ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.7447C>T (p.Arg2483Ter)

gnomAD frequency: 0.00001  dbSNP: rs863225064
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München RCV000201265 SCV000680212 pathogenic Vici syndrome 2017-11-16 criteria provided, single submitter clinical testing
SIB Swiss Institute of Bioinformatics RCV000201265 SCV000899140 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-Moderate => PVS1 downgraded in strength to Moderate. PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:26917586).
Invitae RCV000201265 SCV004297833 pathogenic Vici syndrome 2023-07-28 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 217320). This premature translational stop signal has been observed in individual(s) with Vici syndrome (PMID: 32558422). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Arg2483*) 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).
OMIM RCV000201265 SCV000255996 pathogenic Vici syndrome 2014-12-01 no assertion criteria provided literature only

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