ClinVar Genomic variation as it relates to human health

The MSH6 c.4001+2T>A variant, to our knowledge, is not reported in the medical literature or gene-specific databases. However, another variant in the same nucleotide, c.4001+2T>C, is reported in the literature in several individuals and families with Lynch syndrome (Klarskov 2011, Lagerstedt-Robinson 2016, Nilbert 2009). The c.4001+2T>A variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. This variant disrupts the canonical splice donor site of intron 9, which is likely to negatively impact gene function. Considering available information, this variant is classified as pathogenic. References: Klarskov L et al. Challenges in the identification of MSH6-associated colorectal cancer: rectal location, less typical histology, and a subset with retained mismatch repair function. Am J Surg Pathol. 2011 Sep;35(9):1391-9. Lagerstedt-Robinson K et al. Mismatch repair gene mutation spectrum in the Swedish Lynch syndrome population. Oncol Rep. 2016 Nov;36(5):2823-2835. Nilbert M et al. Major contribution from recurrent alterations and MSH6 mutations in the Danish Lynch syndrome population. Fam Cancer. 2009;8(1):75-83.

The c.4001+2T>A intronic variant results from a T to A substitution two nucleotides after coding exon 9 in the MSH6 gene. This variant has been identified in a proband(s) whose Lynch syndrome-associated tumor demonstrated loss of MSH6 expression by immunohistochemistry (Ambry internal data). This alteration occurs at the 3' terminus of the MSH6 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 93 AA of the protein. The exact functional effect of this alteration is unknown; however, the impacted region is critical for protein function (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved on limited sequence alignment. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic.