ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.7333C>T (p.Arg2445Ter)

gnomAD frequency: 0.00001  dbSNP: rs780889226
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000691031 SCV000818770 pathogenic Vici syndrome 2023-11-01 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg2445*) in the EPG5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EPG5 are known to be pathogenic (PMID: 23222957, 23674064). This variant is present in population databases (rs780889226, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with Vici syndrome (PMID: 26917586). ClinVar contains an entry for this variant (Variation ID: 570218). For these reasons, this variant has been classified as Pathogenic.
SIB Swiss Institute of Bioinformatics RCV000691031 SCV000899152 likely pathogenic Vici syndrome 2019-01-17 criteria provided, single submitter curation This variant is interpreted as a Likely pathogenic for Vici syndrome, autosomal recessive. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PVS1-strong => PVS1 downgraded in strength to Strong.
PreventionGenetics, part of Exact Sciences RCV003953237 SCV004771854 pathogenic EPG5-related condition 2024-01-02 criteria provided, single submitter clinical testing The EPG5 c.7333C>T variant is predicted to result in premature protein termination (p.Arg2445*). This variant has been reported in the apparently homozygous state in an individual with Vici syndrome (Table 1, Byrne S et al 2016. PubMed ID: 26917586). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in EPG5 are expected to be pathogenic. This variant is interpreted as pathogenic.

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