ClinVar Genomic variation as it relates to human health

In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with a personal or family history of breast and/or pancreatic cancer (PMID: 25479140, 25186627, 33471991, 34326862); This variant is associated with the following publications: (PMID: 23621914, 25186627, 25479140, 33471991, 34326862, 17531815, 21120944)

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752].

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

The MSH6 p.Lys676Arg variant was identified in 1 of 580 proband chromosomes (frequency: 0.002) from individuals or families with pancreatic cancer (Grant_2015_25479140). A bioinformatics tool, CoDP (Combination of the Different Properties) integrating the prediction results of three methods (MAPP, PolyPhen-2 and SIFT) and two structural properties, found the variant did not impact the MSH6 protein (Terui_2013_23621914). The variant was also identified in dbSNP (ID: rs143643688) “With Uncertain significance allele”, ClinVar (classified as uncertain significance by Ambry Genetics, GeneDx, Invitae and Counsyl), Clinvitae (4x), and in control databases in 15 of 276506 chromosomes at a frequency of 0.00005 (Genome Aggregation Database Feb 27, 2017). Observations by population include Latino in 2 of 34392 chromosomes (freq: 0.00006), European Non-Finnish in 13 of 126094 chromosomes (freq: 0.0001); it was not observed in the African, “Other”, Ashkenazi Jewish, East Asian, European Finnish, and South Asian populations. The variant was not identified in COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or the Insight Hereditary Tumors Database. The p.Lys676 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 the Arg residue has an impact on the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. 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.

The MSH6 c.2027A>G variant is predicted to result in the amino acid substitution p.Lys676Arg. This variant has been reported in individuals with breast cancer (Table S2, Tung et al. 2014. PubMed ID: 25186627; Table S4, Bhai et al. 2021. PubMed ID: 34326862; Supplemental File, Breast Cancer Association Consortium et al 2021. PubMed ID: 33471991) or pancreatic cancer (Table S1, Grant et al. 2014. PubMed ID: 25479140). In each of these reports this variant was reported along with the MSH6 c.2827G>T (p.Asp943Tyr) variant suggesting they are on the same allele. This variant is reported in 0.010% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations in ClinVar of likely benign and uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/142496/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.