Submissions for variant NM_000249.4(MLH1):c.244A>G (p.Thr82Ala)

gnomAD frequency: 0.00001  dbSNP: rs587778998

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000490565	SCV000106599	likely pathogenic	Lynch syndrome 1	2018-06-13	reviewed by expert panel	curation	Variant reclassification due to new tumour Likelihood Ratios: Multifactorial likelihood analysis posterior probability > 0.95 (0.965)
Ambry Genetics	RCV000166056	SCV000216818	likely pathogenic	Hereditary cancer-predisposing syndrome	2020-03-28	criteria provided, single submitter	clinical testing	The p.T82A variant (also known as c.244A>G), located in coding exon 3 of the MLH1 gene, results from an A to G substitution at nucleotide position 244. The threonine at codon 82 is replaced by alanine, an amino acid with similar properties. This variant has been identified in probands with HNPCC or HNPCC-related cancers and concordant tumors when available (Pastrello C et al. Genet Med. 2011 Feb;13(2):115-24,Hardt K et al. Fam Cancer. 2011 Jun;10(2):273-84, Borras E et al. Hum Mutat. 2012 Nov;33(11):1576-88, Simbolo M et al. Hered. Cancer Clin Pract. 2015 Aug 21;13(1), Ambry internal data). This variant is located in the ATPase functional domain and impaired MMR activity compared to wild-type (Borras E et al. Hum Mutat. 2012 Nov;33(11)). This paper also cites literature demonstrating alterations at the same codon, including p.T82K, p.T82M, and p.T82I, to be defective in MMR activity in yeast and/or human cells. This alteration has been classified as pathogenic 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 majority of available evidence to date, this variant is likely to be pathogenic.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000506252	SCV000604231	likely pathogenic	not specified	2016-12-27	criteria provided, single submitter	clinical testing
Invitae	RCV000542720	SCV000625139	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-02-08	criteria provided, single submitter	clinical testing	This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 82 of the MLH1 protein (p.Thr82Ala). This variant is present in population databases (rs587778998, gnomAD 0.01%). This missense change has been observed in individuals with Lynch syndrome (PMID: 21239990, 21404117, 22736432, 26300997, 28514183). ClinVar contains an entry for this variant (Variation ID: 90116). 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 expected to disrupt MLH1 protein function. Experimental studies have shown that this missense change affects MLH1 function (PMID: 22736432). This variant disrupts the p.Thr82 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10422993, 17510385, 19690142, 20587412, 23403630). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000075602	SCV000696155	likely pathogenic	Lynch syndrome	2016-03-14	criteria provided, single submitter	clinical testing	Variant summary: This c.244A>G variant affects a conserved nucleotide, resulting in amino acid change from Thr to Ala. 4/4 in-silico tools predict this variant to be damaging. This variant was found in 1/122056 control chromosomes from the broad and large populations of ExAC at a frequency of 0.0000082, which does not exceed maximal expected frequency of a pathogenic allele (0.0007105) in this gene. This variant has been reported in multiple patients (at least five independent occurrences) affected with HNPCC or HNPCC-related cancers. There are no reported cosegregation studies for this variant. The variant has been functionally characterized to impair the MMR activity, strongly suggesting for pathogenic outcome. Multiple clinical laboratories as well as reputable databases have classified this variant as likely pathogenic. Multifactorial likelihood analysis for the variant is also in line with likely pathogenic outcome. Taken together this variant has currently been classfied as a Probable Disease Variant/Likely Pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV000166056	SCV000908603	pathogenic	Hereditary cancer-predisposing syndrome	2023-05-16	criteria provided, single submitter	clinical testing	This missense variant replaces threonine with alanine at codon 82 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 shows <10% of normal DNA-mismatch repair activity in vitro (PMID: 22736432, 31881334). This variant has been reported in individuals affected with Lynch syndrome (PMID: 21239990, 26300997) and in individuals affected with colorectal cancer with tumors showing microsatellite instability (PMID: 21404117, 22736432). This variant has been identified in 2/251394 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different missense variant occurring at the same codon, p.Thr82Ile, is known to be disease-causing, indicating the importance of threonine residue at this position for MLH1 function. Based on the available evidence, this variant is classified as Pathogenic.
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV002467439	SCV002762817	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2022-12-09	criteria provided, single submitter	research	PS3, PS4_STR, PM2_SUP, PM5, PP1
Myriad Genetics, Inc.	RCV002467439	SCV004189463	likely pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-12	criteria provided, single submitter	clinical testing	This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 22736432]. This variant is expected to disrupt protein structure [Myriad internal data].
Baylor Genetics	RCV002467439	SCV004192963	likely pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-23	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000075602	SCV004835261	pathogenic	Lynch syndrome	2023-03-02	criteria provided, single submitter	clinical testing	This missense variant replaces threonine with alanine at codon 82 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 shows <10% of normal DNA-mismatch repair activity in vitro (PMID: 22736432, 31881334) (PMID: 22736432, 31881334). This variant has been reported in individuals affected with Lynch syndrome (PMID: 21239990, 26300997) and in individuals affected with colorectal cancer with tumors showing microsatellite instability (PMID: 21404117, 22736432). This variant has been identified in 2/251394 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different missense variant p.Thr82Ile is known to be pathogenic, indicating the importance of threonine residue at this position for MLH1 function. Based on the available evidence, this variant is classified as Pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000075602	SCV004848136	pathogenic	Lynch syndrome	2020-05-13	criteria provided, single submitter	clinical testing	The p.Thr82Ala variant in MLH1 has been reported in 10 European individuals with Lynch syndrome or MLH1-associated cancers (Sjursen 2010, Hardt 2011, Pastrello 2011, Simbolo 2015, Stradella 2019). It has also been identified in 2/123,762 European/Ashkenazi Jewish chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies provide some evidence that this variant impacts protein function (Ellison 2004, Borras 2012). This variant was classified as Likely Pathogenic on June 13, 2018 by the ClinGen-approved InSiGHT expert panel (Variation ID 90116). Another variant involving this codon (p.Thr82Ile) has been identified in individuals with Lynch syndrome and is classified as pathogenic by the ClinGen-approved InSiGHT expert panel. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PM2, PS4_Strong, PP3, PS3_Supporting, PM5.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001353582	SCV000592341	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The p.Thr82Ala variant has been previously reported in the literature and by our laboratory. It was identified in one individual who was reported to have high microsatellite instability and was MLH1 deficient. In addition, it was shown to segregate in one affected family member (Pastrello_2011_21239990). Our laboratory has identified this variant in one family and the variant segregated with disease in 5 affected individuals. Although the pattern of MSI and IHC deficient tumours was inconsistent across individuals from this family, the observation of this variant segregating with Lynch syndrome related cancers increases the likelihood this variant is pathogenic. In addition, functional studies in yeast demonstrated that different variants at this same amino acid residue (T82S, T82K, T82M) were associated with a loss of mismatch repair function between 8% and 67%, increasing the likelihood that this variant may affect normal protein function (Ellison_2004_15475387). In summary, based on the above information, this variant is classified as pathogenic.