ClinVar Genomic variation as it relates to human health

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: protein stability, microsatellite instability, and resistance to MNNG similar to wildtype (Rath et al., 2022) and intermediate loss of mismatch repair function (Ellison et al., 2004); Observed in individuals with colorectal cancer with presence of MLH1 protein on tumor immunohistochemistry analysis (Hampel et al., 2008; Bartley et al., 2012; Shirts et al., 2016; Borras et al., 2017); This variant is associated with the following publications: (PMID: 26333163, 12824425, 26845104, 12202775, 28466842, 25871441, 22086678, 15475387, 18809606, 28765196, 36054288, 16083711, 21120944, 22753075, 29212164, 31697235, 32849802, 17510385, 17210669)

This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 100 of the MLH1 protein (p.Arg100Gln). This variant is present in population databases (rs63750266, gnomAD 0.003%). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 18809606, 22086678, 26845104). This missense change has been observed to be homozygous or hemizygous in an individual who did not have the expected clinical features for that genetic result (Invitae). ClinVar contains an entry for this variant (Variation ID: 90132). An algorithm developed specifically for the MLH1 gene suggests that this missense change is likely to be deleterious (PMID: 26333163). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 15475387). Studies have shown that this missense change is associated with inconclusive levels of altered splicing (Invitae). This variant disrupts the Arg100 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17210669, 17510385, 29212164, 31697235, 32849802). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 glutamine at codon 100 of the MLH1 protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on protein structure and function. A functional study that examined this variant in the context of a human-yeast hybrid protein reported partial loss-of-function (PMID: 15475387). In another functional study done in human embryonic stem cells, the variant demonstrated a similar lack of response to DNA damage to a functionally abnormal variant, but resulted in limited microsatellite instability (PMID: 36054288). This variant has been reported in four individuals affected with colorectal cancer (PMID: 18809606, 22086678, 26845104 and the InSiGHT database) with tumor samples from at least three individuals that exhibited microsatellite instability (PMID: 18809606, 22086678 and the InSiGHT database). This variant also has been reported in breast cancer case-control meta-analysis in 1 affected and 3 unaffected individuals (PMID: 33471991; LOVD DB-ID: MLH1_000129). This variant failed to exhibit a significant association with pancreatic cancer (PMID: 32980694). This variant has been identified in 4/251360 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same position, p.Arg100Pro, is considered to be disease-causing (ClinVar variation ID: 90133), suggesting that arginine or similar amino acid at this position is important for the protein function. Although there is a suspicion that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The p.R100Q variant (also known as c.299G>A), located in coding exon 3 of the MLH1 gene, results from a G to A substitution at nucleotide position 299. The arginine at codon 100 is replaced by glutamine, an amino acid with highly similar properties. This variant was previously reported in the germline of two individuals with MSI-H colorectal cancers who had no family history of colon cancer (Hampel H et al. J Clin Oncol. 2008; 26:5783-8; Bartley AN et al. Cancer Prev Res (Phila) 2012; 5:320-7). In a hybrid yeast-human experiment, this variant was previously found to be associated with a decrease in mismatch repair activity and was considered intermediate deficiency (Ellison AR et al. Nucleic Acids Res. 2004; 32:5321-38). This alteration has been classified as an uncertain variant by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, mutation co-occurrence, and functional assay results (Thompson B et al. Nat Genet. 2014 Feb;46(2):107-15; available at [www.insight-group.org/variants/classifications/]). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear.

This missense variant replaces arginine with glutamine at codon 100 of the MLH1 protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on protein structure and function. A functional study that examined this variant in the context of a human-yeast hybrid protein reported partial loss-of-function (PMID: 15475387). In another functional study done in human embryonic stem cells, the variant demonstrated a similar lack of response to DNA damage to a functionally abnormal variant, but resulted in limited microsatellite instability (PMID: 36054288). This variant has been reported in multiple individuals affected with colorectal cancer (PMID: 18809606, 22086678, 26845104). All tumors tested demonstrated no loss of mismatch repair protein via immunohistochemistry, but two tumor samples exhibited microsatellite instability (PMID: 18809606, 22086678, 26845104). This variant has also been reported in a homozygous or hemizygous individual who did not demonstrate expected clinical features (ClinVar: SCV000284057.10). This variant also has been reported in breast cancer case-control meta-analysis in 1 affected and 3 unaffected individuals (PMID: 33471991; LOVD DB-ID: MLH1_000129). This variant failed to exhibit a significant association with pancreatic cancer (PMID: 32980694). This variant has been identified in 4/251360 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same position, p.Arg100Pro, is considered to be disease-causing (ClinVar variation ID: 90133), suggesting that arginine or similar amino acid at this position is important for the protein function. Although there is a suspicion that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

Variant summary: MLH1 c.299G>A (p.Arg100Gln) results in a conservative amino acid change located in the DNA mismatch repair protein family, N-terminal domain of the encoded protein sequence. Four 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 251360 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.299G>A has been reported in the literature in individuals affected with CRC or HBOC (Bartley_2011, Hampel_2008, Shirts_2016). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. One functional study shows 34-66% loss of MMR function but was performed in hybrid human-yeast genes (Ellison_2004). The following publications have been ascertained in the context of this evaluation (PMID: 15475387, 18809606, 22086678, 26845104). ClinVar contains an entry for this variant (Variation ID: 90132). Based on the evidence outlined above, the variant was classified as uncertain significance.

The MLH1 c.299G>A (p.Arg100Gln) variant has been reported in the published literature in individuals with colorectal cancer (PMIDs: 31391288 (2020), 28765196 (2017), 26845104 (2016), 22086678 (2012), and 18809606 (2008)). Additionally, this variant was reported as a somatic variant in a brain metastasis of a breast cancer patient (PMID: 29755676 (2018)). In a study measuring DNA mismatch repair capacity, this variant showed intermediate function (PMID: 15475387 (2004)). In a study measuring DNA mismatch repair capacity, this variant showed intermediate function (PMID: 15475387 (2004)). The frequency of this variant in the general population, 0.000026 (3/113664 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

Variant interpreted as Uncertain significance and reported on 11-01-2019 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.