ClinVar Miner

Submissions for variant NM_002618.4(PEX13):c.977T>C (p.Ile326Thr)

dbSNP: rs61752115
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001851730 SCV002221637 uncertain significance Peroxisome biogenesis disorder 11A (Zellweger) 2023-11-20 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 326 of the PEX13 protein (p.Ile326Thr). This variant is present in population databases (rs61752115, gnomAD 0.0009%). This missense change has been observed in individual(s) with neonatal adrenoleukodystrophy (PMID: 10332040). ClinVar contains an entry for this variant (Variation ID: 7704). 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 PEX13 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects PEX13 function (PMID: 10332040, 16006427, 27827795). 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.
GeneDx RCV002269257 SCV002552696 likely pathogenic not provided 2022-01-25 criteria provided, single submitter clinical testing Published functional studies suggest a damaging effect on peroxisome assembly (Shimozawa et al., 1999); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 10332040, 16006427)
OMIM RCV000008143 SCV000028348 pathogenic Peroxisome biogenesis disorder 11B 1999-09-01 no assertion criteria provided literature only

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