rs397516643
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The ENST00000261448.6(CASQ2):c.578_580delinsAC(p.Ile193AsnfsTer17) 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: 32)
Consequence
CASQ2
ENST00000261448.6 frameshift
ENST00000261448.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.70
Genes affected
CASQ2 (HGNC:1513): (calsequestrin 2) The protein encoded by this gene specifies the cardiac muscle family member of the calsequestrin family. Calsequestrin is localized to the sarcoplasmic reticulum in cardiac and slow skeletal muscle cells. The protein is a calcium binding protein that stores calcium for muscle function. Mutations in this gene cause stress-induced polymorphic ventricular tachycardia, also referred to as catecholaminergic polymorphic ventricular tachycardia 2 (CPVT2), a disease characterized by bidirectional ventricular tachycardia that may lead to cardiac arrest. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 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 1-115732927-TGA-GT is Pathogenic according to our data. Variant chr1-115732927-TGA-GT is described in ClinVar as [Likely_pathogenic]. Clinvar id is 44169.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASQ2 | NM_001232.4 | c.578_580delinsAC | p.Ile193AsnfsTer17 | frameshift_variant | 5/11 | ENST00000261448.6 | NP_001223.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASQ2 | ENST00000261448.6 | c.578_580delinsAC | p.Ile193AsnfsTer17 | frameshift_variant | 5/11 | 1 | NM_001232.4 | ENSP00000261448 | P1 | |
CASQ2 | ENST00000488931.2 | c.302_304delinsAC | p.Ile101AsnfsTer17 | frameshift_variant, NMD_transcript_variant | 6/13 | 3 | ENSP00000518226 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Catecholaminergic polymorphic ventricular tachycardia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 03, 2012 | The Ile193fs variant in CASQ2 has not been reported in the literature nor previo usly identified by our laboratory. This frameshift variant is predicted to alter the protein?s amino acid sequence beginning at position 193 and lead to a prema ture termination codon 17 amino acids downstream. This alteration is then predic ted to lead to a truncated or absent protein. Homozygous or compound heterozygou s variants in CASQ2 are strongly associated with CPVT and include loss-of-functi on variants (Roux-Buisson 2011). In summary, the severity of the predicted impac t of the Ile193fs variant supports that it is likely pathogenic and combination with a second disease-causing variant in CASQ2 would result in CPVT. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at