ClinVar Genomic variation as it relates to human health

For these reasons, this variant has been classified as Pathogenic. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 32363481). ClinVar contains an entry for this variant (Variation ID: 90317). This variant has been observed in individuals with Lynch syndrome (PMID: 23354634, 24344984, 28874130, 32363481). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 8 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product.

The c.677+5G>A pathogenic mutation results from a G to A substitution 5 nucleotides after coding exon 8 in the MLH1 gene. This nucleotide position is highly conserved in available vertebrate species. This alteration was identified and segregated with disease in individuals meeting Amsterdam Criteria II with colorectal tumors demonstrating MSI-H and/or loss of MLH1 protein expression by IHC (Wielandt AM et al. Rev Med Chil, 2012 Sep;140:1132-9; Ambry internal data) and has been reported in individuals of South American decent (Dominguez-Valentin M et al. Hered Cancer Clin Pract 2013 Dec;11:18; Rossi BM et al. BMC Cancer 2017 Sep;17:623). In addition, this variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The MLH1 c.677+5G>A variant has been reported in the published literature in a small number of Lynch syndrome families (PMIDs: 24344984 (2013), 27606285 (2016), 28874130 (2017)). Splicing studies using minigenes and patient RNA have shown that this variant causes the skipping of exon 8 that results in a frameshift in the coding sequence of the MLH1 mRNA and reduces the amount of MLH1 protein (PMID: 32363481 (2020)). Family studies have also shown that this variant co-segregates with disease, including colorectal cancer (PMID: 32363481 (2020)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic.

This variant causes a G to A nucleotide substitution at the +5 position of intron 8 of the MLH1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. Studies using carrier RNA from blood and minigene assay have shown that this variant causes skipping of exon 8 or skipping of exon 6 and 8 in the RNA transcripts (PMID: 32363481). The aberrant transcripts are expected to create a premature translation stop signal and result in an absent or non-functional protein product. This variant has been reported in individuals affected with Lynch syndrome-associated cancers and to segregate with disease (PMID: 24344984, 28874130, 32363481, 32549215). Microsatellite instability and loss of MLH1 and PMS2 protein expression have been reported in tumor samples from these individuals (PMID: 32363481). 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.

This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID: 12655562].