11-47342928-AGG-AGGG

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_000256.3(MYBPC3):​c.1358dupC​(p.Val454CysfsTer21) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)

Consequence

MYBPC3
NM_000256.3 frameshift

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 9.51
Variant links:
Genes affected
MYBPC3 (HGNC:7551): (myosin binding protein C3) MYBPC3 encodes the cardiac isoform of myosin-binding protein C. Myosin-binding protein C is a myosin-associated protein found in the cross-bridge-bearing zone (C region) of A bands in striated muscle. MYBPC3 is expressed exclusively in heart muscle and is a key regulator of cardiac contraction. Mutations in this gene are a frequent cause of familial hypertrophic cardiomyopathy. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-47342928-A-AG is Pathogenic according to our data. Variant chr11-47342928-A-AG is described in ClinVar as [Likely_pathogenic]. Clinvar id is 181147.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
MYBPC3NM_000256.3 linkc.1358dupC p.Val454CysfsTer21 frameshift_variant Exon 16 of 35 ENST00000545968.6 NP_000247.2 Q14896-1A5YM48

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYBPC3ENST00000545968.6 linkc.1358dupC p.Val454CysfsTer21 frameshift_variant Exon 16 of 35 5 NM_000256.3 ENSP00000442795.1 Q14896-1
MYBPC3ENST00000399249.6 linkc.1358dupC p.Val454CysfsTer21 frameshift_variant Exon 15 of 34 5 ENSP00000382193.2 A8MXZ9
MYBPC3ENST00000544791.1 linkn.1358dupC non_coding_transcript_exon_variant Exon 16 of 27 5 ENSP00000444259.1 F5GZR4

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

Hypertrophic cardiomyopathy 4 Pathogenic:2
-
Laboratory of Genetics and Molecular Cardiology, University of São Paulo
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 27, 2020
Clinical Genetics Laboratory, Region Ostergotland
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PVS1, PS4, PM2, PP5 -

Cardiomyopathy Pathogenic:1
Dec 07, 2011
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

An insertion of a single “C” nucleotide in exon 16 of the MYBPC3 gene. The normal sequence with the base that is inserted in braces is: GCCCCC{C}TGTGC. This mutation is denoted c.1358dupC at the cDNA level or p.Val454CysfsX21 at the protein level. Although the c.1358dupC mutation in the MYBPC3 gene has not been reported previously, this mutation causes a shift in reading frame starting at codon Valine 454, changing it to a Cysteine, and creates a premature stop codon at position 21 of the new reading frame. The c.1358dupC mutation is expected to result in an abnormal, truncated protein or in absence of protein from this allele due to mRNA decay. Multiple frameshift mutations in the MYBPC3 gene have been reported in association with HCM The variant is found in HCM panel(s). -

Cardiovascular phenotype Pathogenic:1
Jan 02, 2025
Ambry Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1358dupC pathogenic mutation, located in coding exon 16 of the MYBPC3 gene, results from a duplication of C at nucleotide position 1358, causing a translational frameshift with a predicted alternate stop codon (p.V454Cfs*21). This variant was reported in individual(s) with features consistent with hypertrophic cardiomyopathy (HCM) (Singh SR et al. Circ Heart Fail, 2017 Oct;10:[ePub ahead of print]; Jääskeläinen P et al. ESC Heart Fail, 2019 Apr;6:436-445; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs727503203; hg19: chr11-47364479; API