Submissions for variant NM_000249.4(MLH1):c.1421G>A (p.Arg474Gln)

gnomAD frequency: 0.00001  dbSNP: rs63751083

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Counsyl	RCV000662517	SCV000785062	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2017-03-29	criteria provided, single submitter	clinical testing
Invitae	RCV000685340	SCV000812818	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2023-12-28	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 474 of the MLH1 protein (p.Arg474Gln). This variant is present in population databases (rs63751083, gnomAD 0.003%). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 18383312, 18561205, 22736432). ClinVar contains an entry for this variant (Variation ID: 89737). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MLH1 protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change does not substantially affect MLH1 function (PMID: 17510385, 18561205, 22736432, 30998989). 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.
Color Diagnostics, LLC DBA Color Health	RCV000776166	SCV000911231	likely benign	Hereditary cancer-predisposing syndrome	2016-08-06	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000776166	SCV001171839	uncertain significance	Hereditary cancer-predisposing syndrome	2023-07-11	criteria provided, single submitter	clinical testing	The p.R474Q variant (also known as c.1421G>A), located in coding exon 13 of the MLH1 gene, results from a G to A substitution at nucleotide position 1421. The arginine at codon 474 is replaced by glutamine, an amino acid with highly similar properties. This alteration has been reported in individuals fulfilling Amsterdam II criteria (Tournier I et al. Hum Mutat, 2008 Dec;29:1412-24; Martin-Morales L et al. PLoS One, 2018 Sep;13:e0203885). This alteration was also detected in a patient with colon cancer who had at least two family members with colorectal and/or endometrial cancer in two generations (Stojcev Z et al. Acta Biochim Pol, 2013 Jun;60:195-8), and was identified in a cohort of 3,579 African males diagnosed with prostate cancer who underwent multi-gene panel testing of 19 DNA repair and cancer predisposition genes (Matejcic M et al. JCO Precis Oncol, 2020 Jan;4:32-43). An in vitro functional study showed that p.R474Q had ATPase activity similar to wild-type MLH1 (Räschle M et al. J. Biol. Chem. 2002 Jun;277:21810-20). Another yeast-based functional assay showed that this alteration retained 81.1% of mismatch repair activity compared to wild-type and also showed greater than 75% relative MLH1 protein expression compared to wild-type (Takahashi M et al. Cancer Res. 2007 May;67:4595-604). The p.R474Q variant also demonstrated evidence of being benign in a methylation tolerance-based functional assay (Bouvet D et al. Gastroenterology, 2019 08;157:421-431). This variant also demonstrated normal function in a human cell-based functional study that examined protein stability, damage response signaling and DNA repair function of MLH1 variants (Rath A et al. Hum Mutat, 2022 Dec;43:2295-2307). 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.
Mendelics	RCV002247468	SCV002518246	uncertain significance	not specified	2022-05-04	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV003129770	SCV003808827	uncertain significance	not provided	2019-03-01	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000662517	SCV004018199	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-03-15	criteria provided, single submitter	clinical testing	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.
Baylor Genetics	RCV000662517	SCV004192993	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-06-04	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV003129770	SCV004220069	uncertain significance	not provided	2023-06-28	criteria provided, single submitter	clinical testing	In the published literature, this variant has been reported in individuals with Lynch syndrome (PMID: 18561205 (2008), 30256826 (2018)), colon cancer (PMID: 23741719 (2013)), and breast cancer (PMID: 33471991 (2021), see also LOVD (https://databases.lovd.nl/shared/variants/MLH1)). Functional studies have reported this variant does not have a damaging effect on protein function (PMID: 17510385 (2007), 18561205 (2008), 30998989 (2019)). The frequency of this variant in the general population, 0.000008 (2/251418 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 benign. Based on the available information, we are unable to determine the clinical significance of this variant.
All of Us Research Program, National Institutes of Health	RCV003997111	SCV004841006	likely benign	Lynch syndrome	2023-06-26	criteria provided, single submitter	clinical testing