Submissions for variant NM_000249.4(MLH1):c.1668-1G>A

dbSNP: rs267607845

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075300	SCV000106296	likely pathogenic	Lynch syndrome	2019-06-21	reviewed by expert panel	curation	Interrupts canonical donor splice site
University of Washington Department of Laboratory Medicine, University of Washington	RCV000075300	SCV000266075	likely pathogenic	Lynch syndrome	2018-05-01	criteria provided, single submitter	clinical testing	MLH1 NM_000249.3:c.1668-1G>A was observed in one family with several cases of early-onset colon and endometrial cancer (Shirts et al 2016, PMID 26845104). It was also seen as an apparent passenger mutation in a tumor with other somatic mutations apparently responsible for the observed MSI status, reducing the likelihood of pathogenicity (Shirts et al 2018, PMID 29887214). This has been reported as likely pathogenic by the InSiGHT consortium and as pathogenic by several laboratories. We currently consider this variant to be likely pathogenic.
Ambry Genetics	RCV000214110	SCV000278026	pathogenic	Hereditary cancer-predisposing syndrome	2021-05-19	criteria provided, single submitter	clinical testing	The c.1668-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 15 of the MLH1 gene. This alteration has been previously reported in several individuals with colorectal cancers demonstrating microsatellite instability and absent MLH1 and/or PMS2 IHC staining, including individuals meeting Amsterdam criteria (Taylor CF, et al. Hum. Mutat. 2003 Dec; 22(6):428-33; Piñol V, et al. JAMA 2005 Apr; 293(16):1986-94; Lamberti C, et al. Digestion 2006 ; 74(1):58-67; Pérez-Carbonell L, et al. Gut 2012 Jun; 61(6):865-72; Walker M et al. Br J Surg, 2007 Dec;94:1567-71). One splicing assay using cell lines from mutation carriers found that this alteration results in out-of-frame skipping of exon 15 (Arnold S, et al. Hum. Mutat. 2009 May; 30(5):757-70). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site; however, direct evidence is insufficient at this time (Ambry internal data). 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.
Color Diagnostics, LLC DBA Color Health	RCV000214110	SCV000684764	pathogenic	Hereditary cancer-predisposing syndrome	2022-01-01	criteria provided, single submitter	clinical testing	This variant causes a G to A nucleotide substitution at the -1 position of intron 14 of the MLH1 gene. Functional RNA studies have shown that this variant causes out-of-frame deletion of exon 15 (PMID: 2707453). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with Lynch syndrome or colorectal cancer with tumors showing microsatellite instability and loss of MLH1 protein expression (PMID: 2707453, 15855432, 17095871, 19267393, 21868491). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000075300	SCV000731290	pathogenic	Lynch syndrome	2019-04-19	criteria provided, single submitter	clinical testing	The c.1668-1G>A variant in MLH1 has been reported in at least 4 individuals with Lynch Syndrome (Lamberti 2006, Arnold 2009, Pérez-Carbonell 2012, Shirts 2016) and was found to segregate with disease in 2 additional affected individuals in one family (Arnold 2009). This variant was absent from large population studies. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and has been observed to cause altered splicing leading to an abnormal or absent protein (Arnold 2009, Pérez-Carbonell 2012). Heterozygous loss of function of the MLH1 gene is an established disease mechanism in Lynch Syndrome. Additionally, this variant has been classified as Likely pathogenic on Sep 5, 2013 by the ClinGen-approved InSiGHT panel (ClinVar SCV000106296.2). In summary, this variant meets criteria to be classified as pathogenic for Lynch Syndrome in an autosomal dominant manner. ACMG/AMP criteria applied: PM2, PS4_Supporting, PVS1.
Invitae	RCV000629693	SCV000750649	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-03-14	criteria provided, single submitter	clinical testing	ClinVar contains an entry for this variant (Variation ID: 89826). Disruption of this splice site has been observed in individual(s) with Lynch syndrome (PMID: 14635101, 15855432, 17095871, 19267393, 21868491). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 14 of the MLH1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. Studies have shown that disruption of this splice site results in exon skipping and introduces a premature termination codon (PMID: 19267393). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Academic Department of Medical Genetics, University of Cambridge	RCV000214110	SCV000992193	likely pathogenic	Hereditary cancer-predisposing syndrome	2018-01-26	criteria provided, single submitter	research	Application of AMCG guidelines 2015. Used other ClinVar submission evidence where relevant. Loss of heterozygosity in tumours or immunohistochemistry abnormalities considered functional evidence of pathogenicity.
Myriad Genetics, Inc.	RCV003451048	SCV004186354	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-21	criteria provided, single submitter	clinical testing	This variant is considered 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. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 27363726].
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001353428	SCV000592416	uncertain significance	not provided		no assertion criteria provided	clinical testing