ClinVar Genomic variation as it relates to human health

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. 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: 11948175, 16083711, 17569143, 17594722, 21120944). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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. This missense change has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 23733757, 30521064). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 63 of the MLH1 protein (p.Asp63Val).

This missense variant replaces aspartic acid with valine at codon 63 in the ATP binding domain 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with colorectal cancer that demonstrated loss of MLH1 and PMS2 proteins via immunohistochemistry analysis (PMID: 23733757; communication with an external laboratory, ClinVar SCV002722481.1), and in an individual affected with unspecified cancer (PMID: 34172528). Several different missense variants at this codon have been classified as pathogenic (ClinVar Variation ID: 89920, 89934, 422297, 957817), supporting that this position is important for protein 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.

The p.D63V pathogenic mutation (also known as c.188A>T), located in coding exon 2 of the MLH1 gene, results from an A to T substitution at nucleotide position 188. The aspartic acid at codon 63 is replaced by valine, an amino acid with highly dissimilar properties. This variant was previously reported in a 35 year old male diagnosed with colorectal cancer whose tumor analysis showed microsatellite instability and loss of MLH1 and PMS2 protein by immunohistochemistry (Ward R.L. et al., J. Clin. Oncol. 2013 Jul; 31(20):2554-62). Crystal structural analysis shows that this amino acid residue directly interacts with ATP and is indicated to be part of the ATP binding motif (Ambry internal data). A pathogenic mutation at the same codon, p.D63N, has been reported in a Hungarian family satisfying Amsterdam I criteria for HNPCC/Lynch syndrome. 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 (Papp J et al. World J. Gastroenterol. 2007 May; 13(19):2727-32). The p.D63N variant has also been identified in multiple individuals with tumors demonstrating loss of MLH1 and PMS2 by immunohistochemistry (Ambry internal data). Another amino acid change at the same codon, p.D63E, 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 variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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 supporting evidence, this alteration is interpreted as a disease-causing mutation.