ClinVar Genomic variation as it relates to human health

Variant summary: MSH6 c.3727A>T (p.Thr1243Ser) results in a conservative amino acid change located in the DNA mismatch repair protein MutS, C-terminal domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00027 in 251210 control chromosomes, predominantly at a frequency of 0.0011 within the South Asian subpopulation in the gnomAD database, including 1 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 7.7 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 South Asian origin. c.3727A>T has been reported in the literature in individuals with a variety of cancer types such as epithelial ovarian cancer (example, Pal_2012), kidney renal clear cell carcinoma in the TGCA cohort (Lu_2015), as a VUS in Malignant pleural mesothelioma (MPM) (example, Betti_2017), as a VUS in breast/ovarian cancer (example, Tsaousis_2019, Akcay_2020, Moradian_2021). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Fifteen 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 (likely benign, n=3; VUS, n=12). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as likely benign.

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.

MSH6: BP1, BS1

DNA sequence analysis of the MSH6 gene demonstrated a sequence change, c.3727A>T, in exon 8 that results in an amino acid change, p.Thr1243Ser. This sequence change has been described in the gnomAD database with a frequency of 0.11% in South Asian populations (dbSNP rs147453999). The p.Thr1243Ser change has been identified in an individual with mesothelioma and exposure to asbestos (PMID: 28687356). The p.Thr1243Ser change affects a highly conserved amino acid residue located in a domain of the MSH6 protein that is known to be functional. The p.Thr1243Ser substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Thr1243Ser change remains unknown at this time.

BS1_Strong,BS2

BS1

The MSH6 c.3727A>T; p.Thr1243Ser variant (rs147453999) is reported in the literature in individuals with hereditary cancer predisposition syndrome, ovarian cancer, or mesothelioma (Betti 2017, Pal 2012, Tsaousis 2019). This variant is also reported in ClinVar (Variation ID: 127589). It is found in the general South Asian population with an allele frequency of 0.1% (35/30614 alleles, including 1 homozygote) in the Genome Aggregation Database. The threonine at codon 1243 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant may be deleterious. However, due to limited information, the clinical significance of this variant is uncertain at this time. REFERENCES Betti M et al. Germline mutations in DNA repair genes predispose asbestos-exposed patients to malignant pleural mesothelioma. Cancer Lett. 2017 Oct 1;405:38-45. Pal T et al. Frequency of mutations in mismatch repair genes in a population-based study of women with ovarian cancer. Br J Cancer. 2012 Nov 6;107(10):1783-90. Tsaousis GN et al. Analysis of hereditary cancer syndromes by using a panel of genes: novel and multiple pathogenic mutations. BMC Cancer. 2019 Jun 3;19(1):535.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23047549, 23621914, 28687356, 26338694, 31159747)

ACMG Guidelines 2015 criteria PM1 Pathogenic Moderate: A domain mutATP5 (V1127-1321R aa) functioning in ATPase activity. Hot-spot has 30 non-VUS coding variants (19 pathogenic and 11 benign), pathogenicity = 63.3%, proximity score 9.180 > threshold 2.472. PP3 Pathogenic Supporting: 7 pathogenic predictions from DEOGEN2, FATHMM-MKL, M-CAP, MVP, MutationTaster, PrimateAI and SIFT vs 4 benign predictions from DANN, EIGEN, MutationAssessor and REVEL. BS1 Benign Strong: GnomAD exomes South Asian allele frequency = 0.00114 > 0.000649 derived from the 3,884 clinically reported variants in gene MSH6 of which 739 PATH, 2,198 VUS and 947 benign. BP1 Benign Supporting: 85 out of 114 non-VUS missense variants in gene MSH6 are BEN = 74.6% > threshold of 51.0%, and 947 out of 3,884 clinically reported variants in gene MSH6 are BEN = 24.4% > threshold of 24.0%. BP6: Multiple reputable databases/clinical laboratories cite the variant with conflicting classifications "uncertain significance" or "likely benign." Therefore, it has been classified as a Variant of Uncertain Significance.

The MSH6 p.Thr1243Ser variant was identified in 2 of 3972 proband chromosomes (frequency: 0.001) from individuals or families with malignant pleural mesothelioma, epithelial ovarian cancer (Betti 2017, Pal 2012). The variant was also identified in dbSNP (ID: rs147453999) as “With other allele”, in ClinVar (classified as uncertain significance by GeneDx, Ambry Genetics, Color Genomics; as likely benign by Invitae, IGLCA), Clinvitae, COGR, MutDB, and the Insight Hereditary Tumors Database. The variant was not identified in Cosmic, UMD-LSDB, Zhejiang Colon Cancer Database, or the Mismatch Repair Genes Variant Database. The variant was identified in control databases in 77 of 276950 chromosomes (1 homozygous) at a frequency of 0.0003 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: “Other” in 7 of 6454 chromosomes (freq: 0.001), Latino in 21 of 34370 chromosomes (freq: 0.001), European in 14 of 126502 chromosomes (freq: 0.0001), and South Asian in 35 of 30782 chromosomes (freq: 0.001); it was not observed in the African, Ashkenazi Jewish, East Asian, or Finnish populations. The p.Thr1243 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume 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 a study that integrated the prediction results of three in silico programs and two other structural properties, namely solvent accessibility and the change in the number of heavy atoms of amino acids in the MSH6 protein, the authors concluded the variant has an impact on the MSH6 protein (Terui 2013). 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.