NM_000249.4:c.589-2A>G
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000249.4(MLH1):c.589-2A>G variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).
Frequency
Consequence
NM_000249.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460462Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726702
GnomAD4 genome
ClinVar
Submissions by phenotype
Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:3
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This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID: 15713769]. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 25085752]. -
Lynch syndrome Pathogenic:3
Variant summary: MLH1 c.589-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Five predict the variant abolishes a 3 acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Thompson_2013). The variant was absent in 246208 control chromosomes (gnomAD). The variant, c.589-2A>G has been reported in the literature in individuals affected with Lynch Syndrome (Syngal_1999, Susswein_2016, Tannergard_1995, Capozzi_1999). These data indicate that the variant is likely to be associated with disease. Multiple ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic. -
Variant causes splicing aberrations: full inactivation of variant allele. Multifactorial likelihood analysis posterior probability >0.99. -
The c.589-2A>G variant in MLH1 has been reported in >15 individuals with Lynch syndrome and segregated with disease in >15 affected relatives from multiple families (Luce 1995, Casey 2005, Tomsic 2012, DeRycke 2017). This variant is considered a founder variant (Tomsic 2015). This variant was absent from large population studies, but has been reported in ClinVar (Variation ID: 90291). This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. In vitro studies demonstrate that this variant causes activation of a cryptic splice site, leading to a frameshift variant (Luce 1995, Arnold 2009). Loss of function of the MLH1 gene is an established disease mechanism in autosomal dominant Lynch syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PVS1, PS4, PM2, PP1_Strong, PS3_Moderate. -
not provided Pathogenic:3
This variant disrupts a canonical splice-acceptor site and interferes with normal MLH1 mRNA splicing. It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in individuals with Lynch syndrome (PMIDs: 30019097 (2019), 28944238 (2017), 25980754 (2015), 21671475 (2012)). Based on the available information, this variant is classified as pathogenic. -
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Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 10422993, 19690142, 25345868, 28888541, 15713769, 25530820, 22949379, 7557107, 21671475, 22624972, 19267393, 12067992, 14970868, 10448273, 17192056, 26681312, 28944238, 29288294, 29228462, 25525159, 25980754, 30787465) -
Hereditary cancer-predisposing syndrome Pathogenic:2
This variant causes an A to G nucleotide substitution at the -2 position of intron 7 of the MLH1 gene. Functional RNA studies have shown that this variant causes use of a cryptic splice site and skipping of exon 8, resulting in a frameshift and premature truncation (PMID: 7557107, 19267393, 22949379). This variant has been reported in multiple individuals affected with Lynch syndrome or Lynch syndrome-associated disease (PMID: 7557107, 8521398, 19267393, 21671475, 26681312, 29228462, 30019097). 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. -
The c.589-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides upstream from coding exon 8 of the MLH1 gene. This mutation has been reported in numerous Lynch syndrome families to date (Luce MC et al. Gastroenterology. 1995 Oct;109(4):1368-74; Viel A et al. Community Genet. 1998;1(4):229-36; Capozzi E et al. Eur. J. Cancer. 1999 Feb;35(2):289-95; Syngal S et al. JAMA. 1999 Jul 21;282(3):247-53; Casey G et al. JAMA. 2005 Feb 16;293(7):799-809; DeRycke MS et al. Mol Genet Genomic Med. 2017 Sep;5(5):553-569). In addition, this alteration has been described as an American founder mutation (Tomsic J et al. Int. J. Cancer. 2012 May 1;130(9):2088-95). RNA studies have demonstrated that this alteration activates a cryptic acceptor site resulting in a transcript with a 4 base pair deletion, which is predicted to lead to a translational frameshift (Ambry internal data; Arnold S et al. Hum. Mutat. 2009 May;30(5):757-70). 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. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
This sequence change affects an acceptor splice site in intron 7 of the MLH1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Lynch syndrome (PMID: 7557107, 10422993, 21671475). It has also been observed to segregate with disease in related individuals. Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this MLH1 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 1,370,736 individuals referred to our laboratory for MLH1 testing. ClinVar contains an entry for this variant (Variation ID: 90291). Studies have shown that disruption of this splice site results in activation of a cryptic splice site, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 7557107; internal data). For these reasons, this variant has been classified as Pathogenic. -
Lynch syndrome 1 Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at