ClinVar Miner

Submissions for variant NM_000318.3(PEX2):c.624dup (p.Pro209fs)

gnomAD frequency: 0.00001  dbSNP: rs1438831421
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000599473 SCV000710444 likely pathogenic not provided 2018-01-16 criteria provided, single submitter clinical testing The c.624dupA variant in the PEX2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.624dupA variant causes a frameshift starting with codon Proline 209, changes this amino acid to a Threonine residue, and creates a premature Stop codon at position 24 of the new reading frame, denoted p.Pro209ThrfsX24. This variant is predicted to cause loss of normal protein function through protein truncation. The c.624dupA variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.624dupA as a likely pathogenic variant.
Eurofins Ntd Llc (ga) RCV000599473 SCV000858939 pathogenic not provided 2018-01-03 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000599473 SCV002021671 likely pathogenic not provided 2020-11-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002532697 SCV003560760 pathogenic Inborn genetic diseases 2021-09-01 criteria provided, single submitter clinical testing The c.624dupA (p.P209Tfs*24) alteration, located in exon 4 (coding exon 1) of the PEX2 gene, consists of a duplication of 1 nucleotide at position 624, causing a translational frameshift with a predicted alternate stop codon after 24 amino acids. This alteration occurs at the 3' terminus of the PEX2 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 32% of the protein. Premature stop codons are typically deleterious in nature and the impacted region is critical for protein function (Ambry internal data). Based on data from gnomAD, this allele has an overall frequency of <0.01% (1/31384) total alleles studied. Based on the available evidence, this alteration is classified as pathogenic.
Baylor Genetics RCV004568319 SCV005055257 likely pathogenic Peroxisome biogenesis disorder 5A (Zellweger) 2024-02-13 criteria provided, single submitter clinical testing

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