ClinVar

Description

The MSH6 p.Pro320Thr variant was found to have no impact on MSH6 using a bioinformatics tool (CoDP (Combination of the Different Properties) that integrated the prediction results of MAPP, PolyPhen-2, SIFT and 2 other structural properties (Terui 2013). The variant was identified in the following databases: dbSNP (ID: rs754879198) “With Uncertain significance allele”, ClinVar (classified as uncertain significance by Invitae), and in control databases in 1 of 246084 chromosomes at a frequency of 0.000004 (Genome Aggregation Consortium Feb 27, 2017); it was observed in the European Non-Finnish population in 1 of 111572 chromosomes (freq: 0.000009) and not in other populations. The variant was not identified in the following databases: COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer, Zhejiang Colon Cancer, Mismatch Repair Genes, and the Insight Hereditary Tumors Database. The variant was also identified by our laboratory in 1 individual with breast and endometrial disease, co-occurring with a pathogenic MSH6 variant (c.741delA, p.Lys247AsnfsX32), increasing the likelihood that the p.Pro320Thr variant does not have clinical significance. The p.Pro320 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood Thr impacts the protein; however, 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign.