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NM_020964.3(EPG5):c.3614del (p.Leu1205fs) AND Vici syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 17, 2017
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:
RCV000691082.6

Allele description [Variation Report for NM_020964.3(EPG5):c.3614del (p.Leu1205fs)]

NM_020964.3(EPG5):c.3614del (p.Leu1205fs)

Gene:
EPG5:ectopic P-granules 5 autophagy tethering factor [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
18q21.1
Genomic location:
Preferred name:
NM_020964.3(EPG5):c.3614del (p.Leu1205fs)
HGVS:
  • NC_000018.10:g.45915590del
  • NG_042838.1:g.56750del
  • NM_020964.3:c.3614delMANE SELECT
  • NP_066015.2:p.Leu1205fs
  • LRG_1234t1:c.3614del
  • LRG_1234:g.56750del
  • LRG_1234p1:p.Leu1205fs
  • NC_000018.9:g.43495555del
  • NC_000018.9:g.43495555delA
  • NM_020964.2:c.3614delT
Protein change:
L1205fs
Links:
dbSNP: rs1568150793
NCBI 1000 Genomes Browser:
rs1568150793
Molecular consequence:
  • NM_020964.3:c.3614del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000818825Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Nov 17, 2017)
germlineclinical testing

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

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, SCV000818825.4

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

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in EPG5 are known to be pathogenic (PMID: 23222957, 23674064). This variant has not been reported in the literature in individuals with EPG5-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Leu1205Argfs*6) in the EPG5 gene. It is expected to result in an absent or disrupted protein product.

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

Last Updated: Sep 29, 2024