ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.1958C>T (p.Ser653Leu)

gnomAD frequency: 0.00001  dbSNP: rs267608228
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000180485 SCV000232938 uncertain significance not provided 2015-05-22 criteria provided, single submitter clinical testing
Invitae RCV001852249 SCV002189831 uncertain significance Peroxisome biogenesis disorder 2024-01-22 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 653 of the PEX6 protein (p.Ser653Leu). This variant is present in population databases (rs267608228, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with PEX6-related conditions. ClinVar contains an entry for this variant (Variation ID: 199006). 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 PEX6 protein function with a negative predictive value of 95%. 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.
Fulgent Genetics, Fulgent Genetics RCV002500521 SCV002780608 uncertain significance Peroxisome biogenesis disorder 4A (Zellweger); Peroxisome biogenesis disorder 4B; Heimler syndrome 2 2021-09-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV002516821 SCV003731863 uncertain significance Inborn genetic diseases 2021-02-08 criteria provided, single submitter clinical testing The c.1958C>T (p.S653L) alteration is located in exon 9 (coding exon 9) of the PEX6 gene. This alteration results from a C to T substitution at nucleotide position 1958, causing the serine (S) at amino acid position 653 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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