ClinVar Miner

Submissions for variant NM_000310.3(PPT1):c.234+1G>A (rs796052923)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188710 SCV000242334 pathogenic not provided 2013-08-06 criteria provided, single submitter clinical testing The c.234+1 G>A splice site mutation in the PPT1 gene destroys the canonical splice donor site in intron 2. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsensemediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Although c.234+1 G>A has not been previously reported to our knowledge, it is considered a diseasecausing mutation. The variant is found in CHILD-EPI panel(s).
Invitae RCV001233540 SCV001406140 pathogenic Neuronal ceroid lipofuscinosis 1 2019-10-04 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 2 of the PPT1 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 been observed in individual(s) with Batten disease (PMID: 26510000). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 206642). 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 PPT1 are known to be pathogenic (PMID: 10679943). For these reasons, this variant has been classified as Pathogenic.

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