ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.4501C>T (p.Arg1501Trp)

dbSNP: rs370776793
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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 RCV001350289 SCV001544680 uncertain significance Vici syndrome 2024-11-05 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 1501 of the EPG5 protein (p.Arg1501Trp). This variant is present in population databases (rs370776793, gnomAD 0.009%). 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: 1045816). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) 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 RCV003442865 SCV004170084 uncertain significance not provided 2023-10-12 criteria provided, single submitter clinical testing 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; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004978391 SCV005577480 uncertain significance Inborn genetic diseases 2024-10-24 criteria provided, single submitter clinical testing The c.4501C>T (p.R1501W) alteration is located in exon 26 (coding exon 26) of the EPG5 gene. This alteration results from a C to T substitution at nucleotide position 4501, causing the arginine (R) at amino acid position 1501 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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