chr2-47466718-G-C
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Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_000251.3(MSH2):c.1571G>C(p.Arg524Pro) 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: 33)
Consequence
MSH2
NM_000251.3 missense
NM_000251.3 missense
Scores
14
4
1
Clinical Significance
Conservation
PhyloP100: 9.06
Genes affected
MSH2 (HGNC:7325): (mutS homolog 2) This locus is frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). When cloned, it was discovered to be a human homolog of the E. coli mismatch repair gene mutS, consistent with the characteristic alterations in microsatellite sequences (RER+ phenotype) found in HNPCC. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.979
PP5
Variant 2-47466718-G-C is Pathogenic according to our data. Variant chr2-47466718-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1759.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47466718-G-C is described in Lovd as [Likely_pathogenic]. Variant chr2-47466718-G-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MSH2 | NM_000251.3 | c.1571G>C | p.Arg524Pro | missense_variant | 10/16 | ENST00000233146.7 | NP_000242.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MSH2 | ENST00000233146.7 | c.1571G>C | p.Arg524Pro | missense_variant | 10/16 | 1 | NM_000251.3 | ENSP00000233146 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:11
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Lynch syndrome Pathogenic:3
| Likely pathogenic, reviewed by expert panel | curation | International Society for Gastrointestinal Hereditary Tumours (InSiGHT) | Jun 21, 2019 | Abrogated function & 2 MSI-H tumours - |
| Likely pathogenic, criteria provided, single submitter | research | CSER _CC_NCGL, University of Washington | Oct 01, 2016 | Found in patient having exome sequencing due to suspicion for hereditary colon cancer and/or polyps. Patient is a 37 year old female diagnosed with colon cancer at age 36. This interpretation considers GERP score and allele frequency data, in addition to published reports of the variant in the literature, available at the time of review. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | University of Washington Department of Laboratory Medicine, University of Washington | Nov 20, 2015 | - - |
Lynch syndrome 1 Pathogenic:2
| Likely pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Aug 02, 2023 | This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 12124176, 20672385, 28422960]. This variant is expected to disrupt protein structure [Myriad internal data]. - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 27, 1994 | - - |
not provided Pathogenic:2
| Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 23, 2021 | Published functional studies demonstrate a damaging effect: defective mismatch repair, abolishment of the dominant mutator phenotype, deficient ATPase activity, reduced mismatch-binding in vitro and MNNG-induced chromatin-binding in cells, and decreased MMR protein complex assembly (Boyer 1995, Guerrette 1998, Clark 1999, Drotschmann 1999, Heinen 2002, Mastrocola 2010, Jia 2020); Observed in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (Mangold 2004, Roberts 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 16995940, 14526391, 23741719, 16327991, 28422960, 20672385, 22290698, 7937795, 8521394, 18383312, 12124176, 9889267, 10469597, 17720936, 9774676, 15340264, 15235030, 17074586, 17594722, 24362816, 16321766, 19062740, 26078562, 21665242, 29345684, 28125613, 12760035, 33357406) - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Apr 18, 2018 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:2
| Likely pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Aug 31, 2020 | This missense variant replaces arginine with proline at codon 524 in the MSH3/MSH6 interaction and clamp domain of the MSH2 protein. Computational prediction tool suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold ‚â•0.7, PMID: 27666373). Functional studies have shown that this variant reduces interactions with MSH3 or MSH6 and impairs mismatch repair (MMR) activities (PMID: 8521394, 12124176, 17594722, 20672385). This variant has been reported in individuals with or suspected with Lynch syndrome (PMID: 15849733, 18931482) and in one individual affected with colorectal cancer (PMID: 26845104). This variant has also been reported in one individual with Muir-Torre syndrome (PMID: 15235030). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2022 | The p.R524P variant (also known as c.1571G>C), located in coding exon 10 of the MSH2 gene, results from a G to C substitution at nucleotide position 1571. The arginine at codon 524 is replaced by proline, an amino acid with dissimilar properties. This alteration was first reported in an individual diagnosed at age 38 with a microsatellite instability high ovarian cancer with loss of heterozygosity (Orth K et al. Proc. Natl. Acad. Sci. U.S.A. 1994 Sep; 91(20):9495-9). This alteration has also been reported in an individual with the Muir-Torre variant of Lynch syndrome and an individual meeting Bethesda criteria (Mangold E et al. J. Med. Genet. 2004 Jul; 41(7):567-72; Shirts BH et al. Genet Med. 2016 Oct;18(10):974-81). This alteration is located in the clamp domain and in vitro DNA binding, ATPase and sliding clamp dissociation studies have shown an effect on the mismatch-dependent molecular switch function of the hMSH2-hMSH6 heterodimer (Heinen CD et al. Cancer Cell 2002 Jun; 1(5):469-78). Multiple functional assays have demonstrated that this protein was repair-deficient, unstable, and unable to elicit a DNA checkpoint in response to DNA alkylation damage (Boyer JC et al. Cancer Res. 1995 Dec; 55(24):6063-70; Mastrocola AS et al. Hum. Mutat. 2010 Oct; 31(10):E1699-708; Nielsen SV et al. PLoS Genet. 2017 Apr 19;13(4):e1006739). In addition, in a massively parallel cell-based functional assay testing susceptibility to a DNA damaging agent, 6-thioguanine (6-TG), this variant was reported to be functionally deleterious (Jia X et al. Am J Hum Genet, 2021 01;108:163-175). This amino acid position is highly conserved in available vertebrate species, and the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. - |
Hereditary nonpolyposis colon cancer Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 29, 2020 | Variant summary: MSH2 c.1571G>C (p.Arg524Pro) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS, clamp (IPR007861) and DNA mismatch repair protein MutS, core (IPR007696) domains of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251380 control chromosomes. c.1571G>C has been reported in the literature in individuals affected with Muir-Torre syndrome (e.g. Mangold_2004), ovarian cancer (e.g. Orth_1994), and colon cancer (e.g. Shirts_2016). These data indicate that the variant may be associated with disease. Several publications report experimental evidence evaluating an impact on protein function (e.g. Drotschmann_1999, Heinen_2002, Gammie_2007, Mastrocola_2010). The most pronounced variant effect results in <10% of normal activity. Eight other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 12, 2023 | This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 524 of the MSH2 protein (p.Arg524Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 7937795, 15235030, 15849733, 18931482, 26845104; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1759). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 33357406) indicates that this missense variant is expected to disrupt MSH2 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects MSH2 function (PMID: 7937795, 10469597, 17594722, 20672385). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
M;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;.;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;.;D
Sift4G
Uncertain
D;D;.;D
Polyphen
D;.;.;D
Vest4
MutPred
Loss of catalytic residue at R524 (P = 0.0336);.;Loss of catalytic residue at R524 (P = 0.0336);Loss of catalytic residue at R524 (P = 0.0336);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at