ClinVar Genomic variation as it relates to human health

This missense variant replaces valine with glutamic acid at codon 1253 of the MSH6 protein. Computational prediction tool suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been performed for this variant. This variant has been reported in individuals affected with Lynch syndrome-associated cancer and/or polyps (PMID: 25142776, 25980754) and other non-Lynch or unspecified cancers (PMID: 26689913, 29684080, 31921681, 31391288), and in an unaffected individual (PMID: 31422574). This variant has also been identified in 42/282588 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The p.V1253E variant (also known as c.3758T>A), located in coding exon 8 of the MSH6 gene, results from a T to A substitution at nucleotide position 3758. The valine at codon 1253 is replaced by glutamic acid, an amino acid with dissimilar properties. This alteration has been reported in multiple cohorts of patients undergoing multigene panel testing, including individuals diagnosed with a Lynch syndrome-associated cancer and/or polyps (Tsaousis GN et al. BMC Cancer. 2019 Jun;19:535; Yehia L et al. PLoS Genet. 2018 04;14:e1007352; Yurgelun MB et al. Gastroenterology. 2015 Sep;149:604-13.e20; Young EL et al. BMC Cancer. 2018 Jun;18:697). It was identified in a 70-year-old individual with microsatellite-stable, mismatch repair protein-proficient colorectal cancer (Kraus C et al. Int. J. Cancer. 2015 Mar;136:E559-68), as well as two patients, one with breast and the other with renal cancer, from a cohort of 4034 cancer cases from The Cancer Genome Atlas (Lu C et al. Nat Commun. 2015 Dec;6:10086). Additionally, this alteration was identified in 1/2515 controls and 0/165 individuals with colorectal cancer and/or polyps (Rosenthal EA et al. Hum. Genet. 2018 Oct;137:795-806). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Variant summary: MSH6 c.3758T>A (p.Val1253Glu) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS, C-terminal domain (IPR000432) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00016 in 251190 control chromosomes, predominantly at a frequency of 0.00023 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 1.62 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 Non-Finnish European origin. c.3758T>A has been reported in the literature in individuals affected with or being tested for Lynch Syndrome, as well as in patients with breast or ovarian cancer (e.g. Kraus_2015, Lu_2015, Young_2018, Yurgelun_2015, Tsaousis_2019, Morak_2019, Li_2020, Kraemer_2019, Oliver_2019, Dorling_2021, Pereira_2022). However, the variant was also identified in many healthy controls (e.g., Dorling_2021, Rosenthal_2018). These reports therefore do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. One publication reports experimental evidence evaluating an impact on RNA splicing and found that the variant had no effect (e.g., Frederiksen_2021). The following publications have been ascertained in the context of this evaluation (PMID: 31422574, 25142776, 31391288, 26689913, 31332305, 31921681, 23621914, 31159747, 29945567, 25980754, 34445333, 35980532, 29684080, 30267214, 33471991). Ten ClinVar submitters (evaluation after 2014) have cited the variant with conflicting assessments: VUS (n = 8) and likely benign (n = 2). Based on the evidence outlined above, the variant was classified as likely benign.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with colorectal, ovarian, breast, or other cancers, as well as in unaffected control groups (PMID: 29684080, 25142776, 26689913, 29945567, 33471991, 34326862, 35980532); This variant is associated with the following publications: (PMID: 28166811, 22949387, 23621914, 25142776, doi:10.5923/j.bioinformatics.20160602.03, 29684080, 25980754, 29945567, 31159747, 26689913, 31422574, 31391288, 31332305, 31921681, 30267214, 34445333, 33471991, Giacomazzi2022[preprint], 17531815, 21120944, 35980532, 36461907, 34326862)

MSH6: BP1, BS1:Supporting

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant has been reported in one individual with CRC. MaxMAF is 0.09%. Classified as DM? in HGMD. Classified in ClinVar as VUS by Invitae, Ambry, GeneDx (2 stars). MAF is greater than or equal to disease prevalence

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

This missense variant replaces valine with glutamic acid at codon 1253 of the MSH6 protein. Computational prediction tool suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been performed for this variant. This variant has been reported in individuals affected with Lynch syndrome-associated cancer and/or polyps (PMID: 25142776, 25980754) and other non-Lynch or unspecified cancers (PMID: 26689913, 29684080, 31921681, 31391288), and in an unaffected individual (PMID: 31422574). This variant has also been identified in 42/282588 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The MSH6 p.Val1253Glu variant was identified in 1 of 304 proband chromosomes (frequency: 0.003) from individuals or families with colorectal cancer (Kraus 2014). The variant was also identified in dbSNP (ID: rs202066386) as "With Uncertain significance allele”, ClinVar (classified as uncertain significance by Invitae, GeneDx, Ambry Genetics, and three other submitters), and in UMD-LSDB. The variant was identified in control databases in 41 of 276934 chromosomes at a frequency of 0.0002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 5 of 6460 chromosomes (freq: 0.0008), Latino in 1 of 34382 chromosomes (freq: 0.00002), European in 25 of 126474 chromosomes (freq: 0.0002), Finnish in 10 of 25788 chromosomes (freq: 0.0004); it was not observed in the African, Ashkenazi Jewish, East Asian, or South Asian populations. An experimental study on predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein identified the p.Val1253Glu has an impact on MSH6 (Terui 2013). The p.Val1253 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 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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.3758T>A variant is predicted to result in the amino acid substitution p.Val1253Glu. This variant has been reported with uncertain significance in individuals with colorectal, suspected Lynch syndrome, or breast cancer (Table 4, ID 48, Kraus et al. 2015. PubMed ID: 25142776; able S5, Li et al. 2020. PubMed ID: 31391288; Supplementary Data, Breast Cancer Association Consortium et al. 2021. PubMed ID: 33471991; Table S4, Bhai et al. 2021. PubMed ID: 34326862; Pereira et al. 2022. PubMed ID: 35980532). It was also reported as a variant of uncertain significance in a study of individuals with hereditary cancer syndromes, however specific clinical features were not noted (Table S5, Tsaousis et al. 2019. PubMed ID: 31159747). This variant has also been reported in control populations (Supplementary Table 2, Rosenthal et al. 2018. PubMed ID: 30267214; Supplementary Data, Breast Cancer Association Consortium et al. 2021. PubMed ID: 33471991). This variant is reported in 0.044% of alleles in individuals of European (Finnish) descent in gnomAD and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from uncertain significance to likely benign (https://www.ncbi.nlm.nih.gov/clinvar/variation/127591/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.