ClinVar Genomic variation as it relates to human health

Variant summary: MLH1 c.2173C>T (p.Arg725Cys) results in a non-conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain (IPR032189) 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 1.6e-05 in 251148 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2173C>T has been reported in the literature as a germline VUS in settings of multigene panel testing of individuals affected with microsatellite stable (MSS) colorectal cancer, Hereditary Breast and Ovarian Cancer (HBOC) and in settings of Lynch-like syndrome where the tumors harbored other pathogenic variants in MLH1 and MSH2 genes of presumably somatic origin (example, Chao_2008, Quezada_2018, Xu_2020). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect reporting reduced expression but proficient mismatch repair (MMR) activity (example, Hinrichsen_2013). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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.

This variant is denoted MLH1 c.2173C>T at the cDNA level, p.Arg725Cys (R725C) at the protein level, and results in the change of an Arginine to a Cysteine (CGC>TGC). This variant has been observed in at least one patient with early-onset colon cancer whose tumor was microsatellite stable (Chao 2008). Functional studies showed Arg725Cys had reduced MLH1 protein expression, but normal mismatch repair (MMR) activity (Hinrichsen 2013). Additionally, a yeast two-hybrid assay revealed this variant retained interaction with PMS2 similar to wild-type, suggesting that Arg725Cys does not impact PMS2 binding (Wang 2012). This variant 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. Since Arginine and Cysteine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. MLH1 Arg725Cys occurs at a position that is conserved across species and is located within the region of interaction with PMS2/MLH3/PMS1 (Pang 1997, Raevaara 2005, Hardt 2011). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available evidence, it is unclear whether MLH1 Arg725Cys is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 725 of the MLH1 protein (p.Arg725Cys). This variant is present in population databases (rs138584384, gnomAD 0.006%). This missense change has been observed in individual(s) with colorectal cancer (PMID: 18383312). ClinVar contains an entry for this variant (Variation ID: 90081). An algorithm developed specifically for the MLH1 gene suggests that this missense change is likely to be deleterious (PMID: 18383312). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 23403630). 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.

This missense variant replaces arginine with cysteine at codon 725 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that the mutant protein had reduced expression but normal mismatch repair activity (PMID: 23403630), and interacted with PMS2 similar to wild type protein (PMID: 22252508). This variant has been reported in individuals affected with colorectal cancer (PMID: 18383312, 33294277). This variant has been identified in 4/251148 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.