ClinVar Miner

Submissions for variant NM_000318.3(PEX2):c.374G>A (p.Arg125Gln)

gnomAD frequency: 0.00003  dbSNP: rs199845625
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001066793 SCV001231813 uncertain significance Peroxisome biogenesis disorder 5A (Zellweger) 2024-01-11 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 125 of the PEX2 protein (p.Arg125Gln). This variant is present in population databases (rs199845625, gnomAD 0.009%). 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: 860482). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae 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 RCV003346297 SCV004061183 uncertain significance Inborn genetic diseases 2023-07-12 criteria provided, single submitter clinical testing The c.374G>A (p.R125Q) alteration is located in exon 4 (coding exon 1) of the PEX2 gene. This alteration results from a G to A substitution at nucleotide position 374, causing the arginine (R) at amino acid position 125 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001833648 SCV002083370 uncertain significance Zellweger spectrum disorders 2020-02-21 no assertion criteria provided clinical testing

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