Submissions for variant NM_000249.4(MLH1):c.1616C>A (p.Ala539Asp)

dbSNP: rs267607843

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001844474	SCV002103416	uncertain significance	not specified	2022-02-27	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1616C>A (p.Ala539Asp) results in a non-conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain (IPR032189) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251320 control chromosomes. c.1616C>A has been reported in the literature as segregating with colorectal cancer in two affected gene carriers from one family and has subsequently been cited by others (example, Parc_2003, Bonadona_2011). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. At least one publication reports experimental evidence evaluating an impact on protein function (example, Bouvet_2019). The most pronounced variant effect results in classification as pathogenic based on a methylation tolerance based functional assay. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
Ambry Genetics	RCV002397764	SCV002707985	likely pathogenic	Hereditary cancer-predisposing syndrome	2022-09-20	criteria provided, single submitter	clinical testing	The p.A539D variant (also known as c.1616C>A), located in coding exon 14 of the MLH1 gene, results from a C to A substitution at nucleotide position 1616. The alanine at codon 539 is replaced by aspartic acid, an amino acid with dissimilar properties. This variant was identified in the germline along with a somatic likely pathogenic MLH1 variant in an individual that met Amsterdam II criteria for Lynch syndrome and tumor displayed high microsatellite instability (MSI-H) with loss of both MLH1/PMS2 on immunohistochemistry (IHC) (Ambry internal data). Furthermore, this variant co-segregated with disease in three other affected family members (Ambry internal data). This variant was first reported in a French individual with colorectal cancer who satisfied at least one of the modified Amsterdam criteria and co-segregation with disease occurred in two affected carriers from this family (Parc Y et al. J. Med. Genet., 2003 Mar;40:208-13). This variant was also reported in three French families suspected of having Lynch syndrome (Bonadona V et al. JAMA, 2011 Jun;305:2304-10). This alteration had no effect on splicing in a minigene assay performed on HeLa cells (Tournier I et al. Hum. Mutat., 2008 Dec;29:1412-24). Based on an internal structural analysis, this variant is anticipated to result in a significant decrease in structural stability. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is well conserved in available vertebrate species. This alteration is predicted to be inconclusive by in silico analyses. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Invitae	RCV002545235	SCV003525105	likely pathogenic	Hereditary nonpolyposis colorectal neoplasms	2022-01-25	criteria provided, single submitter	clinical testing	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. Experimental studies have shown that this missense change affects MLH1 function (PMID: 30998989). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). This missense change has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 12624141, 21642682; external communication). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 539 of the MLH1 protein (p.Ala539Asp).
PreventionGenetics, part of Exact Sciences	RCV003416490	SCV004107910	likely pathogenic	MLH1-related disorder	2023-03-27	criteria provided, single submitter	clinical testing	The MLH1 c.1616C>A variant is predicted to result in the amino acid substitution p.Ala539Asp. This variant has been reported in individuals with a personal and/or family history of non-polyposis colorectal cancer (Table S3, Parc et al. 2003. PubMed ID: 12624141; eTable 1, Bonadona et al. 2011. PubMed ID: 21642682; Table S2, Bouvet et al. 2019. PubMed ID: 30998989). This variant has been reported to segregate with MLH1-associated tumors in a multigenerational kindred (Internal Data, Prevention Genetics LCC). The proband's tumor displayed complete loss of MLH1 and PMS2 expression by immunohistochemistry (Internal Data, Prevention Genetics LCC). In vitro experimental studies using a methylation tolerance assay suggest this variant impacts protein function (Table S2, Bouvet et al. 2019. PubMed ID: 30998989). Additional experimental studies using RT-PCR analysis suggest this variant does not impact pre-mRNA splicing (Table 1, Tournier et al. 2008. PubMed ID: 18561205). In silico analyses predict this variant to be pathogenic (Table 3, Ali et al. 2012. PubMed ID: 22290698). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. It has conflicting interpretations of likely pathogenic and uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/1343456/). This variant is interpreted as likely pathogenic.
Myriad Genetics, Inc.	RCV003451969	SCV004188511	likely pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-21	criteria provided, single submitter	clinical testing	This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 30998989, Myriad internal data]. This variant is expected to disrupt protein structure [Myriad internal data].