ClinVar Miner

Submissions for variant NM_001351132.2(PEX5):c.1718+5G>A

dbSNP: rs1085307998
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489259 SCV000577800 likely pathogenic not provided 2015-05-07 criteria provided, single submitter clinical testing The c.1718+5G>A variant in the PEX5 gene has not been reported previously as a disease-causing variant nor as a benign polymorphism, to our knowledge. This variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This variant is predicted to damage or destroy the natural splice donor site of intron 15, which may cause abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore c.1718+5G>A is a strong candidate for a disease-causing variant, however the possibility it may be a rare benign variant cannot be excluded
Labcorp Genetics (formerly Invitae), Labcorp RCV002526044 SCV003447099 uncertain significance Peroxisome biogenesis disorder 2B 2023-01-26 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. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 427165). This variant has not been reported in the literature in individuals affected with PEX5-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change falls in intron 15 of the PEX5 gene. It does not directly change the encoded amino acid sequence of the PEX5 protein. It affects a nucleotide within the consensus splice site.

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