rs137852764
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Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The ENST00000265968.9(CSRP3):āc.206A>Gā(p.Lys69Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,613,678 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 (ā ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.000052 ( 0 hom. )
Consequence
CSRP3
ENST00000265968.9 missense
ENST00000265968.9 missense
Scores
6
11
2
Clinical Significance
Conservation
PhyloP100: 7.93
Genes affected
CSRP3 (HGNC:2472): (cysteine and glycine rich protein 3) This gene encodes a member of the CSRP family of LIM domain proteins, which may be involved in regulatory processes important for development and cellular differentiation. The LIM/double zinc-finger motif found in this protein is found in a group of proteins with critical functions in gene regulation, cell growth, and somatic differentiation. Mutations in this gene are thought to cause heritable forms of hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) in humans. Alternatively spliced transcript variants with different 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM1
In a mutagenesis_site Increases PKC/PRKCA activity. (size 0) in uniprot entity CSRP3_HUMAN
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.885
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSRP3 | NM_003476.5 | c.206A>G | p.Lys69Arg | missense_variant | 3/6 | ENST00000265968.9 | NP_003467.1 | |
CSRP3 | NM_001369404.1 | c.113-1863A>G | intron_variant | NP_001356333.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSRP3 | ENST00000265968.9 | c.206A>G | p.Lys69Arg | missense_variant | 3/6 | 1 | NM_003476.5 | ENSP00000265968 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251312Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135820
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GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461520Hom.: 0 Cov.: 32 AF XY: 0.0000495 AC XY: 36AN XY: 727052
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
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ClinVar
Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Dilated cardiomyopathy 1M;C2677491:Hypertrophic cardiomyopathy 12 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 26, 2022 | This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 69 of the CSRP3 protein (p.Lys69Arg). This variant is present in population databases (rs137852764, gnomAD 0.003%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy or dilated cardiomyopathy with endocardial fibroelastosis (PMID: 8994428, 14567970, 28790153). ClinVar contains an entry for this variant (Variation ID: 8780). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25"). Experimental studies have shown that this missense change affects CSRP3 function (PMID: 14567970, 18250163, 27353086). 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 09, 2021 | - - |
Dilated cardiomyopathy 1M Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2003 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 08, 2024 | Initially reported in two deceased infant siblings diagnosed with DCM associated with endocardial fibroelastosis; the variant was also identified in their unaffected mother (PMID: 14567970); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In vitro studies demonstrated that the K69R variant abolishes the interaction between MLP and alpha-actinin-2 and also demonstrated differential localization in the cell as compared with wild-type protein (PMID: 14567970); however, additional studies are needed to validate the functional effect of this variant in vivo; Reported in ClinVar as a variant of uncertain significance by other clinical laboratories (ClinVar Variant ID# 8780; ClinVar); This variant is associated with the following publications: (PMID: 22337857, 27896284, 23299917, 28790153, 14567970, 35626289) - |
Hypertrophic cardiomyopathy Uncertain:1
Uncertain significance, no assertion criteria provided | research | Agnes Ginges Centre for Molecular Cardiology, Centenary Institute | Dec 06, 2019 | The CSRP3 Lys69Arg variant has been previously reported in 2 unrelated DCM cases (Zimmerman RS, et al., 2010; Mohaptra B, et al., 2003). In the case reported by Mohaptra B, et al. (2003) 2 siblings died (both around 2 years of age) from DCM no family history of disease was reported. The variant is present in the Exome Aggregation Consortium dataset (MAF=0.0000165; http://exac.broadinstitute.org/). We identified the CSRP3 Lys69Arg in a HCM proband with no family history of disease or sudden cardiac death. A second variant (MYBPC3 Ser871fs) classified as "pathogenic" has also been identified in this proband. Computational tool SIFT and and MutationTaster predict this variant to be "deleterious" and "disease causing", however PolyPhen-2 predicts this variant to be "benign". In summary, based on current literature, rarity in general populations, and our limited familial data we classify CSRP3 Lys69Arg as variant of "uncertain significance". - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 27, 2023 | The p.K69R variant (also known as c.206A>G), located in coding exon 2 of the CSRP3 gene, results from an A to G substitution at nucleotide position 206. The lysine at codon 69 is replaced by arginine, an amino acid with highly similar properties. This alteration was detected in a proband with dilated cardiomyopathy and endocardiofibroelastosis; however, it was also present in the phenotypically normal mother. In vitro analysis suggested that the mutant protein had an altered cellular localization and failed to bind α-actinin-2 (Mohapatra B et al. Mol. Genet. Metab.;80:207-15). In addition, this alteration was reported to enhance PKCα phosphorylation in vitro (Lange S et al. Nat Commun, 2016 Jun;7:12120). 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. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D;.;D;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D;.;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;.;M;M
MutationTaster
Benign
A;A
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;.;D
REVEL
Pathogenic
Sift
Uncertain
D;.;.;D
Sift4G
Uncertain
T;.;.;T
Polyphen
P;.;P;P
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at