ClinVar Miner

Submissions for variant NM_000286.3(PEX12):c.680+1G>A

gnomAD frequency: 0.00001  dbSNP: rs904972651
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000674616 SCV000799984 likely pathogenic Peroxisome biogenesis disorder type 3B; Peroxisome biogenesis disorder 3A (Zellweger) 2018-05-16 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001861845 SCV002312352 pathogenic Peroxisome biogenesis disorder 3A (Zellweger) 2023-08-21 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 2 of the PEX12 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 present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PEX12-related conditions. ClinVar contains an entry for this variant (Variation ID: 558363). 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 PEX12 protein in which other variant(s) (p.Gln349del) have been determined to be pathogenic (PMID: 15542397, 21031596, 33123925; Invitae). 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.
Baylor Genetics RCV001861845 SCV004201432 likely pathogenic Peroxisome biogenesis disorder 3A (Zellweger) 2023-09-21 criteria provided, single submitter clinical testing

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