ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.1954G>T (p.Gly652Cys)

dbSNP: rs754417895
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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 RCV001979955 SCV002219112 uncertain significance Vici syndrome 2022-07-03 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 652 of the EPG5 protein (p.Gly652Cys). This variant is present in population databases (no rsID available, 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: 1447767). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.
PreventionGenetics, part of Exact Sciences RCV003395312 SCV004121172 uncertain significance EPG5-related disorder 2022-10-10 criteria provided, single submitter clinical testing The EPG5 c.1954G>T variant is predicted to result in the amino acid substitution p.Gly652Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.012% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/18-43519711-C-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Ambry Genetics RCV004616911 SCV005118859 uncertain significance Inborn genetic diseases 2024-04-24 criteria provided, single submitter clinical testing The c.1954G>T (p.G652C) alteration is located in exon 10 (coding exon 10) of the EPG5 gene. This alteration results from a G to T substitution at nucleotide position 1954, causing the glycine (G) at amino acid position 652 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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