ClinVar Miner

Submissions for variant NM_001351132.2(PEX5):c.1874C>T (p.Ala625Val)

gnomAD frequency: 0.00004  dbSNP: rs773854263
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001055420 SCV001219810 uncertain significance Peroxisome biogenesis disorder 2B 2022-10-04 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 625 of the PEX5 protein (p.Ala625Val). This variant is present in population databases (rs773854263, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with PEX5-related conditions. ClinVar contains an entry for this variant (Variation ID: 851096). 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 PEX5 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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 RCV003339447 SCV004059579 uncertain significance Inborn genetic diseases 2023-09-13 criteria provided, single submitter clinical testing The c.1874C>T (p.A625V) alteration is located in exon 16 (coding exon 15) of the PEX5 gene. This alteration results from a C to T substitution at nucleotide position 1874, causing the alanine (A) at amino acid position 625 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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