ClinVar Genomic variation as it relates to human health

The p.Arg389Gln variant in MLH1 has been reported in 2 individuals with colorect al cancer (Chao 2008 and Chang 2016, variant reported as p.R291Q). It has also b een identified in 4/10400 of African chromosomes by the Exome Aggregation Consor tium (ExAC, http://exac.broadinstitute.org; dbSNP rs63750361). Please note that for diseases with clinical variability, reduced penetrance, or recessive inherit ance, pathogenic variants may be present at a low frequency in the general popul ation. Computational prediction tools and conservation analysis do not provide s trong support for or against an impact to the protein and in vitro testing did n ot demonstrate an impact on the mismatch repair (Takahashi 2007). In addition, this variant has been classified as a variant of uncertain significance on Septe mber 5, 2013 by the ClinGen approved InSIGHT expert panel (ClinVar SCV000106124. 2). In summary, the clinical significance of the p.Arg389Gln variant is uncertai n.

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 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 variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

The MLH1 c.1166G>A; p.Arg389Gln variant (rs63750361) is reported in the literature in individuals with personal and/or a family history of colorectal cancer (Biscaglia 2022, Chang 2016, variant reported as p.R291Q), and is reported by multiple sources in ClinVar (Variation ID: 41633). One in vitro assay showed mismatch repair activity of 83.6% for the variant protein with >75% relative MLH1 expression (Takahashi 2007). However, another in vitro assay demonstrated mismatch repair activity of 13% for the variant protein compared to wildtype protein, and splicing assays show this variant may have an effect on splicing (Thompson 2020). This variant is found in the general population with an overall allele frequency of 0.007% (20/282620 alleles) in the Genome Aggregation Database. The arginine at codon 389 is moderately conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.594). Based on available information, the clinical significance of this variant is uncertain at this time. References: Biscaglia G et al. Germline Alterations in Patients With IBD-associated Colorectal Cancer. Inflamm Bowel Dis. 2022 Mar 2;28(3):447-454. PMID: 34347074. Chang PY et al. NRAS germline variant G138R and multiple rare somatic mutations on APC in colorectal cancer patients in Taiwan by next generation sequencing. Oncotarget. 2016 Jun 21;7(25):37566-37580. PMID: 27121310. Takahashi M et al. Functional analysis of human MLH1 variants using yeast and in vitro mismatch repair assays. Cancer Res. 2007 May 15;67(10):4595-604. PMID: 17510385. Thompson BA et al. InSiGHT Variant Interpretation Committee. Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation. Front Genet. 2020 Jul 27;11:798. PMID: 32849802.

The MLH1 c.1166G>A (p.Arg389Gln) missense change has a maximum subpopulation frequency of 0.044% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, and functional studies have shown mixed effects. One in vitro study demonstrated a similar mismatch repair activity compared to wildtype, while another showed a significantly reduced activity (PMID: 17510385 and 32849802, respectively). This variant has been reported in individuals with colorectal and ovarian cancer (PMID: 18383312, 23047549, 27121310, 28577310, 29069792, 34347074, 35263119). In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

This variant is associated with the following publications: (PMID: 26817999, 28873162, 16995940, 17510385, 22703879, 23047549, 18383312, 25579085, 25742471, 27300758, 26648449, 24933000, 27121310, 22290698, 32849802)

This variant is considered benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. This variant has been observed in conjunction with multiple pathogenic variants, reducing the likelihood this variant itself is pathogenic.

Variant summary: MLH1 c.1166G>A (p.Arg389Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 5.9e-05 in 252668 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (5.9e-05 vs 0.00071), allowing no conclusion about variant significance. c.1166G>A has been reported in the literature in individuals affected with colorectal or ovarian cancer without strong evidence of causality (e.g. Chao_2008, Pal_2012, Chang_2016, Biscaglia_2022, Delahunty_2022). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. Co-occurrence with another pathogenic variants has been reported (BRCA1 c.2241delC, p.Asp749fsX4, internal database), providing supporting evidence for a benign role. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant (Takahashi_2007). The following publications have been ascertained in the context of this evaluation (PMID: 17510385, 18383312, 22703879, 23047549, 25579085, 26817999, 27121310, 14526391, 34347074, 35263119). ClinVar contains an entry for this variant (Variation ID: 41633). Based on the evidence outlined above, the variant was classified as VUS-possibly benign.

Converted during submission to Uncertain significance.

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).