10-110812303-C-T
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PM5PP3_ModeratePP5_Very_Strong
The NM_001134363.3(RBM20):c.1906C>T(p.Arg636Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000194 in 1,549,338 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R636H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001134363.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBM20 | NM_001134363.3 | c.1906C>T | p.Arg636Cys | missense_variant | Exon 9 of 14 | ENST00000369519.4 | NP_001127835.2 | |
RBM20 | XM_017016103.3 | c.1741C>T | p.Arg581Cys | missense_variant | Exon 9 of 14 | XP_016871592.1 | ||
RBM20 | XM_017016104.3 | c.1522C>T | p.Arg508Cys | missense_variant | Exon 9 of 14 | XP_016871593.1 | ||
RBM20 | XM_047425116.1 | c.1522C>T | p.Arg508Cys | missense_variant | Exon 9 of 14 | XP_047281072.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1397146Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1AN XY: 688808
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 1DD Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2010 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 07, 2025 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 636 of the RBM20 protein (p.Arg636Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of RBM20-related conditions and/or dilated cardiomyopathy (PMID: 20590677, 21483645, 31317183, 31737537; internal data). ClinVar contains an entry for this variant (Variation ID: 43980). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on RBM20 protein function. Experimental studies have shown that this missense change affects RBM20 function (PMID: 30262925). This variant disrupts the p.Arg636 amino acid residue in RBM20. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 19712804, 22466703, 23861363). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 22, 2021 | Reported in ClinVar (ClinVar Variant ID# 43980; Landrum et al., 2016); Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies suggest a damaging effect as this variant may result in a protein trafficking defect (Brodehl et al., 2019); This variant is associated with the following publications: (PMID: 30262925, 21483645, 19712804, 30547036, 32160020, 20590677, 29961767, 30871351, 31317183, 31737537) - |
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The p.R636C pathogenic mutation (also known as c.1906C>T), located in coding exon 9 of the RBM20 gene, results from a C to T substitution at nucleotide position 1906. The arginine at codon 636 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been reported in probands with dilated cardiomyopathy (DCM), has segregated with disease in two affected individuals in one family, and occurs in a RS-rich hot spot region (Li D et al. Clin Transl Sci. 2010;3:90-7; Minoche AE et al. Genet. Med.. 2019 03;21(3):650-662). One in vitro study reported this alteration to result in abnormal protein localization (Brodehl A et al. Genet. Med. 2018 Sep). Based on internal structural analysis, this variant is predicted to be structurally disruptive (Jang S et al. Nucleic Acids Res. 2019 May;47(9):4663-4683; Ambry internal data). In addition, other alterations involving the same amino acid, p.R636H (c.1907G>A) and p.R636S (c.1906C>A), have been detected in families with DCM (Brauch KM et al. J Am Coll Cardiol. 2009;54:930-41). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
not specified Uncertain:1
Uncertain significance, flagged submission | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 29, 2017 | Variant classified as Uncertain Significance - Favor Pathogenic. The p.Arg636Cys variant in RBM20 has been identified in 2 individuals with DCM and segregated w ith disease in 1 affected relative (Li 2010, LMM data). This variant was absent from large population databases; however, this frequency information may be unre liable as metrics indicate poor data quality at this position. This variant has also been reported in ClinVar (Variation ID: 43980). This variant lies within ex on 9, which encodes a conserved protein domain where other pathogenic variants h ave been reported (Brauch 2009, Li 2010). In addition, different disease-causing variants involving this amino acid position (p.Arg636His; p.Arg636Ser) have bee n reported in affected individuals, suggesting that the p.Arg636Cys variant may not be tolerated. In summary, while there is some suspicion for a pathogenic rol e, the clinical significance of the p.Arg636Cys variant is uncertain. ACMG/AMP C riteria applied: PS4_Supporting, PM1, PM5. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at