14-23432703-C-A

Variant names:

• chr14-23432703-C-A
• rs397516212
• NM_000257.4:c.438G>T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_000257.4(MYH7):​c.438G>T​(p.Lys146Asn) variant causes a missense change involving the alteration of a non-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 (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYH7 NM_000257.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 3.30

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 15 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the MYH7 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 341 curated pathogenic missense variants (we use a threshold of 10). The gene has 16 curated benign missense variants. Gene score misZ: 3.9329 (above the threshold of 3.09). Trascript score misZ: 6.7889 (above the threshold of 3.09). GenCC associations: The gene is linked to 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, 0.961
• PP5: Variant 14-23432703-C-A is Pathogenic according to our data. Variant chr14-23432703-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 43013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-23432703-C-A is described in Lovd as [Pathogenic]. Variant chr14-23432703-C-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH7	NM_000257.4	c.438G>T	p.Lys146Asn	missense_variant	Exon 5 of 40	ENST00000355349.4	NP_000248.2
MYH7	NM_001407004.1	c.438G>T	p.Lys146Asn	missense_variant	Exon 4 of 39		NP_001393933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH7	ENST00000355349.4	c.438G>T	p.Lys146Asn	missense_variant	Exon 5 of 40	1	NM_000257.4	ENSP00000347507.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:3

Jun 13, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has been reported in several individuals with hypertrophic cardiomyopathy (HCM) and observed to be de novo in an individual affected with HCM (PMID: 28615295, 18403758, 27532257). ClinVar contains an entry for this variant (Variation ID: 43013). This variant is not present in population databases (ExAC no frequency). This sequence change replaces lysine with asparagine at codon 146 of the MYH7 protein (p.Lys146Asn). The lysine residue is highly conserved and there is a moderate physicochemical difference between lysine and asparagine. -

Feb 26, 2020

Agnes Ginges Centre for Molecular Cardiology, Centenary Institute

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

This MYH7 Lys146Asn variant has been reported as a de novo mutation in a sporadic childhood cardiomyopathy case (Morita H, et al., 2008). This mutation is absent from the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Here we report this variant in 3 unrelated HCM index cases (Ingles, et al., 2005; Ingles et al., 2017). In one of our families this variant segregates to multiple affected individuals (5 meiosis). In silico tools PolyPhen2, SIFT and MutationTaster predict this variant to be deleterious. Furthermore functional studies suggest that this variant disrupts the interaction of the N-terminus and lever arm of the myosin heavy chain protein and the drosophila model recapitulated a cardiomyopathy phenotype (Trujillo et al., 2017). Based on the adapted ACMG criteria (Kelly MA, et al., 2018) this variant has been shown to have a damaging affect on protein in a functional study (PS3), is rare in the general population (PM2), as been reported in a de novo case (PM6), segregates with disease (PP1_moderate), has been reported in HCM probands (PS4_supporting) and multiple in silico tools predict that this variant is deleterious (PP3), therefore we classify MYH7 Lys146Asn as 'Pathogenic'. -

Mar 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

proposed classification - variant undergoing re-assessment, contact laboratory -

Cardiomyopathy Pathogenic:1

May 31, 2021

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
CardioboostCm	Pathogenic	0.98
BayesDel_addAF	Uncertain	0.055	T
BayesDel_noAF	Benign	-0.16
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.85	D
Eigen	Benign	0.17
Eigen_PC	Benign	0.10
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.86	D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.96	D
MetaSVM	Uncertain	0.30	D
MutationAssessor	Benign	0.75	N
PrimateAI	Pathogenic	0.86	D
PROVEAN	Uncertain	-3.1	D
REVEL	Pathogenic	0.75
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0020	D
Polyphen		0.99	D
Vest4		0.86
MutPred		0.77		Gain of catalytic residue at P151 (P = 5e-04);
MVP		0.92
MPC		2.3
ClinPred		0.99	D
GERP RS		2.7
Varity_R		0.73
gMVP		0.91

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: rs397516212; hg19: chr14-23901912;