ClinVar

Description

The p.Met894AsnfsX5 variant in MSH2 has been reported in at least 2 individuals with Lynch syndrome associated cancers (Casey 2005 PMID: 15713769, Lagerstedt-Robinson 2016 PMID: 27601186, Carter 2018 PMID: 30322717). In addition, tumors sampled from 1 of these individuals lacked MSH2 and MSH6 expression. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID: 229809) and has been identified in 0.003% (3/113586) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 894 and leads to a premature termination codon 5 amino acids downstream. This termination codon occurs within the last exon and is therefore, likely to escape nonsense mediated decay (NMD) and result in a truncated protein that is missing ~4% of the coding region, with 36 amino acids removed. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PVS1_Moderate, PM2, PS4_Supporting, PS3_Moderate.