ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.6232C>T (p.Arg2078Ter)

gnomAD frequency: 0.00002  dbSNP: rs587776942
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000033118 SCV000247310 pathogenic Vici syndrome 2015-02-23 criteria provided, single submitter clinical testing
SIB Swiss Institute of Bioinformatics RCV000033118 SCV000899147 pathogenic Vici syndrome 2019-01-17 criteria provided, single submitter curation This variant is interpreted as a 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 => Predicted nullvariant in a gene where LOF is a known mechanism of disease. PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:23222957).
Labcorp Genetics (formerly Invitae), Labcorp RCV000033118 SCV004297835 pathogenic Vici syndrome 2024-01-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg2078*) 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 (rs587776942, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with Vici syndrome (PMID: 23222957). ClinVar contains an entry for this variant (Variation ID: 39984). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV004700299 SCV005201728 pathogenic not provided 2023-09-15 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 28333917, 26917586, 23222957)
OMIM RCV000033118 SCV000056899 pathogenic Vici syndrome 2013-01-01 no assertion criteria provided literature only

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