ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.2059C>T (p.Arg687Trp)

gnomAD frequency: 0.00004  dbSNP: rs138008298
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001336888 SCV001530403 uncertain significance Heimler syndrome 1 2018-01-29 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Invitae RCV001369759 SCV001566207 uncertain significance Zellweger spectrum disorders 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 687 of the PEX1 protein (p.Arg687Trp). This variant is present in population databases (rs138008298, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with PEX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1034227). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PEX1 protein function. 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 RCV002547359 SCV003689278 uncertain significance Inborn genetic diseases 2021-10-26 criteria provided, single submitter clinical testing The c.2059C>T (p.R687W) alteration is located in exon 12 (coding exon 12) of the PEX1 gene. This alteration results from a C to T substitution at nucleotide position 2059, causing the arginine (R) at amino acid position 687 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001369759 SCV002076879 uncertain significance Zellweger spectrum disorders 2018-04-30 no assertion criteria provided clinical testing

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