rs587778523
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BP6
The NM_000251.3(MSH2):c.1601G>A(p.Arg534His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,738 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. R534R) has been classified as Likely benign.
Frequency
Consequence
NM_000251.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSH2 | NM_000251.3 | c.1601G>A | p.Arg534His | 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.1601G>A | p.Arg534His | missense_variant | 10/16 | 1 | NM_000251.3 | ENSP00000233146.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251348Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135858
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461640Hom.: 0 Cov.: 32 AF XY: 0.0000316 AC XY: 23AN XY: 727124
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:4
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | May 29, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Feb 21, 2023 | This missense variant replaces arginine with histidine at codon 534 of the MSH2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). This variant has intermediate MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold -1.32 < LOF score < 0.88, PMID: 33357406). This variant has been reported in individuals affected with colorectal cancer (PMID: 25142776, 29684080), breast cancer (PMID: 33471991), and esophageal squamous cell carcinoma (PMID: 31396961), but also in healthy individuals (PMID: 24728327, 33471991). This variant has been identified in 14/251348 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
Uncertain significance, no assertion criteria provided | clinical testing | True Health Diagnostics | Jul 17, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2024 | The p.R534H variant (also known as c.1601G>A), located in coding exon 10 of the MSH2 gene, results from a G to A substitution at nucleotide position 1601. The arginine at codon 534 is replaced by histidine, an amino acid with highly similar properties. This alteration has been reported in a 68-year-old male patient with colorectal cancer; however this individuals tumor exhibited normal IHC and was MSS (Kraus C et al. Int J Cancer, 2015 Mar;136:E559-68). Another study reported this alteration in a cohort of Chinese esophageal squamous cell carcinoma patients (Ko JM et al. Int J Cancer, 2020 02;146:1042-1051). This variant was reported in 7/60,466 breast cancer cases but also reported in 6/53,461 controls (Dorling et al. N Engl J Med. 2021 02;384:428-439). 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 neutral (Jia X et al. Am J Hum Genet, 2021 01;108:163-175). 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. - |
Lynch syndrome 1 Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 12, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Mar 21, 2023 | This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Dec 14, 2016 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 21, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate mismatch repair function similar to wildtype (PMID: 33357406); Observed in an individual with colorectal cancer whose tumor showed normal immunohistochemistry results and had microsatellite stability (PMID: 25142776); This variant is associated with the following publications: (PMID: 24728327, 28494185, 18822302, 9774676, 21120944, 26824983, 33471991, 31396961, 34326862, 29684080, 33357406, 25142776) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jun 07, 2024 | The MSH2 c.1601G>A (p.Arg534His) variant has been reported in the published literature in individuals with colorectal cancer (PMIDs: 25142776 (2015), 28494185 (2017)), breast cancer (34326862 (2021), 33471991 (2021), see LOVD (https://databases.lovd.nl/shared/)), and esophageal cancer (PMID: 31396961 (2020)). This variant has also been observed in reportedly healthy individuals (PMIDs: 23012121 (2012), 24728327 (2014), 33471991 (2021), see LOVD (https://databases.lovd.nl/shared/)). A cell-survival screening assay suggests this variant has neutral effects on DNA mismatch repair function (PMID: 33357406 (2021)). The frequency of this variant in the general population, 0.000098 (3/30606 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. - |
not specified Uncertain:1Other:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 19, 2018 | Variant summary: MSH2 c.1601G>A (p.Arg534His) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS, clamp domain (IPR007861), which is inserted between the two subdomains of the core domain. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.3e-05 in 246194 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in MSH2 causing Lynch Syndrome (5.3e-05 vs 0.00057), allowing no conclusion about variant significance. c.1601G>A has been reported in the literature in individuals affected with colorectal cancer and in an individual with a positive family history of inherited cancer disorder (Kraus_2015, O'Leary_2014). These reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. Co-occurrences with other pathogenic variant(s) have been reported (MSH2 c.998G>A, p.Cys333Tyr (LOVD)), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five 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 uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
MSH2-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 14, 2024 | The MSH2 c.1601G>A variant is predicted to result in the amino acid substitution p.Arg534His. This variant has been reported in individuals with colorectal cancer (Kraus et al. 2015. PubMed ID: 25142776; Yehia et al. 2018. PubMed ID: 29684080), breast cancer (Bhai et al. 2021. PubMed ID: 34326862), and esophageal cancer (Ko et al. 2019. PubMed ID: 31396961). However, this variant was present at similar frequencies in a large cohort of breast cancer patients (n = 7; 0.12%) compared to unaffected controls (n = 6; 0.011%) (Breast Cancer Association Consortium et al. 2021. PubMed ID: 33471991) and was classified as "functionally neutral" based on the results of a high-throughput DNA damage repair assay (Jia et al. 2021. PubMed ID: 33357406). This variant is reported in 0.0098% of alleles in individuals of South Asian descent in gnomAD and is classified as a variant of uncertain significance by majority of the submitters in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/127632/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Lynch syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Nov 30, 2023 | This missense variant replaces arginine with histidine at codon 534 of the MSH2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). This variant has intermediate MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold -1.32 < LOF score < 0.88, PMID: 33357406). This variant has been reported in individuals affected with colorectal cancer (PMID: 25142776, 29684080), breast cancer (PMID: 33471991), and esophageal squamous cell carcinoma (PMID: 31396961), but also in healthy individuals (PMID: 24728327, 33471991). This variant has been identified in 14/251348 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
Hereditary nonpolyposis colorectal neoplasms Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at