ClinVar

Description

The MSH6 p.Asn223Asp variant was assessed to have no impact on the MSH6 protein using a bioinformatics tool CoDP (Combination of the Different Properties) that integrates the prediction results of MAPP, PolyPhen-2 and SIFT, in addition to 2 other structural properties (solvent accessibility and change in the number of heavy atoms of amino acids (Terui_2013_23621914). The variant was also identified in dbSNP (ID: rs374041375) “With Uncertain significance allele”, ClinVar (classified uncertain significance by Ambry Genetics and Invitae), Clinvitae (2x), and in control databases in 2 of 244386 chromosomes at a frequency of 0.000008 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include European Non-Finnish in 2 of 111096 chromosomes (freq: 0.00002), while not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian, European Finnish, and South Asian populations. The variant was not identified in GeneInSight-COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors Database. The p.Asn223 residue is conserved in in mammals but not in more distantly related organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood the variant Asp impacts the protein; this information is not predictive enough to rule out 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 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.