rs797045097

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP2PP3_ModeratePP5

The NM_000257.4(MYH7):​c.4031G>A​(p.Arg1344Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

MYH7
NM_000257.4 missense

Scores

10
7
3

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3U:7

Conservation

PhyloP100: 7.69
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 Uncertain_significance. Variant got 4 ACMG points.

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, 0.933
PP5
Variant 14-23418348-C-T is Pathogenic according to our data. Variant chr14-23418348-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 208597.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=7, Likely_pathogenic=2}. Variant chr14-23418348-C-T is described in Lovd as [Pathogenic]. Variant chr14-23418348-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYH7NM_000257.4 linkc.4031G>A p.Arg1344Gln missense_variant Exon 30 of 40 ENST00000355349.4 NP_000248.2 P12883
MYH7NM_001407004.1 linkc.4031G>A p.Arg1344Gln missense_variant Exon 29 of 39 NP_001393933.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYH7ENST00000355349.4 linkc.4031G>A p.Arg1344Gln missense_variant Exon 30 of 40 1 NM_000257.4 ENSP00000347507.3 P12883

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152220
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000120
AC:
3
AN:
250948
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135708
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000882
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000109
AC:
16
AN:
1461528
Hom.:
0
Cov.:
32
AF XY:
0.0000124
AC XY:
9
AN XY:
727046
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000809
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152220
Hom.:
0
Cov.:
33
AF XY:
0.0000269
AC XY:
2
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:3Uncertain:7
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Pathogenic:1Uncertain:2
Jan 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

MYH7: PM1, PP3, PS4:Supporting -

Oct 06, 2021
AiLife Diagnostics, AiLife Diagnostics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 03, 2011
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. p.Arg1344Gln (c.4031G>A) in the MYH7 gene. Given the newly reported presence in cases around the world, the absence in unselected populations, we consider this variant likely disease causing. When the patient first had genetic testing the variant was novel, with no published data. Ackerman's group observed the variant in one patient in their cohort of 1053 unrelated patients with HCM who underwent DHLPC-based analysis of 9 sarcomere genes at Mayo (Bos et al 2014). Note that these cases may overlap with prior reports by Ackerman's group (ex. van Driest et al 2005). Arad et al (2014) reported the variant in a patient with HCM in their Israeli cohort. The patient presented at 13yo and had "massive LVH" (also described as "severe distal hypertrophy"), severe heart failure, and, reportedly, growth delay. It is unclear what genes were sequenced. Marsiglia et al (2013) observed the variant in one of 268 unrelated patients with HCM in their Brazilian cohort. Subjects underwent sequencing of MYH7, MYBPC3, TNNT2. There is no ClinVar entry (as of July 22nd, 2015) and there are no other cases in SHaRe. In silico analysis with Polyphen predicts this variant as probably damaging with a score of 0.984. MutationTaster predicts this variant to be disease causing with a score of 43. The Arganine at codon 1344 is completely conserved across species and isoforms. A polar positive Arginine is replaced with a polar neutral Glutamine. Another variant, p.Arg1344Trp has been reported with disease and is in ClinVar as pathogenic by GeneDx and a variant of uncertain significance by LMM. The variant is not listed in dbSNP or 1000 genomes (as of June 20, 2013). The variant is also not currently listed in the NHLBI Exome Sequencing Project dataset, which includes variant calls on ~6,500 Caucasian and African American individuals (as of June 20, 2013). Bos et al (2014) did not observe the variant in 200 "ostensibly healthy" individuals. This variant is not listed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of July 22nd, 2015). However, another variant at that codon (p.Arg1344Trp) is present in 2 of 60,278 individuals. -

Cardiomyopathy Uncertain:2
Dec 06, 2022
Color Diagnostics, LLC DBA Color Health
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This missense variant replaces arginine with glutamine at codon 1344 of the MYH7 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in four unrelated individuals affected with hypertrophic cardiomyopathy (PMID: 24093860, 24793961, 25558701, 29030401, 32894683), in an individual affected with left ventricular noncompaction (PMID: 34853230), and in an individual affected with sudden unexplained death (PMID: 31195250). This variant has been identified in 4/282350 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Aug 06, 2024
All of Us Research Program, National Institutes of Health
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This missense variant replaces arginine with glutamine at codon 1344 of the MYH7 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in four unrelated individuals affected with hypertrophic cardiomyopathy (PMID: 24093860, 24793961, 25558701, 29030401, 32894683), in an individual affected with left ventricular noncompaction (PMID: 34853230), and in an individual affected with sudden unexplained death (PMID: 31195250). This variant has been identified in 4/282350 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Hypertrophic cardiomyopathy Pathogenic:1
Jan 07, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1344 of the MYH7 protein (p.Arg1344Gln). This variant is present in population databases (rs797045097, gnomAD 0.005%). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 24093860, 24793961, 25558701, 27247418, 29030401, 32528171, 32894683). ClinVar contains an entry for this variant (Variation ID: 208597). 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%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Hypertrophic cardiomyopathy 1 Pathogenic:1
-
Laboratory of Genetics and Molecular Cardiology, University of São Paulo
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not specified Uncertain:1
Aug 12, 2019
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.Arg1344Gln variant in MYH7 has been reported in at least 3 individuals with HCM (Marsiglia 2013, Bos 2014, Cirino 2017, LMM data). It was also identified in 4/282350 chromosomes by gnomAD (https://gnomad.broadinstitute.org) and has been reported in ClinVar (Variation ID #208597). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2, PS4_Supporting, PP3. -

Dilated cardiomyopathy 1S Uncertain:1
Feb 02, 2022
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0105 - The mechanism of disease for this gene is not clearly established, however, missense variants have been proposed to act in a dominant negative manner (PMID: 24714796). (I) 0108 - This gene is associated with both recessive and dominant disease. Pathogenic variants in this gene are usually heterozygous, however a recessive inheritance pattern has been observed in severe cases (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 29300372). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (4 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (4 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated myosin tail domain (DECIPHER). (I) 0710 - Another missense variant comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. An alternative change to a tryptophan has been reported as VUS (ClinVar), and in DCM and HCM individuals (PMID: 22464770, 24503780, 27532257). (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported in multiple individuals with HCM (PMID: 24093860, 24793961, 25558701, 29030401) and in one individual who suffered a sudden explained death who also had another VUS in SCN10A (PMID: 31195250). It also has conflicting reports of VUS and likely pathogenic in ClinVar. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Cardiovascular phenotype Uncertain:1
Dec 02, 2019
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.R1344Q variant (also known as c.4031G>A), located in coding exon 28 of the MYH7 gene, results from a G to A substitution at nucleotide position 4031. The arginine at codon 1344 is replaced by glutamine, an amino acid with highly similar properties. This alteration has been reported in multiple individuals with hypertrophic cardiomyopathy (HCM) as well as once in a sudden unexplained death (SUD) cohort (Marsiglia JD et al. Am. Heart J., 2013 Oct;166:775-82; Bos JM et al. Mayo Clin. Proc., 2014 Jun;89:727-37; Arad M et al. Isr. Med. Assoc. J., 2014 Nov;16:707-13; Homburger JR et al. Proc. Natl. Acad. Sci. U.S.A., 2016 06;113:6701-6; Cirino AL et al. Circ Cardiovasc Genet, 2017 Oct;10:; Gando I et al. Forensic Sci. Int., 2019 Aug;301:289-298). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
CardioboostCm
Pathogenic
0.96
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
0.070
CADD
Pathogenic
33
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.82
D
Eigen
Pathogenic
0.81
Eigen_PC
Pathogenic
0.78
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.94
D
M_CAP
Pathogenic
0.96
D
MetaRNN
Pathogenic
0.93
D
MetaSVM
Uncertain
0.50
D
MutationAssessor
Uncertain
2.6
M
PrimateAI
Pathogenic
0.89
D
PROVEAN
Uncertain
-2.9
D
REVEL
Pathogenic
0.74
Sift
Uncertain
0.016
D
Sift4G
Benign
0.22
T
Polyphen
0.98
D
Vest4
0.95
MutPred
0.52
Gain of catalytic residue at L1342 (P = 0.0792);
MVP
0.97
MPC
1.7
ClinPred
0.95
D
GERP RS
5.0
Varity_R
0.40
gMVP
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.13
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: rs797045097; hg19: chr14-23887557; COSMIC: COSV105912883; COSMIC: COSV105912883; API