NC_000018.9:g.(?_43467696)_(43467892_?)del AND Vici syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 19, 2023
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:: RCV004579798.2

Allele description [Variation Report for NC_000018.9:g.(?_43467696)_(43467892_?)del]

NC_000018.9:g.(?_43467696)_(43467892_?)del

Gene:: EPG5:ectopic P-granules 5 autophagy tethering factor [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 18q12.3
Genomic location:: Chr18: 43467696 - 43467892 (on Assembly GRCh37)
Preferred name:: NC_000018.9:g.(?_43467696)_(43467892_?)del
HGVS:: NC_000018.9:g.(?_43467696)_(43467892_?)del
This HGVS expression did not pass validation

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005063796	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 19, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23222957, 23674064, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005063796

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 19, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV005063796.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with EPG5-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 29 of the EPG5 gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in EPG5 are known to be pathogenic (PMID: 23222957, 23674064).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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