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
Consequence
NM_000256.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYBPC3 | ENST00000545968.6 | c.1358dupC | p.Val454CysfsTer21 | frameshift_variant | Exon 16 of 35 | 5 | NM_000256.3 | ENSP00000442795.1 | ||
MYBPC3 | ENST00000399249.6 | c.1358dupC | p.Val454CysfsTer21 | frameshift_variant | Exon 15 of 34 | 5 | ENSP00000382193.2 | |||
MYBPC3 | ENST00000544791.1 | n.1358dupC | non_coding_transcript_exon_variant | Exon 16 of 27 | 5 | ENSP00000444259.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy 4 Pathogenic:2
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PVS1, PS4, PM2, PP5 -
Cardiomyopathy Pathogenic:1
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
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at