ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.1435C>T (p.Leu479Phe)

gnomAD frequency: 0.00051  dbSNP: rs200364337
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000687062 SCV000814613 uncertain significance Vici syndrome 2024-06-06 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 479 of the EPG5 protein (p.Leu479Phe). This variant is present in population databases (rs200364337, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with EPG5-related conditions. ClinVar contains an entry for this variant (Variation ID: 567082). 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 expected to disrupt EPG5 protein function with a positive 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.
GeneDx RCV001731889 SCV001982105 uncertain significance not provided 2022-03-26 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function
Ambry Genetics RCV004619379 SCV005118863 uncertain significance Inborn genetic diseases 2024-04-22 criteria provided, single submitter clinical testing The c.1435C>T (p.L479F) alteration is located in exon 5 (coding exon 5) of the EPG5 gene. This alteration results from a C to T substitution at nucleotide position 1435, causing the leucine (L) at amino acid position 479 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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