ClinVar Miner

Submissions for variant NM_000179.3(MSH6):c.1538T>C (p.Ile513Thr)

dbSNP: rs1060502908
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000456298 SCV000551139 likely benign Hereditary nonpolyposis colorectal neoplasms 2024-12-30 criteria provided, single submitter clinical testing
GeneDx RCV000484466 SCV000572201 uncertain significance not provided 2022-08-18 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 17531815, 21120944)
Ambry Genetics RCV000567923 SCV000670082 uncertain significance Hereditary cancer-predisposing syndrome 2023-09-28 criteria provided, single submitter clinical testing The p.I513T variant (also known as c.1538T>C), located in coding exon 4 of the MSH6 gene, results from a T to C substitution at nucleotide position 1538. The isoleucine at codon 513 is replaced by threonine, an amino acid with similar properties. This amino acid position is not well 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.
Color Diagnostics, LLC DBA Color Health RCV000567923 SCV000685200 uncertain significance Hereditary cancer-predisposing syndrome 2018-08-03 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002480420 SCV002786188 uncertain significance Endometrial carcinoma; Lynch syndrome 5; Mismatch repair cancer syndrome 3 2021-09-23 criteria provided, single submitter clinical testing
Baylor Genetics RCV004568050 SCV005055959 uncertain significance Endometrial carcinoma 2023-11-23 criteria provided, single submitter clinical testing
All of Us Research Program, National Institutes of Health RCV004806322 SCV005429279 uncertain significance Lynch syndrome 2024-09-11 criteria provided, single submitter clinical testing This missense variant replaces isoleucine with threonine at codon 513 of the MSH6 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). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MSH6-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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