chr14-23424059-C-T

Position:

• chr14-23424059-C-T

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The NM_000257.4(MYH7):​c.2770G>A​(p.Glu924Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E924Q) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYH7 NM_000257.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:16
• Conservation: PhyloP100: 7.77

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]

ACMG classification

Verdict is Pathogenic. Variant got 19 ACMG points.

• PM1: In a helix (size 120) in uniprot entity MYH7_HUMAN there are 91 pathogenic changes around while only 3 benign (97%) in NM_000257.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), MYH7. . Gene score misZ 3.9329 (greater than the threshold 3.09). Trascript score misZ 6.7889 (greater than threshold 3.09). GenCC has associacion of gene with hyaline body myopathy, MYH7-related skeletal myopathy, dilated cardiomyopathy 1S, congenital myopathy 7A, myosin storage, autosomal dominant, dilated cardiomyopathy, left ventricular noncompaction, myopathy, myosin storage, autosomal dominant, hypertrophic cardiomyopathy, congenital heart disease, Ebstein anomaly, arrhythmogenic right ventricular cardiomyopathy, myopathy, myosin storage, autosomal recessive, hypertrophic cardiomyopathy 1, familial isolated dilated cardiomyopathy.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.985
• PP5: Variant 14-23424059-C-T is Pathogenic according to our data. Variant chr14-23424059-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 14092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-23424059-C-T is described in Lovd as [Pathogenic]. Variant chr14-23424059-C-T is described in Lovd as [Pathogenic]. Variant chr14-23424059-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYH7	NM_000257.4	c.2770G>A	p.Glu924Lys	missense_variant	23/40	ENST00000355349.4	NP_000248.2
MYH7	NM_001407004.1	c.2770G>A	p.Glu924Lys	missense_variant	22/39		NP_001393933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYH7	ENST00000355349.4	c.2770G>A	p.Glu924Lys	missense_variant	23/40	1	NM_000257.4	ENSP00000347507.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:16

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:5

Pathogenic, no assertion criteria provided	research	Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	Feb 25, 2020	This MYH7 Glu924Lys variant has been identified in multiple unrelated HCM cases. It was first described by Watkins et al. (1992a & 1992b) as a de novo variant in a HCM case whose daughter was also genetically and clinically affected. We have identified the MYH7 Glu924Lys variant in 2 HCM probands (Ingles et al., 2017). One proband has two clinically affected family members who also harbour the variant. This variant is absent from the Genome Aggregation Database (http://gnomad.broadinstitute.org/). An in vitro functional study has shown the MYH7 Glu924Lys completely disrupts binding to another sarcomere protein - MYBPC3 (Gruen M, et al., 1999). In a large HCM population study Walsh et al., showed that MYH7 variants identified in HCM cases were found to cluster between amino acids 181- 937 (2017), this implies that variants in this region are likely to cause a HCM phenotype. Based on the adapted ACMG criteria (Kelly MA, et al., 2018) this variant has been reported in at least 15 probands (PS4), is located in the 'hotspot' of MYH7 (PM1), is rare in the general population (PM2), as been reported in a de novo case (PM6), segregates with disease (PP1_moderate) and multiple in silico tools predict that this variant is deleterious (PP3), therefore we classify MYH7 Gly924Lys as 'pathogenic'. -
Pathogenic, no assertion criteria provided	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 20, 2013	proposed classification - variant undergoing re-assessment, contact laboratory -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 14, 2023	This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 924 of the MYH7 protein (p.Glu924Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 1430197, 1552912, 12818575, 15358028, 15563892, 27247418). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 14092). 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%. Experimental studies have shown that this missense change affects MYH7 function (PMID: 10024460). This variant is found within a region of MYH7 between codons 181 and 937 that contains the majority of the myosin head domain. Missense variants in this region have been shown to be significantly overrepresented in individuals with hypertrophic cardiomyopathy (PMID: 27532257). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jul 29, 2024	This missense variant replaces glutamic acid with lysine at codon 924 of the MYH7 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. This variant is found within a highly conserved region of the myosin head domain. Missense variants in this region have been shown to be significantly overrepresented in individuals with affected with hypertrophic cardiomyopathy (PMID: 27532257). In vitro functional studies have shown that this variant causes disrupted binding to and interaction with cMyBP-C (PMID: 10024460, 34051236). This variant has been reported in more than 30 unrelated individuals affected with hypertrophic cardiomyopathy (PMID: 1430197, 12818575, 15358028, 15563892, 18403758, 18409188, 21425739, 22429680, 22455086, 22857948, 23711808, 24510615, 25611685, 27532257, 27885498, 28356264, 28408708, 28615295, 28790153, 30297972, 30775854, 31737537, 33495596, 33495597, 35026164). It has been shown that this variant segregates with disease in 6 affected individuals across 2 families (PMID: 1430197, 28615295). This variant has been reported to occur de novo in two affected individuals with unaffected family histories (PMID: 1430197, 18403758). This variant has also been reported in one individual affected with left ventricular noncompaction (PMID: 34540771) and in two individuals affected with dilated cardiomyopathy (PMID: 30650640, 35284542). In a study of two large cardiomyopathy cohorts, this variant was observed in 9 of total 6112 individuals affected with hypertrophic cardiomyopathy, while it was absent among 60,706 reference samples from the ExAC population database (PMID: 27532257). 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 Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego	Sep 12, 2017	- -

Hypertrophic cardiomyopathy 1 Pathogenic:4

Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Nov 28, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Feb 23, 2023	The variant is not observed in the gnomAD v2.1.1 dataset. The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PMID: 29300372). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.94; 3Cnet: 0.34). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000014092). Different missense changes at the same codon (p.Glu924Gln, p.Glu924Gly) have been reported to be associated with MYH7 related disorder (ClinVar ID: VCV000560716 / PMID: 12974739, 31737537). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 23, 1992	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory of Genetics and Molecular Cardiology, University of São Paulo	-	- -

not provided Pathogenic:2

Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Jul 23, 2015	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. Glu924Lys (E924K; G>A at the nucleotide level) This variant has been reported in at least 6 unrelated cases of HCM with weak segregation data in one family and just one functional study. Watkins et al. (1992, NEJM and J Clin Invest) detected a de novo Glu924Lys variant in one HCM case of European descent, with transmission of both the variant and the disease to an offspring. [Solomon et al. (1993) may be referring to these same two patients.] Morner et al. (2003) found the variant in one case in Sweden, in a patient who also carried the MYBPC3 variant Val896Met. Van Driest et al. (2004) detected the Glu924Lys variant in one case of HCM at the Mayo Clinic. Xie et al. (2004) apparently found it in a Chinese family, but the article is in Chinese so this can’t be confirmed. Song et al. (2005) found it in 2 unrelated Chinese cases of HCM. Morita et al. (2008) found it had occurred de novo in a sporadic HCM patient. Both parents were clinically unaffected. Kaski et al. (2009) identified it in an HCM patient. There is functional data available: Gruen & Gautel (1999) showed the variant to significantly reduce myosin binding to MYBPC. Another change at this same codon, Glu924Gln, has been associated with HCM (Harvard Sarcomere Protein Gene Mutation Database). Variation at nearby loci of MYH7 (within 10 amino acids to either side) has been associated with disease, supporting the functional importance of this region of the protein. These HCM variants include Glu921Lys, Glu927Lys, Asp928Asn, Glu930Lys, and Glu931Lys (Harvard Sarcomere Protein Gene Mutation Database). This is a nonconservative amino acid change from an acidic, negatively-charged Glutamic Acid to a basic, positively-charged Lysine. The Glutamic Acid at codon 924 is completely conserved across 44 vertebrate species examined. Some surrounding residues are also highly conserved. In silico analysis with PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) predicts the variant to be “probably damaging”. This variant is in the rod domain of the beta-myosin heavy chain protein (Rayment et al. 1995). In total this Glu924Lys variant has not been seen in ~6190 published controls and publicly available population datasets. No variation codon 924 is present in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~3500 Caucasian and ~1800 African American individuals (as of 1/15/2012). There is no variation at this codon listed in dbSNP or in 1000 genomes (as of 1/15/2012). The variant was not observed in published controls: Watkins et al. (1992) did not observe the variant in 90 (Caucasian?) controls. Morner et al. (2003) did not find it in 100 controls. Van Driest et al. (2004) did not observe the variant in 100 Caucasian and 100 African American controls. Song et al. (2005) did not find it in 120 Chinese controls. Morita et al. (2008) did not find it in 180 ethnicity-matched controls. Kaski et al. (2009) did not find it in 200 controls. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 09, 2022	Reported in a Saudi Arabian infant with DCM and her mildly-affected mother; the infant also harbored a paternally-inherited variant in the LAMA4 gene (Abdallah et al., 2019); Identified in numerous other individuals referred for HCM genetic testing at GeneDx and found to segregate with disease in at least two families; Not 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 have demonstrated that E924K, which lies in the S2 segment of the myosin rod, completely abolishes normal binding to MYBPC3 (Gruen et al., 1999); This variant is associated with the following publications: (PMID: 7731997, 25125180, 24093860, 28606303, 16630449, 25351510, 1430197, 30775854, 34542152, 10024460, 21425739, 23074333, 21310275, 25524337, 22857948, 15358028, 12818575, 18403758, 23711808, 22455086, 18409188, 1552912, 27247418, 28166811, 27532257, 15563892, 20031618, 24510615, 22429680, 15569455, 29743414, 31006259, 30650640, 34540771, 32894683, 34051236, 33906374, 29300372) -

Cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

May 31, 2022

- -

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 submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Left ventricular noncompaction cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Klaassen Lab, Charite University Medicine Berlin

-

- -

MYH7-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 07, 2022

The MYH7 c.2770G>A variant is predicted to result in the amino acid substitution p.Glu924Lys. This variant was reported in numerous individuals with hypertrophic cardiomyopathy (Watkins et al. 1992. PubMed ID: 1552912; Dataset S1, Homburger et al. 2016. PubMed ID: 27247418; Jääskeläinen et al. 2019. PubMed ID: 30775854; Table S1, Norrish et al. 2019. PubMed ID: 31006259; Table S1A, Walsh et al. 2017. PubMed ID: 27532257). Functional studies showed that the p.Glu924Lys substitution impacts normal protein function (Gruen and Gautel. 1999. PubMed ID: 10024460; Singh et al. 2021. PubMed ID: 34051236). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 18, 2021

The p.E924K pathogenic mutation (also known as c.2770G>A), located in coding exon 21 of the MYH7 gene, results from a G to A substitution at nucleotide position 2770. The glutamic acid at codon 924 is replaced by lysine, an amino acid with similar properties. This alteration has been reported across ethnicities in individuals with hypertrophic cardiomyopathy (HCM), including at least two de novo cases (Watkins H et al. J. Clin. Invest., 1992 Nov;90:1666-71; Morita H et al. N. Engl. J. Med., 2008 May;358:1899-908; Fokstuen S et al. Hum. Mutat., 2008 Jun;29:879-85; Santos S et al. BMC Med. Genet., 2012 Mar;13:17). Segregation with disease in affected family members has also been described (Watkins H et al. J. Clin. Invest., 1992 Nov;90:1666-71; Liu WL et al. Zhonghua Xin Xue Guan Bing Za Zhi, 2006 Mar;34:202-7). Additionally, this alteration has been reported in HCM cohorts, although clinical details were limited (Kapplinger JD et al. J Cardiovasc Transl Res. 2014;7(3):347-61; Lopes LR et al. Heart, 2015 Feb;101:294-301; Walsh R et al. Genet. Med., 2017 Feb;19:192-203). Functional studies in rat cardiomyocytes have shown no apparent structural changes, but total loss of MyBP-C binding was observed (Gruen M. J. Mol. Biol. 1999 Feb;286:933-949). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.80
CardioboostCm	Uncertain	0.74
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.51
CADD	Pathogenic	29
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.80	D
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.95
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.93	D
M_CAP	Pathogenic	0.96	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.9	H
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-3.1	D
REVEL	Pathogenic	0.94
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.057	T
Polyphen		1.0	D
Vest4		0.96
MutPred		0.86		Gain of ubiquitination at E924 (P = 0.009);
MVP		0.99
MPC		0.79
ClinPred		1.0	D
GERP RS		5.5
Varity_R		0.66
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs121913628; hg19: chr14-23893268; COSMIC: COSV100805670;