Submissions for variant NM_000249.4(MLH1):c.1732-1G>A

dbSNP: rs267607854

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075333	SCV000106330	pathogenic	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Variant causes splicing aberration (not quantified), 4 MSI-H tumours, co-segregation with disease & MAF 0.00.
Ambry Genetics	RCV002408578	SCV002715691	pathogenic	Hereditary cancer-predisposing syndrome	2021-11-16	criteria provided, single submitter	clinical testing	The c.1732-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 16 of the MLH1 gene. This mutation was reported in HNPCC patients including in a German patient with MSI-H colon cancer showing absent MLH1 staining by IHC; this individual's family met Amsterdam I criteria (Mangold E et al. Int. J. Cancer, 2005 Sep;116:692-702; Mueller-Koch Y et al. Gut 2005 Dec;54:1733-40). This mutation was found in conjunction with a chromosomal deletion encompassing MLH1 in an MSI-H melanoma cell line demonstrating absence of MLH1 and PMS2 expression by IHC. Authors showed this mutation results in in-frame skipping of exon 16, which is required for interaction with PMS2 and conclude it results in functional inactivation of mismatch repair (Castiglia D et al. Genes Chromosomes Cancer 2003 Jun;37:165-75). This alteration has been classified as pathogenic using the following lines of evidence: in silico prediction models, segregation with disease, clinical phenotype including tumor characteristics, mutation co-occurrence, and functional studies (Thompson BA et al. Hum. Mutat. 2013 Jan;34:200-9; Thompson BA et al. Nat. Genet. 2014 Feb;46:107-15; available at [www.insight-group.org/variants/classifications/]). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation.
Invitae	RCV002514342	SCV003525134	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2022-09-27	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Ala619 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10612827, 18561205, 21404117, 21520333, 28514183). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Studies have shown that disruption of this splice site results in skipping of exon 16, but is expected to preserve the integrity of the reading-frame (PMID: 19267393). ClinVar contains an entry for this variant (Variation ID: 89859). Disruption of this splice site has been observed in individual(s) with hereditary nonpolyposis colorectal cancer and/or Lynch syndrome (PMID: 8571956, 15849733, 24090359; Invitae). 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 affects an acceptor splice site in intron 15 of the MLH1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product.
Myriad Genetics, Inc.	RCV003451057	SCV004189486	likely pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-21	criteria provided, single submitter	clinical testing	This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001355292	SCV001550135	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The MLH1 c.1732-1G>A variant was identified in 2 of 3524 proband chromosomes (frequency: 0.001) from individuals or families with HNPCC (Mangold 2005, Mueller-Koch 2005); however, control chromosomes were not evaluated in these studies, thus the prevalence of this variant in the general population could not be determined. The variant was also identified in dbSNP (ID: rs267607854) as with pathogenic allele , in the ClinVar database as pathogenic by InSIGHT; in the Cosmic database 2X as pathogenic; in the Insight Colon Cancer Gene Variant Database 6X, in the Mismatch Repair Genes Variant Database 3X, and 6X in the Insight Hereditary Tumors Database. The variant was not identified in COGR, MutDB, UMD-LSDB, and Zhejiang Colon Cancer databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, and the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). Two functional studies showed that the c.1732-1G>A variant results in an in frame skipping of exon 16 given that it falls at position -1 of a 3’ acceptor splice site (Arnold_2009, Castiglia_2003). The c.1732-1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.