ClinVar Miner

Submissions for variant NM_000249.3(MLH1):c.1409+1G>T (rs267607825)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000482715 SCV000568946 pathogenic not provided 2016-11-18 criteria provided, single submitter clinical testing This variant is denoted MLH1 c.1409+1G>T or IVS12+1G>T and consists of a G>T nucleotide substitution at the +1 position of intron 12 of the MLH1 gene. This variant destroys a canonical splice donor site and is predicted 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. Although MLH1 c.1409+1G>T has not, to our knowledge, been published in the literature, an alternate base change at the same position, MLH1 c.1409+1G>C, has been observed in at least one family meeting Amsterdam Criteria for Lynch Syndrome (Peltomäki 1997, Kurzawski 2002). Based on the current evidence, we consider MLH1 c.1409+1G>T to be pathogenic.
Invitae RCV000548182 SCV000625061 likely pathogenic Hereditary nonpolyposis colorectal neoplasms 2017-08-09 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 12 of the MLH1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MLH1-related disease. ClinVar contains an entry for this variant (Variation ID: 420226). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants 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). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000781541 SCV000919661 likely pathogenic Lynch syndrome 2018-09-13 criteria provided, single submitter clinical testing Variant summary: MLH1 c.1409+1G>T 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 5 prime splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 30956 control chromosomes. To our knowledge, no occurrence of c.1409+1G>T in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Color RCV001184206 SCV001350144 likely pathogenic Hereditary cancer-predisposing syndrome 2018-10-24 criteria provided, single submitter clinical testing

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