ClinVar Genomic variation as it relates to human health

Multifactorial likelihood analysis posterior probability 0.95-0.99

This variant is denoted MSH2 c.2021G>A at the cDNA level, p.Gly674Asp (G674D) at the protein level, and results in the change of a Glycine to an Aspartic Acid (GGT>GAT). This variant was observed in at least four individuals with a personal history of one or more Lynch Syndrome-associated cancers and was reported to co-segregate with cancer in one family (Raedle 2001, Brieger 2011, Parc 2003). The corresponding variant in yeast, G693D, has been studied in numerous assays, and although it does not appear to impact Msh2p-Msh6p binding (Alani 1997, Gammie 2007), it has exhibited features supportive of pathogenicity including a dominant negative, high mutator phenotype (Studamire 1999, Gammie 2007), a reduction of protein expression (Gammie 2007), and at least a partial defect in ATP binding and ATPase activity (Kijas 2003, Bowers 2000). The International Society for Gastrointestinal Hereditary Tumours Incorporated (InSiGHT) classifies this variant as likely pathogenic (Thompson 2014). MSH2 Gly674Asp was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Glycine and Aspartic Acid differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. MSH2 Gly674Asp occurs at a position that is conserved across species and is located in the ATPase domain, ATP-binding motif and region of interaction with EXO1 (Lutzen 2008, UniProt). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on the currently available information, we consider MSH2 Gly674Asp to be a likely pathogenic variant.

Variant summary: MSH2 c.2021G>A (p.Gly674Asp) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS, C-terminal domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 246190 control chromosomes. c.2021G>A has been reported in the literature in multiple individuals affected with Lynch Syndrome, including cosegregation with disease in one family (Parc_2003). In addition, several other variants at the same codon (p.G674A, p.G674R, and p.G674S) are reported as being associated with colorectal cancer, suggesting it is important for protein function. These data indicate that the variant is likely to be associated with disease. Multiple publications report experimental evidence evaluating an impact on protein function. Although protein:protein interactions such as MSH2-MSH6 binding were not affected by the variant (Gammie_2007), MMR function was found to be defective and ATP-mediated dissocation in the presence of mismatch DNA was also impaired (Gammie_2007; Kijas_2003). Overall, the most pronounced variant effect in these functional studies results in <10% of normal activity. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The p.G674D pathogenic mutation (also known as c.2021G>A), located in coding exon 13 of the MSH2 gene, results from a G to A substitution at nucleotide position 2021. The glycine at codon 674 is replaced by aspartic acid, an amino acid with similar properties. This variant has been identified in probands whose family histories met Amsterdam I/II criteria for Lynch syndrome and colorectal tumors demonstrated high microsatellite instability (MSI-H) or loss of MSH2/MSH6 protein expression on immunohistochemistry (IHC) (Ambry internal data; Raedle J et al. Ann. Intern. Med., 2001 Oct;135:566-76; Brieger A et al. Fam. Cancer, 2011 Sep;10:591-5). This variant has also been identified in other unrelated families that met either Amsterdam criteria or Bethesda guidelines for Lynch syndrome (Schneider NB et al. Cancer Med, 2018 05;7:2078-2088; Parc Y et al. J. Med. Genet., 2003 Mar;40:208-13). In an in vitro complementation assay, this variant had deficient relative mismatch repair (MMR) activity and in a cell-based assay, cells expressing this variant became resistant to an alkylating agent demonstrating elevated mutation frequencies (Drost M et al. Genet. Med., 2019 07;21:1486-1496; Hayashida G et al. Exp. Cell Res., 2019 04;377:24-35). Functional studies performed using the homologous yeast allele, p.G693D, also demonstrated reduced function for this variant (Studamire B et al. Mol. Cell. Biol., 1999 Nov;19:7558-67; Bowers J et al. J. Mol. Biol., 2000 Sep;302:327-38; Kijas AW et al. J. Mol. Biol., 2003 Aug;331:123-38; Gammie AE et al. Genetics, 2007 Oct;177:707-21). Lastly, knock-in mice that conditionally expressed this variant in intestinal tissues developed smaller but more tumors with delayed onset compared to MSH2 null mice and tumors were responsive to Cisplatin, FOLFOX chemotherapeutic agents, but did demonstrate deficient MMR (Kucherlapati MH et al. Gastroenterology, 2010 Mar;138:993-1002.e1). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 22102614, 18822302, 19931261]. This variant is expected to disrupt protein structure [Myriad internal data].