ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.2275+1G>T

dbSNP: rs1554294393
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000528011 SCV000625606 pathogenic Hereditary nonpolyposis colorectal neoplasms 2023-11-28 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 13 of the PMS2 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 PMS2 are known to be pathogenic (PMID: 21376568, 24362816). The frequency data for this variant in the population databases (gnomAD) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. Disruption of this splice site has been observed in individuals with clinical features of Lynch syndrome (PMID: 31992580, 33193653; Invitae). ClinVar contains an entry for this variant (Variation ID: 455697). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Myriad Genetics, Inc. RCV003449547 SCV004187624 likely pathogenic Lynch syndrome 4 2023-09-22 criteria provided, single submitter clinical testing This variant is considered likely 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.

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