ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.4205G>A (p.Arg1402Lys)

gnomAD frequency: 0.00003  dbSNP: rs749547713
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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 RCV000805104 SCV000945048 uncertain significance Vici syndrome 2022-08-16 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 1402 of the EPG5 protein (p.Arg1402Lys). This variant also falls at the last nucleotide of exon 23, which is part of the consensus splice site for this exon. This variant is present in population databases (rs749547713, gnomAD 0.01%). 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: 650030). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus 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 RCV002537194 SCV003748374 uncertain significance Inborn genetic diseases 2021-04-28 criteria provided, single submitter clinical testing The c.4205G>A (p.R1402K) alteration is located in exon 23 (coding exon 23) of the EPG5 gene. This alteration results from a G to A substitution at nucleotide position 4205, causing the arginine (R) at amino acid position 1402 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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