rs727504578
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024422.6(DSC2):c.394C>T(p.Arg132Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000223 in 1,613,808 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R132H) has been classified as Uncertain significance.
Frequency
Consequence
NM_024422.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSC2 | NM_024422.6 | c.394C>T | p.Arg132Cys | missense_variant | 4/16 | ENST00000280904.11 | |
DSC2 | NM_004949.5 | c.394C>T | p.Arg132Cys | missense_variant | 4/17 | ||
DSC2 | NM_001406506.1 | c.-36C>T | 5_prime_UTR_variant | 4/16 | |||
DSC2 | NM_001406507.1 | c.-36C>T | 5_prime_UTR_variant | 4/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSC2 | ENST00000280904.11 | c.394C>T | p.Arg132Cys | missense_variant | 4/16 | 1 | NM_024422.6 | P1 | |
DSC2 | ENST00000251081.8 | c.394C>T | p.Arg132Cys | missense_variant | 4/17 | 1 | |||
DSC2 | ENST00000648081.1 | c.-36C>T | 5_prime_UTR_variant | 5/17 | |||||
DSC2 | ENST00000682357.1 | c.-36C>T | 5_prime_UTR_variant | 4/16 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251182Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135764
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461732Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727168
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74280
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 24, 2018 | The p.Arg132Cys variant in DSC2 has been identified in 3 individuals with ARVC, one of whom carried a likely pathogenic variant in PKP2 and another of whom also carried a frameshift variant in DSC2 (Fressart 2010, Ohno 2013, Wada 2017, LMM data). This variant has been identified in 10/282564 chromosomes by the gnomAD ( http://gnomad.broadinstitute.org). Computational prediction tools and conservati on analysis suggest that the p.Arg132Cys variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary , the clinical significance of the p.Arg132Cys variant is uncertain. ACMG/AMP Cr iteria applied: PP3. - |
Arrhythmogenic right ventricular dysplasia 11 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 132 of the DSC2 protein (p.Arg132Cys). This variant is present in population databases (rs727504578, gnomAD 0.02%). This missense change has been observed in individual(s) with arrhythmogenic right ventricular cardiomyopathy (PMID: 20400443, 23514727, 33784018). ClinVar contains an entry for this variant (Variation ID: 178972). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt DSC2 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects DSC2 function (PMID: 33784018). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Dec 16, 2022 | This missense variant replaces arginine with cysteine at codon 132 of the DSC2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). A functional study has shown that, unlike wildtype, this variant can't rescue the cardiovascular phenotypes in DSC2 knockdown zebrafish model (PMID: 33784018). This variant has been reported in an individual affected with cardiac arrest (ClinVar SCV001245073.1) and in four unrelated individuals affected with arrhythmogenic cardiomyopathy (PMID: 20400443, 23514727, 29178656, 33784018, ClinVar SCV000205460.4). Two of these probands also carried a truncating variant in DSC2 or PKP2 genes (PMID: 20400443, ClinVar SCV001245073.1). Studies with heart samples and cardiomyocytes derived from one of the probands revealed altered electric activity and a marked reduction of DSC2 in both mRNA and protein levels (PMID: 33784018, 35297182). This variant has been identified in 10/282564 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. - |
Aborted sudden cardiac death Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Agnes Ginges Centre for Molecular Cardiology, Centenary Institute | Jul 26, 2018 | DSC2 Arg132Cys has been reported previously in 2 ARVC patients, however both patients also had other DSC2 variants (Fressart V et al., 2010; Ohno S, et al., 2013). We have identified this variant in a proband of south-east asian descent whom presented with cardiac arrest. The patient was also found to have a second variant (PKP2 p.Leu744Serfs*3). Clinical screening did not uncover any abnormal findings, but it is possible that the patient may have a 'concealed' ARVC phenotype. The proband has no family history of any inherited cardiac disease or sudden death. The variant is present at an elevated frequency in the Genome Aggregation Database (MAF= 0.000036, http://gnomad.broadinstitute.org/). In silico tools SIFT, MutationTaster, CADD and PolyPhen-2 all predict the variant to be deleterious. In summary, the variant has been reported in at least 3 probands with multiple variants, it is present in population databases but is still considered rare and in silico tools predict it to be deleterious, therefore based on this conflicting information we classify DSC2 Arg132Cys as a variant of 'uncertain significance'. - |
Primary dilated cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University | Jun 01, 2023 | - - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2019 | The p.R132C variant (also known as c.394C>T), located in coding exon 4 of the DSC2 gene, results from a C to T substitution at nucleotide position 394. The arginine at codon 132 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been reported in individuals with arrhythmogenic right ventricular cardiomyopathy (ARVC), who also had additional cardiac-related variants detected (Fressart V et al. Europace, 2010 Jun;12:861-8; Ohno S et al. Circ. J., 2013 Mar;77:1534-42). This alteration has also been seen in an exome cohort, but detailed cardiovascular history was not provided (Haggerty CM et al. Genet. Med., 2017 11;19:1245-1252). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Familial isolated arrhythmogenic right ventricular dysplasia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Dec 18, 2023 | This missense variant replaces arginine with cysteine at codon 132 of the DSC2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). A functional study has shown that, unlike wildtype, this variant can't rescue the cardiovascular phenotypes in DSC2 knockdown zebrafish model (PMID: 33784018). This variant has been reported in an individual affected with cardiac arrest (ClinVar SCV001245073.1) and in four unrelated individuals affected with arrhythmogenic cardiomyopathy (PMID: 20400443, 23514727, 29178656, 33784018, ClinVar SCV000205460.4). Two of these probands also carried a truncating variant in DSC2 or PKP2 genes (PMID: 20400443, ClinVar SCV001245073.1). Studies with heart samples and cardiomyocytes derived from one of the probands revealed altered electric activity and a marked reduction of DSC2 in both mRNA and protein levels (PMID: 33784018, 35297182). This variant has been identified in 10/282564 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at