ClinVar Genomic variation as it relates to human health

Variant summary: MSH6 c.1696G>A (p.Gly566Arg) results in a non-conservative amino acid change located in the DNA mismatch repair protein MuT S, connector domain (IPR007860) of the encoded protein sequence. 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 0.00024 in 250316 control chromosomes, predominantly at a frequency of 0.0015 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 11 fold of the estimated maximal expected allele frequency for a pathogenic variant in MSH6 causing Lynch Syndrome phenotype (0.00014), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. c.1696G>A has been reported in the literature in at-least one non-HNPCC familial case in the population based series studied (Kolodner_1999). This report does not provide unequivocal conclusions about association of the variant with Lynch Syndrome. Several publications report conflicting experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in a reduction of mismatch- stimulated ATPase activity (approx 11% of WT) despite normal ability of the protein to interact with MSH2 and a normal MSH6 nuclear import (example, Kariola_2002, Cyr_2008, Belvederesi_2012). Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (benign/likely benign, n=2; VUS, n=5). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as likely benign.

This variant is considered benign. This variant has been observed in trans with a known pathogenic variant in one or more individuals lacking clinical features consistent with gene-specific recessive disease. 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].

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are conflicting: reduced MMR activity, ATP binding, and ATPase activities (Kolodner 1999, Cyr 2008) but MMR activity and nuclear distribution pattern comparable to wild-type (Kariola 2002, Belvederesi 2012, Houlleberghs 2017); This variant is associated with the following publications: (PMID: 27899619, 22290698, 17594722, 22851212, 21120944, 12019211, 18790734, 15354210, 23621914, 26333163, 19766128, 10508506, 26269718, 28531214, 10537275, 31391288)

The MSH6 c.1696G>A variant is predicted to result in the amino acid substitution p.Gly566Arg. This variant has been reported in an individual with a history of colorectal cancer (Kolodner et al. 1999. PubMed ID: 10537275) and in patient from a large osteosarcoma cohort study (eTable 5. Mirabello L et al 2020. PubMed ID: 32191290). A yeast 2-hybrid assay indicated this variant resulted in partial loss of MSH6 function (Kolodner et al. 1999. PubMed ID: 10537275). However, additional in vitro functional studies also indicated this variant retained function similar to wildtype (Kariola R et al 2002. PubMed ID: 12019211) and another study indicated this variant retained mismatch repair function in mESCs (Houlleberghs H et al 2017. PubMed ID: 28531214). This variant has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/89217/?new_evidence=true). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.