ClinVar Miner

Submissions for variant NM_004565.3(PEX14):c.474C>A (p.Ser158Arg)

gnomAD frequency: 0.00057  dbSNP: rs145867351
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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) RCV000081152 SCV000113060 uncertain significance not provided 2017-10-26 criteria provided, single submitter clinical testing
Invitae RCV001068404 SCV001233516 uncertain significance Peroxisome biogenesis disorder, complementation group K 2024-01-22 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 158 of the PEX14 protein (p.Ser158Arg). This variant is present in population databases (rs145867351, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with PEX14-related conditions. ClinVar contains an entry for this variant (Variation ID: 95146). 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 PEX14 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.
Illumina Laboratory Services, Illumina RCV001101249 SCV001257848 uncertain significance Peroxisome biogenesis disorder 13A (Zellweger) 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
PreventionGenetics, part of Exact Sciences RCV003407459 SCV004110496 uncertain significance PEX14-related condition 2023-08-04 criteria provided, single submitter clinical testing The PEX14 c.474C>A variant is predicted to result in the amino acid substitution p.Ser158Arg. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.091% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-10683165-C-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Mayo Clinic Laboratories, Mayo Clinic RCV000081152 SCV004227742 uncertain significance not provided 2022-07-08 criteria provided, single submitter clinical testing BP4, PM2

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