ClinVar Genomic variation as it relates to human health
NM_001134363.3(RBM20):c.1913C>T (p.Pro638Leu)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001134363.3(RBM20):c.1913C>T (p.Pro638Leu)
Variation ID: 268 Accession: VCV000000268.20
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q25.2 10: 110812310 (GRCh38) [ NCBI UCSC ] 10: 112572068 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Feb 20, 2024 Oct 24, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001134363.3:c.1913C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001127835.2:p.Pro638Leu missense NC_000010.11:g.110812310C>T NC_000010.10:g.112572068C>T NG_021177.1:g.172914C>T LRG_382:g.172914C>T LRG_382t1:c.1913C>T - Protein change
- P638L
- Other names
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p.P638L:CCG>CTG
- Canonical SPDI
- NC_000010.11:110812309:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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RBM20 | - | - |
GRCh38 GRCh37 |
1888 | 1924 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Oct 24, 2023 | RCV000000292.14 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 16, 2014 | RCV000211851.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 26, 2022 | RCV000183865.4 | |
Pathogenic (1) |
no assertion criteria provided
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May 1, 2016 | RCV000490927.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 1, 2021 | RCV000619200.2 | |
Pathogenic (1) |
criteria provided, single submitter
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May 4, 2020 | RCV001256960.2 | |
RBM20-related disorder
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Pathogenic (1) |
criteria provided, single submitter
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Jun 12, 2023 | RCV003407245.4 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Oct 31, 2018)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1DD
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000893836.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
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Pathogenic
(May 04, 2020)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1A
Affected status: yes
Allele origin:
germline
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Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
Accession: SCV001433497.1
First in ClinVar: Sep 27, 2020 Last updated: Sep 27, 2020 |
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Pathogenic
(Jul 26, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000236347.14
First in ClinVar: Jul 05, 2015 Last updated: Mar 04, 2023 |
Comment:
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; … (more)
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate a damaging effect as a cell-based splice reporter assay showed complete loss of protein function (Guo et al., 2012) and human cardiac tissue cell culture showed an abnormal cytoplasmic localization of the protein (Gaertner et al., 2020); This variant is associated with the following publications: (PMID: 24584570, 24503780, 24033266, 22004663, 27532257, 29367541, 28798025, 30547036, 20590677, 32969603, 29650543, 30871351, 30871348, 29253866, 32840935, 30847666, 32746448, 19712804, 22466703, 31737537) (less)
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Pathogenic
(Dec 16, 2014)
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criteria provided, single submitter
Method: clinical testing
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Primary dilated cardiomyopathy
(Autosomal dominant inheritance)
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000060611.6
First in ClinVar: May 03, 2013 Last updated: Aug 26, 2019 |
Comment:
The p.Pro638Leu variant in RBM20 has been reported in 3 families with DCM, segre gated with disease in >10 affected individuals (including 2 affected obligate … (more)
The p.Pro638Leu variant in RBM20 has been reported in 3 families with DCM, segre gated with disease in >10 affected individuals (including 2 affected obligate ca rriers) and was absent from 2160 control chromosomes (Brauch 2009, Refaat 2012) and other large population studies. Additionally, this variant has been identifi ed by our laboratory in 2 individuals with DCM and LV dilation/dysfunction, 1 in dividual with atypical ARVC, and segregated with disease in 2 affected relatives . In vitro studies suggest that the p.Pro638Leu variant may impact protein funct ion (Guo 2012). Proline (Pro) at position 638 is highly conserved in mammals and evolutionarily distant species and lies within a conserved protein domain in wh ich other pathogenic variants have been reported (Brauch 2009, Li 2010). In summ ary, this variant meets our criteria to be classified as pathogenic for DCM in a n autosomal dominant manner (http://www.partners.org/personalizedmedicine/LMM) based upon segregation studies, absence from controls, and functional evidence. (less)
Number of individuals with the variant: 6
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Pathogenic
(Mar 22, 2022)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1DD
Affected status: yes
Allele origin:
germline
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3billion
Accession: SCV002318820.1
First in ClinVar: Apr 02, 2022 Last updated: Apr 02, 2022 |
Comment:
Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000000268, PMID:19712804). A different … (more)
Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000000268, PMID:19712804). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000202063). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.81>=0.6). A missense variant is a common mechanism associated with Cardiomyopathy, dilated, 1DD . It is not observed in the gnomAD v2.1.1 dataset. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Asthma (present) , Ventriculomegaly (present) , Hypertensive disorder (present) , Gastric polyposis (present)
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Pathogenic
(Jul 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000737224.4
First in ClinVar: Apr 14, 2018 Last updated: Nov 29, 2022 |
Comment:
The p.P638L pathogenic mutation (also known as c.1913C>T), located in coding exon 9 of the RBM20 gene, results from a C to T substitution at … (more)
The p.P638L pathogenic mutation (also known as c.1913C>T), located in coding exon 9 of the RBM20 gene, results from a C to T substitution at nucleotide position 1913. The proline at codon 638 is replaced by leucine, an amino acid with similar properties. This alteration has been detected in individuals with dilated cardiomyopathy (DCM), and has been reported to segregate with disease in multiple families (Brauch KM et al. J Am Coll Cardiol. 2009 Sep;54:930-41; Refaat MM et al. Heart Rhythm. 2012;9:390-6; Pugh TJ et al. Genet Med. 2014;16:601-8; Long PA et al. J Cardiovasc Dev Dis, 2017 Aug;4; Klauke B et al. PLoS One, 2017 Dec;12:e0189489; Gaertner A et al. Hum Mutat, 2020 11;41:1931-1943). In addition, this alteration has been noted as occurring in the RS-rich hot spot region, and studies have suggested this alteration results in cytoplasmic mislocalization and altered protein function (Guo W et al. Nat Med. 2012;18:766-73; Gaertner A et al. Hum Mutat, 2020 11;41:1931-1943). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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Pathogenic
(Jun 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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RBM20-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004109671.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
The RBM20 c.1913C>T variant is predicted to result in the amino acid substitution p.Pro638Leu. This variant has been reported in many individuals with dilated cardiomyopathy … (more)
The RBM20 c.1913C>T variant is predicted to result in the amino acid substitution p.Pro638Leu. This variant has been reported in many individuals with dilated cardiomyopathy and has been shown to segregate with disease in multiple large families (see for example, Brauch et al 2009. PubMed ID: 19712804; Gaertner A et al 2020. PubMed ID: 32840935; Long PA et al 2017. PubMed ID: 29367541). In addition, functional analysis in vitro, suggests that the p.Pro638Leu variant is deleterious (Guo W et al 2012. PubMed ID: 22466703; Gaertner A et al 2020. PubMed ID: 32840935). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating it is rare. This variant is interpreted as pathogenic. (less)
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Pathogenic
(Aug 03, 2023)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1DD
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV004238121.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
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Pathogenic
(Oct 24, 2023)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1DD
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000552923.6
First in ClinVar: May 29, 2016 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 638 of the RBM20 protein (p.Pro638Leu). … (more)
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 638 of the RBM20 protein (p.Pro638Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with dilated cardiomyopathy (DCM) and dilated cardiomyopathy (PMID: 19712804, 22004663). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 268). 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) has been performed at Invitae 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: 22466703). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Sep 01, 2009)
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no assertion criteria provided
Method: literature only
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CARDIOMYOPATHY, DILATED, 1DD
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000020436.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
In affected members from 2 large multigenerational families with dilated cardiomyopathy (CMD1DD; 613172), 1 of Norwegian ancestry ('DC-12') and 1 of German ancestry ('DC-50'), Brauch … (more)
In affected members from 2 large multigenerational families with dilated cardiomyopathy (CMD1DD; 613172), 1 of Norwegian ancestry ('DC-12') and 1 of German ancestry ('DC-50'), Brauch et al. (2009) identified heterozygosity for a 1913C-T transition in exon 9 of the RBM20 gene, resulting in a pro638-to-leu (P638L) substitution at a conserved residue in the RS domain. (less)
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Pathogenic
(May 01, 2016)
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no assertion criteria provided
Method: clinical testing
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Dilated cardiomyopathy 1S
Affected status: yes
Allele origin:
inherited
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Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen
Accession: SCV000298124.1
First in ClinVar: Jun 25, 2017 Last updated: Jun 25, 2017 |
Number of individuals with the variant: 3
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Genomic study of dilated cardiomyopathy in a group of Mexican patients using site-directed next generation sequencing. | Carnevale A | Molecular genetics & genomic medicine | 2020 | PMID: 32969603 |
Cardiomyopathy-associated mutations in the RS domain affect nuclear localization of RBM20. | Gaertner A | Human mutation | 2020 | PMID: 32840935 |
Variant panorama in 1,385 index patients and sensitivity of expanded next-generation sequencing panels in arrhythmogenic disorders. | Marschall C | Cardiovascular diagnosis and therapy | 2019 | PMID: 31737537 |
Pathogenic RBM20-Variants Are Associated With a Severe Disease Expression in Male Patients With Dilated Cardiomyopathy. | Hey TM | Circulation. Heart failure | 2019 | PMID: 30871348 |
Large next-generation sequencing gene panels in genetic heart disease: yield of pathogenic variants and variants of unknown significance. | van Lint FHM | Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation | 2019 | PMID: 30847666 |
RBM20 Mutations Induce an Arrhythmogenic Dilated Cardiomyopathy Related to Disturbed Calcium Handling. | van den Hoogenhof MMG | Circulation | 2018 | PMID: 29650543 |
Diagnostic Yield of Whole Exome Sequencing in Pediatric Dilated Cardiomyopathy. | Long PA | Journal of cardiovascular development and disease | 2017 | PMID: 29367541 |
High proportion of genetic cases in patients with advanced cardiomyopathy including a novel homozygous Plakophilin 2-gene mutation. | Klauke B | PloS one | 2017 | PMID: 29253866 |
Novel Genetic Triggers and Genotype-Phenotype Correlations in Patients With Left Ventricular Noncompaction. | Miszalski-Jamka K | Circulation. Cardiovascular genetics | 2017 | PMID: 28798025 |
Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. | Walsh R | Genetics in medicine : official journal of the American College of Medical Genetics | 2017 | PMID: 27532257 |
Rbm20-deficient cardiogenesis reveals early disruption of RNA processing and sarcomere remodeling establishing a developmental etiology for dilated cardiomyopathy. | Beraldi R | Human molecular genetics | 2014 | PMID: 24584570 |
The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. | Pugh TJ | Genetics in medicine : official journal of the American College of Medical Genetics | 2014 | PMID: 24503780 |
RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing. | Guo W | Nature medicine | 2012 | PMID: 22466703 |
Genetic variation in the alternative splicing regulator RBM20 is associated with dilated cardiomyopathy. | Refaat MM | Heart rhythm | 2012 | PMID: 22004663 |
Identification of novel mutations in RBM20 in patients with dilated cardiomyopathy. | Li D | Clinical and translational science | 2010 | PMID: 20590677 |
Mutations in ribonucleic acid binding protein gene cause familial dilated cardiomyopathy. | Brauch KM | Journal of the American College of Cardiology | 2009 | PMID: 19712804 |
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Text-mined citations for rs267607003 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.