ClinVar Miner

Submissions for variant NM_000249.3(MLH1):c.1976G>T (p.Arg659Leu) (rs63749900)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000075448 SCV000106446 pathogenic Lynch syndrome 2013-09-05 reviewed by expert panel research Multifactorial likelihood analysis posterior probability >0.99
Ambry Genetics RCV000572238 SCV000676046 pathogenic Hereditary cancer-predisposing syndrome 2016-05-20 criteria provided, single submitter clinical testing The p.R659L variant (also known as c.1976G>T), located in coding exon 17 of the MLH1 gene, results from a G to T substitution at nucleotide position 1976. The arginine at codon 659 is replaced by leucine, an amino acid with dissimilar properties. This alteration has been reported in multiple individuals either meeting classic ‘Amsterdam’ criteria for HNPCC, or a modified set of criteria (Cravo M et al. Gut 2002 Mar; 50(3):405-12; Fidalgo P et al. Eur. J. Hum. Genet. 2000 Jan; 8(1):49-53; Lage PA et al. Cancer 2004 Jul; 101(1):172-7; Nyström-Lahti M et al. Genes Chromosomes Cancer 1999 Dec; 26(4):372-5). Further, this alteration has been shown to segregate with disease in one family, as two affected members were shown to carry this alteration while one unaffected member did not (Cravo M et al. Gut 2002 Mar; 50(3):405-12). This alteration is located in the c-terminal ATP binding and hydrolysis domain of the MLH1 protein, which is responsible for constitutive dimerization with PMS2. In a study examining pathogenic effects due to interference with dimerization with PMS2, this alteration was reported to results in statistically significant reduction of MLH1 expression by multiple independent Western blot transfection experiments (Kosinski J et al. Hum. Mutat. 2010 Aug; 31(8):975-82). This alteration has also 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, clinical phenotype including 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/]). Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to create a new alternate splice acceptor site. Functional analysis of this alteration using patient RNA sequencing via RT-PCR revealed a deletion of 93 base pairs due to skipping of exon 17; authors note that no sequence alterations of the intron-exon boundaries were identified suggesting this alteration will thereby lead to a non-functional protein (Nyström-Lahti M et al. Genes Chromosomes Cancer 1999 Dec; 26(4):372-5).Based on the available evidence, p.R659Lis classified as a pathogenic mutation.
Color Health, Inc RCV000572238 SCV001346828 likely pathogenic Hereditary cancer-predisposing syndrome 2020-04-23 criteria provided, single submitter clinical testing

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