rs730880732

chr14-23426039-T-C

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.2087A>G(p.Asn696Ser) 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. N696H) 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:3
• Conservation: PhyloP100: 7.58

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 hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 7 uncertain 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 chr14-23426040-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1345397.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP2: Missense variant where missense usually causes diseases, MYH7
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.944
• PP5: Variant 14-23426039-T-C is Pathogenic according to our data. Variant chr14-23426039-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 181173.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-23426039-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH7	NM_000257.4	c.2087A>G	p.Asn696Ser	missense_variant	19/40	ENST00000355349.4
MYH7	NM_001407004.1	c.2087A>G	p.Asn696Ser	missense_variant	18/39

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH7	ENST00000355349.4	c.2087A>G	p.Asn696Ser	missense_variant	19/40	1	NM_000257.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:2

Likely pathogenic, criteria provided, single submitter	research	Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	Aug 24, 2018	The MYH7 Asn696Ser variant has been reported previously in 6 HCM probands (GeneDx, Pers. Comm.; Jaaskelainen P, et al., 2014; Teirlinck CH, et al., 2012; Millat G, et al., 2010; Jaaskelainen P, et al., 1998). One of the probands was also reported to carry MYH7 Met982Thr (Millat G, et al., 2010), however this variant is found at high frequency in population databases (MAF=0.0009; http://exac.broadinstitute.org/), which is highly suggestive of a benign polymorphism. The MYH7 Asn696Ser is very rare, being absent from the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/). We identified this variant in one HCM proband (Ingles J et al., 2017), who was diagnosed at 12 years after suffering a resuscitated cardiac arrest. The proband has no family history of HCM or sudden cardiac death, and neither of the parents were found to harbour this variant, therefore this variant has arisen de novo. Computational tools SIFT, PolyPhen-HCM, MutationTaster predict this variant to have a deleterious effect, however PolyPhen2 predicts this variant to be "benign". 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. In summary, based on the adapted ACMG guidelines (Kelly MA, et al., 2018) the variant is located in a known functional domain of MYH7 (PM1), is rare in the general population (PM2), has been identified in a de novo case (PM6) and has been reported in a total of 7 HCM probands (PS4_moderate), therefore we classify MYH7 Asn696Ser as 'likely pathogenic'. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Apr 17, 2023	For these reasons, this variant has been classified as Pathogenic. 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: 181173). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 9822100, 28615295; Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 696 of the MYH7 protein (p.Asn696Ser). -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jun 30, 2022

Identified in patients with HCM referred for genetic testing at GeneDx and in published literature (Jskelinen et al., 1998; Millat et al., 2010; Teirlinck et al., 2012; Ross et al., 2017; Mattivi et al., 2020); 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; This variant is associated with the following publications: (PMID: 23140321, 9822100, 24888384, 27532257, 29300372, 28615295, 28265379, 31006259, 32894683, 20800588) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.94
CardioboostCm	Pathogenic	0.98
BayesDel_addAF	Uncertain	0.048	T
BayesDel_noAF	Benign	-0.17
Cadd	Uncertain	24
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.87	D
Eigen	Uncertain	0.22
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.94	D
M_CAP	Pathogenic	0.78	D
MetaRNN	Pathogenic	0.94	D
MetaSVM	Uncertain	0.13	D
MutationAssessor	Benign	1.1	L
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.73	T
PROVEAN	Pathogenic	-4.4	D
REVEL	Pathogenic	0.68
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.028	D
Polyphen		0.060	B
Vest4		0.84
MutPred		0.80		Gain of catalytic residue at G697 (P = 0);
MVP		0.97
MPC		1.6
ClinPred		0.99	D
GERP RS		5.0
Varity_R		0.72
gMVP		0.96

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: rs730880732; hg19: chr14-23895248; COSMIC: COSV100806153;