ClinVar

Description

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.