ClinVar Genomic variation as it relates to human health

Variant summary: MSH6 c.1063G>A (p.Gly355Ser) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 251204 control chromosomes, predominantly at a frequency of 0.0014 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 9.9 fold of the estimated maximal expected allele frequency for a pathogenic variant in MSH6 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00014), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.1063G>A has been reported in the literature in individuals affected with a variety of cancers (example, Yu_2015, Chao_2019). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome. At-least one co-occurrence with other pathogenic variant(s) have been reported (BRCA1 c.5527G>C, p.Ala1843Pro), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (VUS, n=3; likely benign, n=3). Based on the evidence outlined above, the variant was classified as likely benign.

This variant is denoted MSH6 c.1063G>A at the cDNA level, p.Gly355Ser (G355S) at the protein level, and results in the change of a Glycine to a Serine (GGT>AGT). This variant has been reported in two related individuals with non-medullary thyroid cancer (Yu 2015), and in an Asian patient with early-onset colorectal cancer (DeRycke 2017). This variant was also observed in 1/62 healthy East Asian individuals undergoing whole genome sequencing (Bodian 2014); of note, the participants in this study were younger than 50 years old, thus the unaffected status of this individual may not be significant. MSH6 Gly355Ser was observed at an allele frequency of 0.15% (29/18,868) in individuals of East Asian ancestry in large population cohorts (Lek 2016). Since Glycine and Serine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. MSH6 Gly355Ser is located within the nuclear localization signals (Gassman 2011). In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure or function. Based on currently available evidence, it is unclear whether MSH6 Gly355Ser is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

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.Gly355Ser variant was identified in 1 of 76 proband chromosomes (frequency: 0.01) from individuals or families with familial or sporadic non-medullary thyroid cancer, being identified in 2 affected members of the same family; and in 1 of 1362 chromosomes from healthy individuals (frequency: 0.0007) (Yu_2015_26530882, Bodian_2014_24728327). The variant was also identified in dbSNP (ID: rs587778531) “With Uncertain significance allele”, ClinVar (classified with conflicting interpretations of pathogenicity; submitters: likely benign by Invitae, uncertain significance by Ambry Genetics, GeneDx, Counsyl, Fulgent Genetics, and classification not provided by ITMI), Clinvitae (4x), Insight Hereditary Tumors Database (1x). The variant was not identified in GeneInsight-COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, or Mismatch Repair Genes Variant Database. The variant was identified in control databases in 33 of 276930 chromosomes at a frequency of 0.0001 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include Other in 1 of 6466 chromosomes (freq: 0.0002), East Asian in 29 of 18868 chromosomes (freq: 0.002), and South Asian in 3 of 30782 chromosomes (freq: 0.0001) while not observed in the African, Latino, European Non-Finnish, Ashkenazi Jewish and European Finnish populations. The p.Gly355 residue is conserved in mammals but not in more distantly related organisms; however, four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood that the Ser residue impacts the protein; 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.