rs727503260

chr14-23425403-C-Gchr14-23425403-C-T

Variant summary

Our verdict is Pathogenic. Variant got 25 ACMG points: 25P and 0B. PS1_Very_Strong PM1 PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_000257.4(MYH7):c.2302G>C(p.Gly768Arg) 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 Pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Synonymous variant affecting the same amino acid position (i.e. G768G) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYH7 NM_000257.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 7.51

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 25 ACMG points.

• PS1: Transcript NM_000257.4 (MYH7) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 164337
• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 uncertain in NM_000257.4
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, MYH7
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.972
• PP5: Variant 14-23425403-C-G is Pathogenic according to our data. Variant chr14-23425403-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 181180.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-23425403-C-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH7	NM_000257.4	c.2302G>C	p.Gly768Arg	missense_variant	21/40	ENST00000355349.4
MYH7	NM_001407004.1	c.2302G>C	p.Gly768Arg	missense_variant	20/39

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH7	ENST00000355349.4	c.2302G>C	p.Gly768Arg	missense_variant	21/40	1	NM_000257.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Feb 01, 2021

Variant summary: MYH7 c.2302G>C (p.Gly768Arg) results in a non-conservative amino acid change located in the Myosin head, motor domain (IPR001609) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251408 control chromosomes. c.2302G>C has been reported in the literature in multiple individuals affected with Cardiomyopathy (e.g. Hinton_2010, Miller_2013, Kostareva_2016, Vermeer_2017, Mak_2018). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and cited the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Dec 18, 2018

p.Gly768Arg (GGG>CGG): c.2302 G>C in exon 21 of the MYH7 gene (NM_000257.2). The G768R mutation in the MYH7 gene (as a result of a G>C or G>A nucleotide substitution) has been reported previously in association with HCM (Richard P et al., 2003; Millat et al, 2010; Hinton R et al., 2010). In one reported family, the G768R mutation co-segregated with an HCM or restrictive cardiomyopathy phenotype and the age of onset ranged from infancy to adulthood (Hinton R et al., 2010). In two studies, the G768R mutation was not present in 200 and 400 chromosomes of matched healthy adult controls (Richard P et al., 2003, Millat et al, 2010). In addition, the NHLBI Exome Sequencing Project reports G768R was not observed in approximately 6,500 individuals of European and African American backgrounds, indicating it is not a common benign variant in these populations. The G768R mutation results in a non-conservative amino acid substitution of a non-polar Glycine for a positively charged Arginine at a position in the b-myosin heavy chain that is conserved across species. Moreover, missense mutations affecting nearby residues (F764L, F764Y, E774V) have been reported in association with cardiomyopathy, further supporting the functional importance of this region of the protein. In summary, G768R in the MYH7 gene is interpreted as a disease-causing mutation. The variant is found in HCM panel(s). -

Hypertrophic cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 03, 2022

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). 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. ClinVar contains an entry for this variant (Variation ID: 181180). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 12707239, 18076673, 20800588, 25935763, 27600940). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 768 of the MYH7 protein (p.Gly768Arg). For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 04, 2021

The p.G768R pathogenic mutation (also known as c.2302G>C), located in coding exon 19 of the MYH7 gene, results from a G to C substitution at nucleotide position 2302. The glycine at codon 768 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 alteration has been reported in several individuals with hypertrophic cardiomyopathy (HCM) and in a pediatric patient with restrictive cardiomyopathy (RCM) (Miller EM et al. J Genet Couns, 2013 Apr;22:258-67; Cecconi M et al. Int. J. Mol. Med., 2016 Oct;38:1111-24; Ware SM et al. Clin. Genet., 2008 Feb;73:165-70; Hinton RB et al. J. Pediatr., 2010 Jul;157:164-6). In addition, a different alteration located at the same position, resulting in the same protein change, c.2302G>A (p.G768R), has been reported in individuals with HCM and RCM (Ho CY et al. Circ Cardiovasc Imaging, 2013 May;6:415-22; García-Giustiniani D et al. Heart, 2015 Jul;101:1047-53; Walsh R et al. Genet. Med., 2017 02;19:192-203; Wang J et al. Int Heart J, 2019 Mar;60:477-481; Franaszczyk M et al. J Clin Med, 2020 Jan;9:). This variant is considered to be rare based on population 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 supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
CardioboostCm	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.50
Cadd	Pathogenic	28
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.72	D
Eigen	Pathogenic	0.82
Eigen_PC	Pathogenic	0.74
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.92	D
M_CAP	Pathogenic	0.90	D
MetaRNN	Pathogenic	0.97	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.8	M
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.93	D
PROVEAN	Pathogenic	-6.8	D
REVEL	Pathogenic	0.93
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0090	D
Polyphen		1.0	D
Vest4		0.98
MutPred		0.80		Gain of catalytic residue at K766 (P = 0.0045);
MVP		0.98
MPC		2.3
ClinPred		1.0	D
GERP RS		4.6
Varity_R		0.87
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: rs727503260; hg19: chr14-23894612;