14-23427723-C-G

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PP1_ModeratePS4PP3PM1PM2

This summary comes from the ClinGen Evidence Repository: The c.1750G>C (p.Gly584Arg) variant in MYH7 has been reported in >25 individuals with hypertrophic cardiomyopathy (PS4; PMID:1552912; PMID:10567705; PMID:24093860; Partners LMM ClinVar SCV000059395.5; SHaRe consortium, PMID:30297972). This variant segregated with disease in >5 affected individuals (PP1_Moderate; PMID:1552912; Partners LMM ClinVar SCV000059395.5). This variant was absent from large population studies (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). 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 pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PP1_Moderate; PP3 LINK:https://erepo.genome.network/evrepo/ui/classification/CA011186/MONDO:0005045/002

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

MYH7
NM_000257.4 missense

Scores

Clinical Significance

Pathogenic reviewed by expert panel P:14

Conservation

PhyloP100: 7.60

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]

MYH7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PS4

For more information check the summary or visit ClinGen Evidence Repository.

PM1

For more information check the summary or visit ClinGen Evidence Repository.

PM2

For more information check the summary or visit ClinGen Evidence Repository.

PP1

For more information check the summary or visit ClinGen Evidence Repository.

PP3

For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH7	NM_000257.4 link	c.1750G>C	p.Gly584Arg	missense_variant	Exon 16 of 40	ENST00000355349.4	NP_000248.2	P12883
MYH7	NM_001407004.1 link	c.1750G>C	p.Gly584Arg	missense_variant	Exon 15 of 39		NP_001393933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH7	ENST00000355349.4 link	c.1750G>C	p.Gly584Arg	missense_variant	Exon 16 of 40	1	NM_000257.4	ENSP00000347507.3		P12883

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251490

Hom.:

AF XY:

0.00

AC XY:

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:

0.00000879

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000479

AC:

AN:

1461894

Hom.:

Cov.:

AF XY:

0.00000550

AC XY:

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000629

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:14

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

not provided

Pathogenic:6

Oct 25, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MYH7 c.1750G>C; p.Gly584Arg variant (rs121913626, ClinVar Variation ID: 14090) is a common pathogenic variant reported in the literature in numerous individuals affected with hypertrophic cardiomyopathy (Marsiglia 2013, Nier 1999, Walsh 2017, Watkins 1992). This variant is only observed on one allele in the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.922). Based on available information, this variant is considered to be pathogenic. References: 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. PMID: 24093860. Nier V et al. Variability in the ratio of mutant to wildtype myosin heavy chain present in the soleus muscle of patients with familial hypertrophic cardiomyopathy. A new approach for the quantification of mutant to wildtype protein. FEBS Lett. 1999 Nov 19;461(3):246-52. PMID: 10567705. Walsh R et al. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2017 Feb;19(2):192-203. PMID: 27532257. Watkins H et al. Characteristics and prognostic implications of myosin missense mutations in familial hypertrophic cardiomyopathy. N Engl J Med. 1992 Apr 23;326(17):1108-14. PMID: 1552912. -

Oct 07, 2014

Stanford Center for Inherited Cardiovascular Disease, Stanford University

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: 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. MYH7 c.1750G>C p.Gly584Arg g.23896932C>G (chr14.GRCh37) Seen in 1 pt with HCM in our center. First reviewed 4/1/2013, re-reviewed 1 oct 2014 While the variant has been seen in many cases of cardiomyopathy, we consider it likely pathogenic instead of very likely pathogenic because of the absence of a large number of controls matching the published cases (which are nearly all Portuguese) as well as the lack of strong segregation data or animal model data. In total this variant has been seen in at least 29 unrelated individuals with HCM (including one patient in our center) with weak segregation data in two families. We have seen the variant once in our center, in a Portuguese man who was diagnosed at 58 years of age with HCM, with a septum of 3.1 cm. This variant was initially reported in two families with HCM (Watkins et al 1993). In one family a haplotype block containing the variant segregated with 3 affected individuals, and in the second family it segregated with 2 affecteds. Both families were of Portuguese origin, and they had identical haplotypes thus suggesting p.Gly584Arg is a founder variant in this population. In a study on 80 Portuguese patients with HCM Santos et al (2012) observed the variant in one individual with HCM. Vieira et al (1995) appear to have assessed the prevalence of this variant in a Portuguese population. The manuscript is in Portuguese. Using google translate we were able to ascertain that they did not observe this variant in their cohort, but unfortunately it is unclear how many patients they studied or if they published controls. GeneDx shared that they have seen this variant in two other probands, one Caucasian and the other Portuguese. I also contacted the Laboratory for Molecular Medicine and they shared that they have seen it in 23 cases (2013). Unfortunately they have no segregation data nor do they have detailed ancestry data. They shared that most of the cases were listed as Caucasian without further specifics, though they did notice that many of the patients have Portuguese names. Carolyn Ho’s group included a patient with this variant in a paper on extracellular volume expansion, however it is unclear if that individual had hypertrophy or not (Ho et al 2013). In addition, that case likely overlaps with the LMM’s cases. No ancestry or segregation data was reported. Per their ClinVar submissions, LMM classifies it as likely pathogenic (SCV000059395). This is a semi conservative amino acid change with a nonpolar, neutral Glycine replaced with a polar, positively charged Arginine. In silico analysis (SIFT, PolyPhen2, mutationtaster) predicts the amino acid change to be deleterious/probably damaging to the resulting protein. The Laboratory of Molecular Medicine shared that their sarcomere-specific PolyPhen predicts the variant to be pathogenic and the lab notes that the pathogenic prediction is estimated to be correct 94% of the time (Jordan et al 2011). Additional variants at the same codon (p.Gly584Ser (Erdmann et al 2003, per ClinVar LMM classifies as likely pathogenic (SCV000059394)) and nearby codons (p.His576Arg, p.Ala583Val, p.Asp587Val) have been reported in association with cardiomyopathy (per the GeneDx report citing HGMD). Wang et al (2003) observed dramatic myofibril disarray after introducing the variant into chicken embryonic myocytes. Nier et al (1999) studied muscle fibers from a patient with p.Gly584Arg and observed that only 12% of all myosin in the sarcomeres was the variant version. However they did not observe any impact on sarcomere function. In total the variant has not been seen in ~6600 published controls and publicly available general population samples -

May 28, 2021

AiLife Diagnostics, AiLife Diagnostics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 29, 2023

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 28, 2021

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Classified in ClinVar as a pathogenic variant by the ClinGen Inherited Cardiomyopathy Expert Panel (ClinVar Variant ID# 14090; Landrum et al., 2016); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Functional studies demonstrate that this variant causes myofibril disarray in embryonic chicken cardiomyocytes (Wang et al., 2003); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8250038, 7731997, 9062359, 21769673, 23408646, 27639548, 27247418, 1552912, 8335820, 22429680, 24093860, 28606303, 28166811, 21310275, 27532257, 25611685, 28193612, 29300372, 10567705, 30275503, 31447099, 12953063) -

Feb 05, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP1_moderate, PP3, PM1, PM2, PS4 -

Hypertrophic cardiomyopathy

Pathogenic:3

Dec 15, 2016

ClinGen Cardiomyopathy Variant Curation Expert Panel

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.1750G>C (p.Gly584Arg) variant in MYH7 has been reported in >25 individuals with hypertrophic cardiomyopathy (PS4; PMID:1552912; PMID:10567705; PMID:24093860; Partners LMM ClinVar SCV000059395.5; SHaRe consortium, PMID: 30297972). This variant segregated with disease in >5 affected individuals (PP1_Moderate; PMID:1552912; Partners LMM ClinVar SCV000059395.5). This variant was absent from large population studies (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). 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 pathogenic for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (PMID:29300372): PS4; PM1; PM2; PP1_Moderate; PP3 -

Jan 31, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 584 of the MYH7 protein (p.Gly584Arg). This variant is present in population databases (rs121913626, gnomAD 0.0009%). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 8250038, 22429680, 24093860). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 14090). 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%. Experimental studies have shown that this missense change affects MYH7 function (PMID: 12953063). This variant disrupts the p.Gly584 amino acid residue in MYH7. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12974739, 23283745, 24510615, 26187847). 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. -

Feb 19, 2021

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Gly584Arg variant in MYH7 has been reported in at least 8 individuals with HCM (Watkins 1993 PMID:8250038, Nier 1999 PMID:10567705, Santos 2012 PMID: 22429680, Marsiglia 2013 PMID:24093860) and has been identified by our laboratory in >20 individuals with HCM. Furthermore, this variant segregated with disease in 5 affected members (including 1 obligate carrier) from 4 families (Watkins 1993 PMID:8250038, LMM data). It has also been identified in 0.001% (1/113768) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant lies in the head region of the protein and missense variants in this region are statistically more likely to be disease-associated (Walsh 2017 PMID:27532257). In vitro functional studies support an impact on protein function (Fujita 1998 PMID:9062359, Wang 2003 PMID:12953063) and computational prediction tools and conservation analyses are consistent with pathogenicity. Additionally, this variant was classified as pathogenic on 12/15/2016 by the ClinGen-approved Cardiomyopathy expert panel (Variation ID 14090). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HCM. ACMG/AMP criteria applied: PS4, PP1_Moderate, PM2_supporting, PM1, PS3_Supporting, PP3. -

Cardiovascular phenotype

Pathogenic:2

Feb 11, 2025

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS4, PP1_strong, PM1, PM2, PM5, PP3 -

Jan 16, 2025

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.G584R pathogenic mutation (also known as c.1750G>C), located in coding exon 14 of the MYH7 gene, results from a G to C substitution at nucleotide position 1750. The glycine at codon 584 is replaced by arginine, an amino acid with dissimilar properties. This alteration is located in the myosin head domain, which contains a statistically significant clustering of pathogenic missense variants (Homburger JR et al. Proc Natl Acad Sci U S A, 2016 06;113:6701-6; Walsh R et al. Genet Med, 2017 02;19:192-203; Ambry internal data). This variant was identified in one or more individuals with features consistent with hypertrophic cardiomyopathy (HCM) and segregated with disease in at least one family (Solomon SD et al. J. Am. Coll. Cardiol., 1993 Aug;22:498-505; Watkins H et al. Am. J. Hum. Genet., 1993 Dec;53:1180-5; Marsiglia JD et al. Am. Heart J., 2013 Oct;166:775-82; Walsh R et al. Genet. Med., 2017 02;19:192-203). Functional studies have suggested that this alteration leads to impaired function and increased myofibril disarray (Fujita H et al. J. Clin. Invest., 1997 Mar;99:1010-5; Wang Q et al. J. Cell. Sci., 2003 Oct;116:4227-38). Other variant(s) at the same codon,p.G584S (c.1750G>A), have been identified in individual(s) with features consistent with HCM (Erdmann J et al. Clin Genet. 2003;64(4):339-49). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Hypertrophic cardiomyopathy 1

Pathogenic:2

Apr 23, 1992

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Laboratory of Genetics and Molecular Cardiology, University of São Paulo

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiomyopathy

Pathogenic:1

Jul 05, 2022

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

1.0

CardioboostCm

Pathogenic

1.0

BayesDel_addAF

Pathogenic

0.55

BayesDel_noAF

Pathogenic

0.56

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.95

Eigen

Pathogenic

0.94

Eigen_PC

Pathogenic

0.73

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

0.99

M_CAP

Pathogenic

0.97

MetaRNN

Pathogenic

0.99

MetaSVM

Pathogenic

1.0

MutationAssessor

Pathogenic

4.3

PrimateAI

Pathogenic

0.82

PROVEAN

Pathogenic

-7.2

REVEL

Pathogenic

0.92

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.98

MutPred

0.78

Gain of catalytic residue at N589 (P = 8e-04);

MVP

0.99

MPC

2.3

ClinPred

1.0

GERP RS

4.8

Varity_R

0.80

gMVP

0.92

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over