Submissions for variant NM_000249.4(MLH1):c.187G>A (p.Asp63Asn)

dbSNP: rs63750850

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000212515	SCV000211107	likely pathogenic	not provided	2016-09-29	criteria provided, single submitter	clinical testing	This variant is denoted MLH1 c.187G>A at the cDNA level, p.Asp63Asn (D63N) at the protein level, and results in the change of an Aspartic Acid to an Asparagine (GAC>AAC). MLH1 Asp63Asn was observed in a Hungarian family meeting Amsterdam I criteria and reported to co-segregate with disease in two family members with a history of early-onset colon cancer but was not present in seven unaffected family members (Papp 2007). Raschle et. al. (2002) showed that MLH1 Asp63Asn results in a dramatic reduction in MLH1 and PMS2 protein expression. In addition, another variant at the same residue, MLH1 Asp63Glu, is considered pathogenic by the International Society for Gastrointestinal Hereditary Tumours Incorporated (InSiGHT). MLH1 Asp63Glu has been reported to segregate with Lynch syndrome-related cancers in at least one family and has been shown to result in decreased MLH1 protein expression, deficient mismatch repair activity, and decreased nuclear localization of MLH1 and PMS2 (Raevaara 2005, Hardt 2011). MLH1 Asp63Asn was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Aspartic Acid and Asparagine differ in some properties, this is considered a semi-conservative amino acid substitution. MLH1 Asp63Asn occurs at a position that is conserved across species and is located in ATP-binding domain (Raevaara 2005). In addition, in silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available information, we consider MLH1 Asp63Asn to be a likely pathogenic variant.
Ambry Genetics	RCV000160535	SCV000215751	pathogenic	Hereditary cancer-predisposing syndrome	2019-05-14	criteria provided, single submitter	clinical testing	The p.D63N pathogenic mutation (also known as c.187G>A), located in coding exon 2 of the MLH1 gene, results from a G to A substitution at nucleotide position 187. The aspartic acid at codon 63 is replaced by asparagine, an amino acid with highly similar properties. This alteration was reported in a Hungarian family satisfying Amsterdam I criteria for HNPCC/Lynch syndrome (Papp J et al. World J. Gastroenterol. 2007 May; 13(19):2727-32). In this family, p.D63N segregated with disease, being detected in the affected proband (CRC at 25y) and his affected father (CRC at 40y) and was absent from 7 cancer-free relatives. This variant has also been identified in multiple individuals with tumors demonstrating loss of MLH1 and PMS2 by immunohistochemistry (Ambry internal data). An in vitro functional study reported that the p.D63N variant abolished ATP binding in the hMLH1 subunit, deleteriously affecting expression of the heterodimer (Räschle M et al. J. Biol. Chem. 2002 Jun;277:21810-20). This amino acid position is highly conserved in available vertebrate species. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000075399	SCV000696133	likely pathogenic	Lynch syndrome	2019-02-26	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.187G>A (p.Asp63Asn) results in a conservative amino acid change located in the Histidine kinase/HSP90-like ATPase domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 246206 control chromosomes. c.187G>A has been reported in the literature in individuals affected with Lynch Syndrome (Papp_2007, Espenschied_2017). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in dramatically reduced expression of both MLH1 and PMS2 proteins and reduced ATP'ase activity (Raschle_2002). Three 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 pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae	RCV000694220	SCV000822654	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-08-17	criteria provided, single submitter	clinical testing	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 63 of the MLH1 protein (p.Asp63Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 17569143). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 89920). 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: 11948175). This variant disrupts the p.Asp63 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16083711, 17594722, 21120944). 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.
Color Diagnostics, LLC DBA Color Health	RCV000160535	SCV001340137	likely pathogenic	Hereditary cancer-predisposing syndrome	2020-02-05	criteria provided, single submitter	clinical testing	This missense variant replaces aspartic acid with asparagine at codon 63 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). Splice site prediction tools suggest that this variant may not impact RNA splicing. An experimental study has shown that this variant affects protein stability (PMID: 11948175). This variant has been reported in two related individuals affected with colorectal cancer and absent in multiple asymptomatic family members (PMID: 17569143). Different missense variants affecting the same codon, p.Asp63Glu and p.Asp63Gly are associated with disease (Clinvar variation ID: 89934, 422297), indicating that aspartic acid residue at this position is important for MLH1 function. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.
Baylor Genetics	RCV003460707	SCV004193044	likely pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2022-06-30	criteria provided, single submitter	clinical testing