ClinVar

Description

Variant summary: MSH2 c.499G>C (p.Asp167His) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS, connector domain 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 8.7e-05 in 251484 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is not higher than expected for a pathogenic variant in MSH2 causing Hereditary Nonpolyposis Colorectal Cancer (8.7e-05 vs 0.00057), allowing no conclusion about variant significance. c.499G>C has been reported in the literature in individuals affected with Hereditary Nonpolyposis Colorectal Cancer and breast cancer (e.g. Moslein_1996, Scartozzi_2002, Belvederesi_2008, Yurgelun_2015, Lagerstedt-Robinson_2016, Rizzolo_2019, Tsaousis_2019, Ryan_2020, Doling_2021) but it was also reported in controls (e.g. Dorling_2021). In two of the patients from these studies where tumor analysis was carried out, IHC was found to be normal for MSH2 while loss of MLH1 protein expression was noted (Scartozzi_2002, Belvederesi_2008). In a third patient who did not fullfil Amsterdam-II Criteria or Revised Bethesda Criteria, normal IHC results and MSS was observed (Ryan_2020). These results provide supporting evidence for a benign role of the variant. Co-occurrences with pathogenic variants have been reported [MLH1 c.1852_1854delAAG, p.Lys618del (UMD); MLH1 21delG, p.Ile8PhefsX9 (Moslein_1996)], providing further supporting evidence for a benign role. Experimental evidence from multiple studies, including a recent in cellulo functional assay utilizing CRISPR-Cas9 gene editing in human embryonic stem cells, agree in their majority that the variant acts comparable to wild type (e.g. Gammie_2007, Belvederesi_2008, Drost_2011, Rath_2019). Six ClinVar submitters including an expert panel (InSiGHT) (evaluation after 2014) cite the variant as benign/likely benign and three ClinVar submitters (evaluation after 2014) cite it as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.