ClinVar Miner

Submissions for variant NM_000251.3(MSH2):c.1313CTC[1] (p.Pro439del)

dbSNP: rs587779082
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000411959 SCV000488947 uncertain significance Lynch syndrome 1 2016-07-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV000491828 SCV000580573 likely pathogenic Hereditary cancer-predisposing syndrome 2024-06-13 criteria provided, single submitter clinical testing The c.1316_1318delCTC variant (also known as p.P439del) is located in coding exon 8 of the MSH2 gene. This variant results from an in-frame CTC deletion of nucleotide positions 1316 through 1318. This variant was detected in individuals who either met Bethesda/Amsterdam criteria for HNPCC/Lynch syndrome with colorectal tumors that demonstrated high microsatellite instability (MSI-H) and/or absent MSH2 protein expression on immunohistochemistry (IHC) (Nagasaka T, et al. Cancer Res. 2010;70(8):3098-108, Jeong SY, et al. Dis. Colon Rectum 2003;46(8):1069-77; Ambry internal data). This amino acid position is highly conserved in available vertebrate species. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al., PLoS ONE 2012; 7(10):e46688). Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000528474 SCV000625249 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2024-11-13 criteria provided, single submitter clinical testing This variant, c.1316_1318del, results in the deletion of 1 amino acid(s) of the MSH2 protein (p.Pro439del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 15365995, 20388775, 31332305). This variant is also known as c.1316_1318delCCT (p.Leu440del). ClinVar contains an entry for this variant (Variation ID: 90623). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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 RCV000491828 SCV000904680 uncertain significance Hereditary cancer-predisposing syndrome 2018-09-19 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000411959 SCV004043986 uncertain significance Lynch syndrome 1 2023-05-09 criteria provided, single submitter clinical testing This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.
Institute of Human Genetics, University of Wuerzburg RCV000850309 SCV000992484 likely pathogenic Rectal neoplasm no assertion criteria provided clinical testing

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