125, 24047955, 19913502, 26688388, 19808356, 23074333, 22857948, 24704860, 27532257, 27247418, 29300372, 23283745, 20800588, 25351510, 28408708, 28771489, 30165862, 31737537, 31199839, 32344918, 28615295, 16335287, 32686758)
Invitae RCV000461192 SCV000546247 pathogenic Hypertrophic cardiomyopathy 2020-07-15 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid with lysine at codon 1356 of the MYH7 protein (p.Glu1356Lys). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and lysine. This variant is not present in population databases (ExAC no frequency) . This variant has been reported in individuals affected with hypertrophic cardiomyopathy (PMID: 15358028, 15856146 , 19913502, 20800588, 22857948). ClinVar contains an entry for this variant (Variation ID: 164294). Experimental studies have shown that this missense change affects the secondary structure of the MYH7 protein and interferes with its incorporation into thick filaments (PMID: 24047955). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV000619582 SCV000740076 likely pathogenic Cardiovascular phenotype 2020-08-05 criteria provided, single submitter clinical testing The p.E1356K variant (also known as c.4066G>A), located in coding exon 28 of the MYH7 gene, results from a G to A substitution at nucleotide position 4066. The glutamic acid at codon 1356 is replaced by lysine, an amino acid with similar properties. This variant has been reported in several patients with hypertrophic cardiomyopathy (HCM) (Van Driest SL et al. J Am Coll Cardiol. 2004;44:602-10; Perrot A et al. J Mol Med. 2005;83:468-77; Millat G et al. Clin Chim Acta. 2010;411:1983-91; Zou Y et al. Mol Biol Rep. 2013;40:3969-76; Homburger JR et al. Proc Natl Acad Sci U.S.A. 2016;113:6701-6; Walsh R et al. Genet. Med., 2017 Feb;19:192-203). In functional in vitro and in vivo analyses, this variant has been suggested to adversely affect thick filament assembly in the sarcomere; however, the clinical impact of these findings has not been determined (Armel TZ et al. Biochem Biophys Res Commun. 2010;391:352-6; Wolny M et al. J Biol Chem. 2013;288:31952-62). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Color Health, Inc RCV000772181 SCV000905298 likely pathogenic Cardiomyopathy 2019-03-22 criteria provided, single submitter clinical testing
Blueprint Genetics RCV000223815 SCV000927656 pathogenic not provided 2018-04-25 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000151243 SCV000199128 uncertain significance not specified 2014-03-07 no assertion criteria provided clinical testing proposed classification - variant undergoing re-assessment, contact laboratory
Stanford Center for Inherited Cardiovascular Disease, Stanford University RCV000223815 SCV000280345 likely pathogenic not provided 2012-01-18 no assertion criteria provided clinical testing Note 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.Glu1356Lys (c. 4066G>A) in the MYH7 gene. We first reviewed this variant in June 2011, we reviewed it on 1/25/2012, adding additional control data. There was no new case data at that time. We last reviewed it on 4/17/13 adding additional control and case data. We are aware of a total of at least 4 presumably unrelated individuals who have this variant and have cardiomyopathy (not including this family). This variant has been reported in 4 unrelated individuals with HCM (Van Driest et al 2004, Millat et al 2010, Perrot et al 2005, Brito, 2011). Brito et al the variant segregated with disease, although specifics are not given. Theis et al (2009) also reported a case with this variant, however it may be the same case that was reported by Van Driest et al (2004). Moderate segregation data is available within our patient's family. This is a semi conservative amino acid change with a polar, negative glutamic acid replaced by a polar, positive lysine. Conservation analysis illustrates that glutamic acid is highly conserved across species at codon 1356 (Perrot et al 2005). There are no published disease associated variants within 10 codons upstream or downstream of this variant. Functional studies indicate that the presence of p.Glu1356Lys thermodynamically destabilizes the resulting myosin heavy chain protein and affecting its ability to form filaments and to function properly (Armel et al 2009). LMM informed me that a novel computational tool specific to sarcomere genes and based on PolyPhen predicts the variant to be pathogenic. This tool has a reported accuracy of 94% (Jordan 2011). In total, this variant was not observed in ~7,296 published controls, laboratory controls, and publicly available general population samples. Note that the family's ancestry is Asian, and few of these controls are matched to that ancestry. PGxHealth reports that they did not see this variant in 400 presumably healthy controls of mixed ethnic background. Perrot et al did not find the variant in 96 healthy volunteers of unspecified race. Brito did not find the variant in 100 additional samples of unspecified race. Van Driest et al did not identify the variant in 100 Caucasian and 100 African American controls. There is no variation at codon 1356 listed in dbSNP (as of 4/17/13). There are two entries for variant at codon 1356 listed in 1000 genomes, however one points to an HGMD entry and the other is rom COSMIC project (somatic mutations found in human cancers) (April 17th, 2013). There is also no variation at codon 1356 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~6,500 Caucasian and African American individuals (as of 4/17/2013).
Agnes Ginges Centre for Molecular Cardiology,Centenary Institute RCV000584808 SCV000692494 pathogenic Hypertrophic cardiomyopathy; Sudden unexplained death 2019-12-05 no assertion criteria provided research This MYH7 Glu1356Lys variant has previously been identified in >15 unrelated HCM cases (see references, ClinVar submissions), including 1 de novo occurence (Brito et al., 2005). The variant has also been reported to segregate in 2 affected families (Standford University, Pers Comm.). A biochemical and biophysical assay has shown that the variant destabilises the protein and impairs filament formation (Armel TZ & Leinwand LA, 2010), whereas expression in adult rat cardiomyocytes suggests that this variant alters the alpha-helical structure, resulting in improper sarcomeric incorporation (Wolny M, et al., 2013). We identified this variant in 1 individual diagnosed with HCM (Ingles et al., 2017). MYH7 Glu1356Lys is present at a low frequency in the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Computational tools SIFT, PolyPhen-2, PolyPhen-HCM and MutationTaster predict the variant to be deleterious. In summary, based on this information, we classify MYH7 Glu1356Lys as "pathogenic".

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