Submissions for variant NM_000249.4(MLH1):c.1559-1G>A

dbSNP: rs267607837

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075253	SCV000106251	likely pathogenic	Lynch syndrome	2019-06-21	reviewed by expert panel	curation	Interrupts canonical donor splice site
Invitae	RCV001238289	SCV001411092	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2022-03-05	criteria provided, single submitter	clinical testing	Disruption of this splice site has been observed in individuals with Lynch syndrome (PMID: 8776590, 12624141, 15849733, 15926618; Invitae). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 89779). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 13 of the MLH1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MLH1 are known to be pathogenic (PMID: 15713769, 24362816).
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV001267988	SCV001446544	likely pathogenic	not provided	2020-10-23	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002399433	SCV002704933	likely pathogenic	Hereditary cancer-predisposing syndrome	2019-10-10	criteria provided, single submitter	clinical testing	The c.1559-1G>A intronic variant results from a G to A substitution one nucleotide upstream from coding exon 14 of the MLH1 gene. This alteration was detected in 1/1,721 unrelated German HNPCC patients who met Bethesda criteria (Mangold E et al. Int. J. Cancer, 2005 Sep;116:692-702). This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice acceptor site; however, direct evidence is unavailable. 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 likely pathogenic.
Myriad Genetics, Inc.	RCV003451032	SCV004189630	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-20	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	RCV001358119	SCV001553773	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The MLH1 c.1559-1G>A (Alias IVS13-1G>A) variant was identified in 1 of 908 proband chromosomes (frequency: 0.001) from individuals or families with HNPCC (Mangold 2005). The variant was also identified in dbSNP (ID: rs267607837) as “With Likely pathogenic, Pathogenic allele”, ClinVar and Clinvitae (1x classified as likely pathogenic by InSiGHT due to interruption of canonical acceptor splice site), Insight Colon Cancer Gene Variant Database (1x pathogenicity unknown), Mismatch Repair Genes Variant Database, and the Insight Hereditary Tumors Database (1x classified as probably affects function). The variant was not identified in the following databases: GeneInsight-COGR, COSMIC, MutDB, UMD-LSDB, or the Zhejiang Colon Cancer Database. The variant was not identified in the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016) or the gnomAD Genome Aggregation Database (February 27, 2017) control databases. The c.1559-1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer and HumanSpliceFinder) predict a greater than 10% difference in splicing. A different missense variant in this position (c.1559-1G>T) was identified in a Finnish study; one kindred showed a mutation at the splice acceptor site of exon 14 resulting in the deletion of exon 14 from the transcript and a frameshift with premature termination and loss of function (Nystrom-Lahti 1996). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.