ClinVar Miner

Submissions for variant NM_000430.4(PAFAH1B1):c.1159+2T>A

dbSNP: rs587784243
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000147012 SCV000194352 pathogenic Lissencephaly due to LIS1 mutation 2013-02-08 criteria provided, single submitter clinical testing
Invitae RCV001857518 SCV002111090 pathogenic not provided 2023-07-14 criteria provided, single submitter clinical testing Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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 a region of the PAFAH1B1 protein in which other variant(s) (p.His389Tyr) have been determined to be pathogenic (PMID: 19808989). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 159496). This variant has not been reported in the literature in individuals affected with PAFAH1B1-related conditions. This sequence change affects a donor splice site in intron 10 of the PAFAH1B1 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is not present in population databases (gnomAD no frequency).

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