ClinVar Miner

Submissions for variant NM_000251.3(MSH2):c.1177A>C (p.Lys393Gln)

dbSNP: rs863225386
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000231260 SCV000284095 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2024-01-17 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamine, which is neutral and polar, at codon 393 of the MSH2 protein (p.Lys393Gln). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MSH2-related conditions. ClinVar contains an entry for this variant (Variation ID: 237360). 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 with a negative predictive value of 80%. 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.
Color Diagnostics, LLC DBA Color Health RCV001183558 SCV001349339 uncertain significance Hereditary cancer-predisposing syndrome 2019-06-12 criteria provided, single submitter clinical testing
Ambry Genetics RCV001183558 SCV003855799 uncertain significance Hereditary cancer-predisposing syndrome 2022-11-03 criteria provided, single submitter clinical testing The p.K393Q variant (also known as c.1177A>C), located in coding exon 7 of the MSH2 gene, results from an A to C substitution at nucleotide position 1177. The lysine at codon 393 is replaced by glutamine, an amino acid with similar properties. 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.

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