ClinVar Genomic variation as it relates to human health

Interrupts canonical donor splice site

This variant is denoted MLH1 c.1409+1G>A or IVS12+1G>A and consists of a G>A nucleotidesubstitution at the +1 position of intron 12 of the MLH1 gene. This variant destroys a canonical splice donor site and ispredicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. This variant has been reported in at least one family withuterine and colorectal cancer (Irmejs 2007) and an alternate change, MLH1 c.1409+1G>C, has been observed in atleast one family meeting Amsterdam Criteria for Lynch syndrome (Peltomäki 1997, Kurzawski 2002). Based on thecurrent evidence, we consider MLH1 c.1409+1G>A to be pathogenic.

This variant is a substitution of the first nucleotide of intron 12 of the MLH1 gene. This position is highly conserved in human and other genomes. It is expected that this variant affects the correct mRNA splicing and results in the deletion of an entire exon. This causes the formation of a truncated non functional protein. This mutation has been described in international literature in families with suspected Lynch syndrome (PMID: 17348456).

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].

This sequence change affects a donor splice site in intron 12 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). 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: 17348456). ClinVar contains an entry for this variant (Variation ID: 89718). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the c.1409+1G nucleotide in the MLH1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 9322509, 10200055, 12362047, 14574010, 16451135). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The c.1409+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 12 of the MLH1 gene. This variant has been identified in a proband(s) whose Lynch syndrome-associated tumor demonstrated loss of MLH1/PMS2 expression by immunohistochemistry (Ambry internal data). This mutation has also been described in a Latvian individual with suspected HNPCC (Irmejs A et al. Anticancer Res. 2007;27(1):653-8). In addition, another mutation at the same nucleotide position, c.1409+1G>C, has been described in a Baltic/Polish individual fulfilling Amsterdam II criteria for HNPCC (Kurzawski G et al. J Med Genet. 2002;39:e65). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. 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.

Variant summary: MLH1 c.1409+1G>A 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing and loss of MLH1 function. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 250196 control chromosomes. c.1409+1G>A has been reported in the literature in individuals affected with Hereditary Nonpolyposis Colorectal Cancer, colorectal cancer or gastric cancer (e.g. Irmejs_2007, Haron_2019, Tsaousis_2019). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 30803214, 17348456, 31159747). ClinVar contains an entry for this variant (Variation ID: 89718). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This variant causes a G to A nucleotide substitution at the canonical +1 position of intron 12 splice donor site of the MLH1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. Although RNA studies have not been reported, this variant is expected to impair splicing and result in an absent or non-functional protein product. This variant has been reported in an individual affected with colorectal cancer with uterine cancer in the first-degree relative (PMID: 17348456). 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 Likely Pathogenic.

The c.1409+1G>A variant in MLH1 has been previously reported in 1 individual suspected to have Lynch syndrome (Irmejs 2007) and was absent from large population studies. This variant was classified as Pathogenic by several clinical labs in ClinVar and as Likely pathogenic on September 5, 2013 by the ClinGen-approved InSiGHT expert panel (Variation ID 89718). This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. Other variants involving this position (c.1409+1G>C, c.1409+1G>T) have been classified as likely pathogenic/Pathogenic in ClinVar. Heterozygous loss-of-function of the MLH1 gene is an established disease mechanism in individuals with Lynch syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP criteria applied: PVS1, PM2, PM5.