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NM_020964.3(EPG5):c.4132G>T (p.Glu1378Ter) AND Vici syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 4, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003539612.2

Allele description [Variation Report for NM_020964.3(EPG5):c.4132G>T (p.Glu1378Ter)]

NM_020964.3(EPG5):c.4132G>T (p.Glu1378Ter)

Gene:
EPG5:ectopic P-granules 5 autophagy tethering factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q21.1
Genomic location:
Preferred name:
NM_020964.3(EPG5):c.4132G>T (p.Glu1378Ter)
HGVS:
  • NC_000018.10:g.45910594C>A
  • NG_042838.1:g.61746G>T
  • NM_001410858.1:c.4132G>T
  • NM_001410859.1:c.4132G>T
  • NM_020964.3:c.4132G>TMANE SELECT
  • NP_001397787.1:p.Glu1378Ter
  • NP_001397788.1:p.Glu1378Ter
  • NP_066015.2:p.Glu1378Ter
  • LRG_1234t1:c.4132G>T
  • LRG_1234:g.61746G>T
  • LRG_1234p1:p.Glu1378Ter
  • NC_000018.9:g.43490559C>A
Protein change:
E1378*
Molecular consequence:
  • NM_001410858.1:c.4132G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001410859.1:c.4132G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_020964.3:c.4132G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Vici syndrome (VICIS)
Synonyms:
Absent corpus callosum cataract immunodeficiency; Immunodeficiency with cleft lip/palate, cataract, hypopigmentation and absent corpus callosum
Identifiers:
MONDO: MONDO:0009452; MedGen: C1855772; Orphanet: 1493; OMIM: 242840

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004263164Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 4, 2024) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Recessive mutations in EPG5 cause Vici syndrome, a multisystem disorder with defective autophagy.

Cullup T, Kho AL, Dionisi-Vici C, Brandmeier B, Smith F, Urry Z, Simpson MA, Yau S, Bertini E, McClelland V, Al-Owain M, Koelker S, Koerner C, Hoffmann GF, Wijburg FA, ten Hoedt AE, Rogers RC, Manchester D, Miyata R, Hayashi M, Said E, Soler D, et al.

Nat Genet. 2013 Jan;45(1):83-7. doi: 10.1038/ng.2497. Epub 2012 Dec 9.

PubMed [citation]
PMID:
23222957
PMCID:
PMC4012842

Role of Epg5 in selective neurodegeneration and Vici syndrome.

Zhao YG, Zhao H, Sun H, Zhang H.

Autophagy. 2013 Aug;9(8):1258-62. doi: 10.4161/auto.24856. Epub 2013 May 14.

PubMed [citation]
PMID:
23674064
PMCID:
PMC3748201
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004263164.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Glu1378*) 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 not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EPG5-related conditions. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024