chr11-47332894-AAGT-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4_SupportingPP5
The NM_000256.3(MYBPC3):c.3407_3409delACT(p.Tyr1136del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,608,628 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000256.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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MYBPC3 | ENST00000545968.6 | c.3407_3409delACT | p.Tyr1136del | disruptive_inframe_deletion | Exon 31 of 35 | 5 | NM_000256.3 | ENSP00000442795.1 | ||
MYBPC3 | ENST00000399249.6 | c.3407_3409delACT | p.Tyr1136del | disruptive_inframe_deletion | Exon 30 of 34 | 5 | ENSP00000382193.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1456496Hom.: 0 AF XY: 0.00000691 AC XY: 5AN XY: 723952
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy 4 Pathogenic:5
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PS4, PM2, PM4 -
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not provided Pathogenic:3Uncertain:1
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The c.3407_3409delACT variant of uncertain significance in the MYBPC3 gene has been reported previously in two individuals with HCM; however, no detailed clinical or segregation data were provided (Sequeira et al., 2013; Murphy et al., 2016). This variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This three nucleotide deletion results in elimination of a tyrosine residue at position 1136, and does not result in a shift in reading frame. Tyrosine at this position is conserved in mammals and in silio analysis predicts this deletion to be damaging to the protein structer/function. However, the c.3407_3409delACT variant lacks sufficient evidence, including observation in a significant number of affected inidividuals, segregation studies, and functional characterization, that would further clarify its potential pathogenicity. -
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Hypertrophic cardiomyopathy Pathogenic:3
The c.3407_3409del (p.Tyr1136del) variant of the MYBPC3 gene leads to the deletion of 1 amino acid of the MYBPC3 protein (p.Tyr1136del), but otherwise preserves the integrity of the reading frame. This variant has been observed in individuals with hypertrophic cardiomyopathy (PMID: 24835277, 31323898, 29875424, 23508784, 33495596, 26914223, 30685992, 31513939, 33673806). This variant is not present in the general population by the Genome Aggregation Database (gnomAD). Therefore the c.3407_3409del (p.Tyr1136del) variant of the MYBPC3 gene is classified as likely pathogenic. -
This variant, c.3407_3409del, results in the deletion of 1 amino acid(s) of the MYBPC3 protein (p.Tyr1136del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with hypertrophic cardiomyopathy (PMID: 23508784, 26914223, 30685992, 31513939, 33673806, 35626289; internal data). ClinVar contains an entry for this variant (Variation ID: 181102). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. -
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Left ventricular noncompaction 10 Pathogenic:1
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Cardiomyopathy Pathogenic:1
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Brugada syndrome Pathogenic:1
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Primary familial hypertrophic cardiomyopathy Pathogenic:1
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Cardiovascular phenotype Pathogenic:1
The c.3407_3409delACT variant (also known as p.Y1136del) is located in coding exon 31 of the MYBPC3 gene. This variant results from an in-frame ACT deletion at nucleotide positions 3407 to 3409. This results in the in-frame deletion of a tyrosine at codon 1136. This alteration has been reported in several individuals with hypertrophic cardiomyopathy (HCM) (Lopes LR et al. J Med Genet, 2013 Apr;50:228-39; Sequeira V et al. Circ. Res., 2013 May;112:1491-505; Witjas-Paalberends ER et al. Cardiovasc. Res., 2014 Jul;103:248-57; Murphy SL et al. J Cardiovasc Transl Res, 2016 Apr;9:153-61; Dorsch LM et al. Cells, 2019 07;8:[ePub ahead of print]; Mazzarotto F et al. Genet Med, 2019 02;21:284-292; Nagyova E et al. Bratisl Lek Listy, 2019 Oct;120:46-51; Robyns T et al. Eur J Med Genet, 2020 Mar;63:103754; Harper AR et al. Nat Genet, 2021 02;53:135-142; Hathaway J et al. BMC Cardiovasc Disord, 2021 03;21:126; Tadros R et al. Nat Genet, 2021 02;53:128-134; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
not specified Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at