ClinVar Miner

Submissions for variant NM_000251.3(MSH2):c.1469A>G (p.Lys490Arg)

dbSNP: rs1060502008
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002230362 SCV000548194 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2023-01-29 criteria provided, single submitter clinical testing 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. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 33357406) indicates that this missense variant is not expected to disrupt MSH2 function. ClinVar contains an entry for this variant (Variation ID: 408491). This variant has not been reported in the literature in individuals affected with MSH2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 490 of the MSH2 protein (p.Lys490Arg).
Ambry Genetics RCV002393116 SCV002701580 uncertain significance Hereditary cancer-predisposing syndrome 2021-08-18 criteria provided, single submitter clinical testing The p.K490R variant (also known as c.1469A>G), located in coding exon 9 of the MSH2 gene, results from an A to G substitution at nucleotide position 1469. The lysine at codon 490 is replaced by arginine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
All of Us Research Program, National Institutes of Health RCV004000780 SCV004834817 uncertain significance Lynch syndrome 2023-10-06 criteria provided, single submitter clinical testing This missense variant replaces lysine with arginine at codon 490 of the MSH2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MSH2-related disorders in the literature. This variant has not been identified 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.

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