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

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

RBM20
NM_001134363.3 missense

Scores

10
5
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:4U:1

Conservation

PhyloP100: 5.74
Variant links:
Genes affected
RBM20 (HGNC:27424): (RNA binding motif protein 20) This gene encodes a protein that binds RNA and regulates splicing. Mutations in this gene have been associated with familial dilated cardiomyopathy. [provided by RefSeq, Apr 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PM1
In a region_of_interest RS (size 27) in uniprot entity RBM20_HUMAN there are 8 pathogenic changes around while only 1 benign (89%) in NM_001134363.3
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr10-110812304-G-A is described in Lovd as [Likely_pathogenic].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.88
PP5
Variant 10-110812303-C-T is Pathogenic according to our data. Variant chr10-110812303-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 43980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RBM20NM_001134363.3 linkc.1906C>T p.Arg636Cys missense_variant Exon 9 of 14 ENST00000369519.4 NP_001127835.2 Q5T481
RBM20XM_017016103.3 linkc.1741C>T p.Arg581Cys missense_variant Exon 9 of 14 XP_016871592.1
RBM20XM_017016104.3 linkc.1522C>T p.Arg508Cys missense_variant Exon 9 of 14 XP_016871593.1
RBM20XM_047425116.1 linkc.1522C>T p.Arg508Cys missense_variant Exon 9 of 14 XP_047281072.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RBM20ENST00000369519.4 linkc.1906C>T p.Arg636Cys missense_variant Exon 9 of 14 1 NM_001134363.3 ENSP00000358532.3 Q5T481

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152192
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000143
AC:
2
AN:
1397146
Hom.:
0
Cov.:
32
AF XY:
0.00000145
AC XY:
1
AN XY:
688808
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000186
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152192
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:4Uncertain:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Dilated cardiomyopathy 1DD Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMJun 01, 2010- -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 07, 2025This 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 submitterclinical testingGeneDxNov 22, 2021Reported 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 submitterclinical testingAmbry GeneticsOct 25, 2023The 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 submissionclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineDec 29, 2017Variant 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.55
BayesDel_addAF
Pathogenic
0.33
D
BayesDel_noAF
Pathogenic
0.24
CADD
Pathogenic
27
DANN
Pathogenic
1.0
Eigen
Uncertain
0.61
Eigen_PC
Uncertain
0.57
FATHMM_MKL
Uncertain
0.95
D
M_CAP
Pathogenic
0.44
D
MetaRNN
Pathogenic
0.88
D
MetaSVM
Pathogenic
0.97
D
PrimateAI
Uncertain
0.78
T
PROVEAN
Pathogenic
-4.6
D
REVEL
Pathogenic
0.68
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0010
D
Vest4
0.68
MutPred
0.56
Loss of MoRF binding (P = 0.0154);
MVP
0.88
ClinPred
0.99
D
GERP RS
5.7
gMVP
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs267607002; hg19: chr10-112572061; API