ClinVar Miner

Submissions for variant NM_000318.3(PEX2):c.304C>A (p.Gln102Lys)

gnomAD frequency: 0.00030  dbSNP: rs200065382
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000734498 SCV000862648 uncertain significance not provided 2018-07-25 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001066961 SCV001231987 uncertain significance Peroxisome biogenesis disorder 5A (Zellweger) 2025-01-06 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 102 of the PEX2 protein (p.Gln102Lys). This variant is present in population databases (rs200065382, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with PEX2-related conditions. ClinVar contains an entry for this variant (Variation ID: 598165). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt PEX2 protein function with a negative predictive value of 80%. 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.
Ambry Genetics RCV003165994 SCV003865412 uncertain significance Inborn genetic diseases 2023-01-17 criteria provided, single submitter clinical testing The c.304C>A (p.Q102K) alteration is located in exon 4 (coding exon 1) of the PEX2 gene. This alteration results from a C to A substitution at nucleotide position 304, causing the glutamine (Q) at amino acid position 102 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001825483 SCV002083373 uncertain significance Zellweger spectrum disorders 2019-10-28 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003965552 SCV004787590 uncertain significance PEX2-related disorder 2024-09-04 no assertion criteria provided clinical testing The PEX2 c.304C>A variant is predicted to result in the amino acid substitution p.Gln102Lys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.045% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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