chr10-110821356-G-A

Position:

• chr10-110821356-G-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_001134363.3(RBM20):​c.2737G>A​(p.Glu913Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RBM20 NM_001134363.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 9.36

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]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.768
• PP5: Variant 10-110821356-G-A is Pathogenic according to our data. Variant chr10-110821356-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 43998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM20	NM_001134363.3	c.2737G>A	p.Glu913Lys	missense_variant	11/14	ENST00000369519.4	NP_001127835.2
RBM20	XM_017016103.3	c.2572G>A	p.Glu858Lys	missense_variant	11/14		XP_016871592.1
RBM20	XM_017016104.3	c.2353G>A	p.Glu785Lys	missense_variant	11/14		XP_016871593.1
RBM20	XM_047425116.1	c.2353G>A	p.Glu785Lys	missense_variant	11/14		XP_047281072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM20	ENST00000369519.4	c.2737G>A	p.Glu913Lys	missense_variant	11/14	1	NM_001134363.3	ENSP00000358532	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Dilated cardiomyopathy 1DD Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	May 06, 2021	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with dilated cardiomyopathy, 1DD (MIM#613172). While some publications suggest a dominant negative mechanism for variants in the hotspot affecting residues between 630 and 640 (PMID: 32187365, PMID: 29895960), this has been recently disproven (PMID: 32840935). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to lysine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated glutamic acid-rich region (PMID: 30547036, PDB). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been previously reported as pathogenic in at least five unrelated individuals with dilated cardiomyopathy (DCM) (ClinVar, PMID: 27496873, PMID: 30547036). (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has been shown to segregate in at least one family with eight affected individuals with DCM (PMID: 27496873). (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. Studies with both an affected individual’s heart cells and cell lines have showed that this variant strongly decreases protein levels. In addition, it alters TTN gene splicing and protein isoform composition, leading to an increase in the larger titin isoform (PMID: 27496873). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 13, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 913 of the RBM20 protein (p.Glu913Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with dilated cardiomyopathy (DCM) (PMID: 24503780, 27496873; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 43998). 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 not expected to disrupt RBM20 protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects RBM20 function (PMID: 27496873). For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 17, 2023	Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate that E913K results in reduced RBM20 protein expression, which alters titin splicing in the heart (Beqqali et al., 2016; Khan et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27496873, 27531932, 24503780, 27532257, 29304022, 28941705, 30050558, 30871348, 30871351, 26582918, 35288587, 33019804, 34540771) -
Likely pathogenic, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Jun 09, 2017	Our patient is a 13 year-old male listed for heart tranplant due to familial DCM. He had a Comprehensive Cardiomyopathy Panel with the GeneDx laboratory which included sequencing of 76 genes and additional deletion/duplication analysis of 61 of those genes (nuclear genes) associated with various forms of cardiomyopathy: ABCC9 , ACTC (ACTC1), ACTN2, ANKRD1, BAG3 , BRAF, CAV3, CRYAB , CSRP3, DES, DMD, DSC2, DSG2, DSP, DTNA, EMD, FKTN, GATAD1, GLA, HRAS, ILK, JPH2, JUP, KRAS, LAMA4, LAMP2, LDB3 (ZASP), LMNA, MAP2K1, MAP2K2, MTND1, MTND5, MTND6, MTTD, MTTG, MTTH, MTTI, MTTK, MTTL1, MTTL2, MTTM, MTTQ, MTTS1, MTTS2, MYBPC3, [no sequence data could be obtained for MYH6], MYH7, MYL2, MYL3, MYLK2, MYOZ2, MYPN, NEBL , NEXN, NRAS, PDLIM3, PKP2, PLN, PRKAG2, PTPN11, RAF1, RBM20, RYR2, SCN5A, SGCD, SOS1, TAZ, TCAP, TMEM43, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR, VCL. Results show that one variant was detected: p.Glu913Lys (E913K; c.2737G>A) in exon 11 of the RBM20 gene. Based on the information reviewed below, including very strong segregation data in a family with DCM, we classify p.Glu913Lys as Likely Pathogenic. This variant has been reported in the literature by Beqqali et al. (2016) in a family with DCM. It segregated with disease in 9 affected family members, which would happen by chance in 1/256 or 0.4% of cases. No other disease-causing variants were found in 83 DCM genes including TTN. The index patient presented with heart failure at age 35. His brother was diagnosed at age 19 and died of heart failure at age 29, His mother died of heart failure at age 72. Upon family-member screening, other family members were diagnosed with DCM at ages 12-17, and one of them underwent heart transplant at age 19. This paper also contains in vitro data on the variant. The authors report that it leads to lower RBM20 protein levels by affecting protein stability. This then causes altered splicing of titin (TTN) in the cardiomyocytes, resulting in a shift from the more stiff N2B isoform to the more compliant titin isoform N2BA, an increased sarcomere resting length, and decreased length-dependent activation (impaired Frank-Starling mechanism). In a separate paper (Khan et al. 2016), this same group shows the variant to alter formation of circular RNAs from TTN. This variant in RBM20 has been identified by LMM laboratory in 2 adults with DCM, according to their submission to ClinVar, for a total of 4 DCM families known to have it, including our patient's. It is absent from the gnomAD population database of 140,000 individuals. However, there is poor sequencing coverage at this location with only 65% of samples covered at 1x, much less 20x. This is a nonconservative amino acid change, resulting in the replacement of a negatively charged Glutamic Acid with a positively charged Lysine. Glutamic Acid at this location is absolutely conserved across ~100 vertebrate species for which we have data. The adjacent residues are also highly conserved. While pathogenic variants in RBM20 have been reported in cases of DCM within exon 9 (Brauch 2009, Li 2010), the impact of variants in other regions of the gene is currently unclear. However, a nearby variant, p.Glu916Lys, is listed as Likely Pathogenic by LMM in ClinVar, as it was found to segregate with disease in 5 affected individuals, including 4 obligate carriers. Variants in the RBM20 gene have been reported in approximately 3% of patients with DCM (Refaat et al., 2012), but specifically in pediatric patients may represent a higher proportion: Pugh et al. (2014) found high-confidence RBM20 variants in over 6% of pediatric patients with DCM. Variants in RBM20 are relatively newly reported with cardiomyopathy, so only minimal data on disease-associated variation in this gene is available. Currently, only 16 Likely Pathogenic or Pathogenic variants in this gene are listed in ClinVar (as of June 2017). -

Primary dilated cardiomyopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Jul 07, 2023	This sequence change in RBM20 is predicted to replace glutamic acid with lysine at codon 913, p.(Glu913Lys). The glutamic acid residue is highly conserved (100 vertebrates, UCSC), and is located in a glutamic acid-rich region (PMID: 27496873). There is a small physicochemical difference between glutamic acid and lysine. This variant is absent from the population database gnomAD v2.1 and v3.1. This variant has been reported in multiple individuals with RBM20-related cardiomyopathy, including dilated cardiomyopathy (DCM), noncompaction cardiomyopathy, or left ventricular noncompaction cardiomyopathy (PMID: 27532257, 29447731, 34540771, 35113650; ClinVar: SCV000924914.1, SCV000060629.7, SCV000768943.6). The variant has been reported to segregate with DCM over three generations in a single family (PMID: 27496873). At least one individual with this variant displayed downregulation of RBM20 protein in heart tissue compared to controls and TTN RNA mis-splicing causing a significant shift from the less compliant toward the highly compliant TTN isoforms (PMID: 27496873). Reduced RBM20 protein expression was also demonstrated in an in vitro cell line assay indicating that this variant impacts protein function (PMID: 27496873). Computational evidence is uninformative for the missense substitution (REVEL = 0.54). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PP1_Strong, PS4_Moderate, PP4_Moderate, PM2_Supporting, PS3_Supporting. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Dec 06, 2021	The p.Glu913Lys variant in RBM20 has been reported in 3 individuals with dilated cardiomyopathy (DCM) and segregated with disease in at least 9 affected relatives from 2 families (Beqqali 2016 PMID 27496873, Walsh 2017 PMID 27532257, van den Hoogenhof 2018 PMID 29650543, Hey 2019 PMID 30871348, Parikh 2019 PMID 30871351, LMM Data). This variant has also been reported by other clinical laboratories in ClinVar (Variant ID: 43998) but is absent from large population studies. RNA sequencing and RT-PCR performed on heart tissue from a patient harboring this variant as well as in vitro studies using transfected cells suggest that this variant affects RBM20 protein function (Beqqali 2016 PMID 27496873, Khan 2016 PMID 27531932, van den Hoogenhof 2018 PMID 29650543). Computational prediction tools and conservation analysis suggest are consistent with pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant DCM. ACMG/AMP criteria applied: PS4_Supporting, PP1_Strong, PM2_Supporting, PS3_Moderate, PP3. -

Cardiomyopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Oct 23, 2017

- -

Left ventricular noncompaction cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Klaassen Lab, Charite University Medicine Berlin

-

- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 12, 2021

The p.E913K pathogenic mutation (also known as c.2737G>A), located in coding exon 11 of the RBM20 gene, results from a G to A substitution at nucleotide position 2737. The glutamic acid at codon 913 is replaced by lysine, an amino acid with similar properties. This alteration has been reported in individuals with dilated cardiomyopathy (DCM) and has shown co-segregation with disease in several families, including one with at least nine affected members (Beqqali A et al. Cardiovasc Res, 2016 10;112:452-63; Invitae pers. comm.). This alteration was reported in one individual with DCM from a genetic testing cohort, who also had variants in other cardiac-related genes (Pugh TJ et al. Genet Med, 2014 Aug;16:601-8;Walsh R et al. Genet Med, 2017 02;19:192-203). Functional studies suggested this variant destabilizes the protein and may impact splicing in TTN; however, the mechanism of disease for RBM20 has not been well-established (Khan MA et al. Circ Res, 2016 Oct;119:996-1003; Beqqali A et al. Cardiovasc Res, 2016 10;112:452-63). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.91
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Pathogenic	31
DANN	Pathogenic	1.0
Eigen	Pathogenic	0.87
Eigen_PC	Pathogenic	0.88
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Benign	0.050	D
MetaRNN	Pathogenic	0.77	D
MetaSVM	Uncertain	0.21	D
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.76	T
PROVEAN	Benign	-2.3	N
REVEL	Uncertain	0.54
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.12	T
Vest4		0.78
MutPred		0.39		Gain of ubiquitination at E913 (P = 0.006);
MVP		0.74
ClinPred		0.98	D
GERP RS		5.8
gMVP		0.55

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

Other links and lift over

dbSNP: rs397516607; hg19: chr10-112581114; COSMIC: COSV65706173; COSMIC: COSV65706173;