ClinVar

Description

The MSH6 p.Thr1243Ser variant was identified in 2 of 3972 proband chromosomes (frequency: 0.001) from individuals or families with malignant pleural mesothelioma, epithelial ovarian cancer (Betti 2017, Pal 2012). The variant was also identified in dbSNP (ID: rs147453999) as “With other allele”, in ClinVar (classified as uncertain significance by GeneDx, Ambry Genetics, Color Genomics; as likely benign by Invitae, IGLCA), Clinvitae, COGR, MutDB, and the Insight Hereditary Tumors Database. The variant was not identified in Cosmic, UMD-LSDB, Zhejiang Colon Cancer Database, or the Mismatch Repair Genes Variant Database. The variant was identified in control databases in 77 of 276950 chromosomes (1 homozygous) at a frequency of 0.0003 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: “Other” in 7 of 6454 chromosomes (freq: 0.001), Latino in 21 of 34370 chromosomes (freq: 0.001), European in 14 of 126502 chromosomes (freq: 0.0001), and South Asian in 35 of 30782 chromosomes (freq: 0.001); it was not observed in the African, Ashkenazi Jewish, East Asian, or Finnish populations. The p.Thr1243 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In a study that integrated the prediction results of three in silico programs and two other structural properties, namely solvent accessibility and the change in the number of heavy atoms of amino acids in the MSH6 protein, the authors concluded the variant has an impact on the MSH6 protein (Terui 2013). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.