ClinVar Genomic variation as it relates to human health

Variant summary: The MLH1 c.-11C>T variant involves the alteration of a non-conserved nucleotide located in the 5'UTR. Mutation Taster predicts a benign outcome for this variant. This variant is absent in 121940 control chromosomes including broad and large population from ExAC. This variant has previously been reported in two colon cancer patients, one with both MSI and MLHI IHC negative tumor, the other with either MSI or MLH1 IHC negative tumor, consistent with disease-causing outcome of the variant (Ward_2013). This report also performed functional studies in which c.-11C>T showed a significant reduction in promoter activity as compared with the wild-type promoter sequence (~49% and ~62% of wild-type activity in HCT116 and HEK293 cells, respectively). Taken together, this variant is currently classified as VUS-possibly pathogenic.

This variant is denoted MLH1 c.-11C>T, and describes a nucleotide substitution 11 base pairs upstream of the MLH1 ATG translational start site in the 5' untranslated region (UTR). The surrounding sequence, with the base that is substituted in brackets, is TCTT[C/T]TGGC. This variant has been observed in at least three individuals with colon cancer whose tumors demonstrated microsatellite instability (MSI-H) and/or absence of MLH1 expression by immunohistochemistry (IHC). While one of these individuals' tumors was also positive for MLH1 promoter hypermethylation, the other two were not (Hampel 2008. Ward 2013). MLH1 c.-11C>T has been reported to reduce promoter activity compared to wild type (Ward 2013). MLH1 c.-11C>T was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. The cytosine (C) nucleotide that is altered is not conserved. This variant does not appear to affect the start codon or the Kozak translational consensus sequence, and is not predicted to affect splicing. However, in the absence of RNA or functional studies, the actual effect of this variant is unknown. Based on currently available evidence, it is unclear whether MLH1 c.-11C>T is pathogenic or benign. We consider it to be a variant of uncertain significance.

MLH1 NM_000249.2 c.-11C>T: This variant has been reported in the literature in at least three individuals with colorectal cancer; these individuals had tumor screening that showed absence of MLH1 on IHC and/or microsatellite instability (MSI) (Hampel 2008 PMID:18809606, Ward 2013 PMID:22878509). This variant is present in 0.006% (1/15290) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/3-36993537-C-T?dataset=gnomad_r3). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population, carrier status, and/or variable expressivity. This variant is present in ClinVar (Variation ID:421030). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant represents a single nucleotide change in the upstream 5' untranslated region (UTR) of the gene. In vitro functional studies showed a significant reduction in promotor activity with this variant compared to the wild-type promotor sequence (Ward 2013 PMID:22878509). However, these studies may not accurately represent in vivo biological function. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

This variant is located in the 5' untranslated region of the MLH1 gene. This variant has been reported in individuals affected with Lynch syndrome and colorectal cancer (PMID: 8809606, 22878509, 37433431, 37270516). Additionally, the variant has been reported to reduce promoter activity (PMID: 22878509). This variant has been identified in 3/251472 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may be associated with disease, additional clinical and functional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

This variant occurs in a non-coding region of the MLH1 gene. It does not change the encoded amino acid sequence of the MLH1 protein. This variant is present in population databases (rs776898290, gnomAD 0.003%). This variant has been observed in individual(s) with colorectal cancer (PMID: 18809606, 22878509). ClinVar contains an entry for this variant (Variation ID: 421030). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects MLH1 function (PMID: 22878509). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

PP4_Moderate

The MLH1 c.-11C>T variant was identified in 2 of 832 proband chromosomes (frequency: 0.002) from individuals with Lynch Syndrome, at least one of whom had abnormal IHC results (Ward 2013). The variant was identified in dbSNP (rs776898290) as “with uncertain significance allele and ClinVar (classified as uncertain significance by Color, GeneDx and Integrated Genetics). The variant was not identified in UMD-LSDB. The variant was identified in control databases in 3 of 246,260 chromosomes at a frequency of 0.00001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 2 of 111,710 chromosomes (freq: 0.00002) and South Asian in 1 of 30,782 chromosomes (freq: 0.00003); it was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian or Finnish populations. The c.-11C>T variant is located upstream of the Kozak sequence and the effect of this variant on promoter activity cannot be predicted with in silico tools. However, the variant demonstrated a significant reduction in promoter activity in a luciferase assay (Ward 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.