rs1060501443

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM2PP2PP3_ModeratePP5_Very_Strong

The NM_000257.4(MYH7):​c.1618T>C​(p.Phe540Leu) 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 (★★).

Frequency

Genomes: not found (cov: 32)

Consequence

MYH7
NM_000257.4 missense

Scores

11
5
4

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4

Conservation

PhyloP100: 9.11
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]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 13 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, 0.923
PP5
Variant 14-23427855-A-G is Pathogenic according to our data. Variant chr14-23427855-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 407186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYH7NM_000257.4 linkc.1618T>C p.Phe540Leu missense_variant Exon 16 of 40 ENST00000355349.4 NP_000248.2 P12883
MYH7NM_001407004.1 linkc.1618T>C p.Phe540Leu missense_variant Exon 15 of 39 NP_001393933.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYH7ENST00000355349.4 linkc.1618T>C p.Phe540Leu missense_variant Exon 16 of 40 1 NM_000257.4 ENSP00000347507.3 P12883

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Cardiomyopathy Pathogenic:1
Aug 05, 2019
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant has been previously reported as a heterozygous change and segregated with disease in a large family with dilated cardiomyopathy (PMID: 26899768). The variant has been classified as Pathogenic by a clinical diagnostic laboratory in the ClinVar database (Variation ID: 407186). The variant is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. The c.1618T>C (p.Phe540Leu) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.1618T>C (p.Phe540Leu) variant is classified as Pathogenic. -

Primary dilated cardiomyopathy Pathogenic:1
May 11, 2021
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.Phe540Leu variant in MYH7 has been reported in 1 individual with dilated cardiomyopathy (DCM) and segregated with disease in 7 affected individuals from one family (Cuenca 2016 PMID: 26899768,). Additionally, it was reported as de novo in one individual with clinical features of left ventricular noncompaction (Invitae data). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 407186) and was absent from large population studies. This variant lies in the head region of the protein (aa 181-937) and while missense variants in this region are statistically more likely to be associated with hypertrophic cardiomyopathy (HCM; Walsh 2017 PMID:27532257), location in this region cannot be used to support pathogenicity for other phenotypes; therefore PM1 is not applicable. In addition, computational prediction tools and conservation analyses are consistent with pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant DCM. ACMG/AMP Criteria applied: PP1_Strong, PM2_Supporting, PP3. -

Hypertrophic cardiomyopathy Pathogenic:1
Jan 16, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

A computational algorithm designed to assess the pathogenicity of missense variants in MYH7 with regard to hypertrophic cardiomyopathy predicted this sequence change to be deleterious. The algorithm has a sensitivity of 94% and a specificity of 89% (PMID: 21310275). However, this prediction has not been confirmed by published functional studies. 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). This variant has been observed to be de novo in an individual affected with clinical features of left ventricular noncompaction. In addition, this variant has been reported in the literature to segregate in a family with dilated cardiomyopathy (PMID: 26899768). ClinVar contains an entry for this variant (Variation ID: 407186). This variant is not present in population databases (ExAC no frequency). This sequence change replaces phenylalanine with leucine at codon 540 of the MYH7 protein (p.Phe540Leu). The phenylalanine residue is highly conserved and there is a small physicochemical difference between phenylalanine and leucine. -

Cardiovascular phenotype Pathogenic:1
Oct 13, 2016
Ambry Genetics
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.F540L variant (also known as c.1618T>C), located in coding exon 14 of the MYH7 gene, results from a T to C substitution at nucleotide position 1618. The phenylalanine at codon 540 is replaced by leucine, an amino acid with highly similar properties. This alteration has been reported to segregate with disease in multiple individuals in a family with dilated cardiomyopathy (Cuenca S et al. J Heart Lung Transplant. 2016;35(5):625-35). 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 majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
CardioboostCm
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.36
D
BayesDel_noAF
Pathogenic
0.28
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.88
D
Eigen
Benign
0.18
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.84
T
M_CAP
Pathogenic
0.78
D
MetaRNN
Pathogenic
0.92
D
MetaSVM
Uncertain
0.50
D
MutationAssessor
Benign
1.8
L
PrimateAI
Pathogenic
0.87
D
PROVEAN
Pathogenic
-5.2
D
REVEL
Pathogenic
0.81
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.036
D
Polyphen
0.0020
B
Vest4
0.88
MutPred
0.74
Gain of relative solvent accessibility (P = 0.0289);
MVP
0.95
MPC
1.7
ClinPred
1.0
D
GERP RS
4.9
Varity_R
0.85
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.

Other links and lift over

dbSNP: rs1060501443; hg19: chr14-23897064; COSMIC: COSV62516695; API