NM_020964.3(EPG5):c.7156G>T (p.Glu2386Ter) AND Vici syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 23, 2020
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:: RCV001051976.5

Allele description [Variation Report for NM_020964.3(EPG5):c.7156G>T (p.Glu2386Ter)]

NM_020964.3(EPG5):c.7156G>T (p.Glu2386Ter)

Gene:

EPG5:ectopic P-granules 5 autophagy tethering factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q12.3

Genomic location:

Preferred name:

NM_020964.3(EPG5):c.7156G>T (p.Glu2386Ter)

HGVS:

NC_000018.10:g.45858636C>A
NG_042838.1:g.113704G>T
NM_020964.3:c.7156G>TMANE SELECT
NP_066015.2:p.Glu2386Ter
LRG_1234t1:c.7156G>T
LRG_1234:g.113704G>T
LRG_1234p1:p.Glu2386Ter
NC_000018.9:g.43438601C>A
NM_020964.2:c.7156G>T

Protein change:

E2386*

Links:

dbSNP: rs373944025

NCBI 1000 Genomes Browser:

rs373944025

Molecular consequence:

NM_020964.3:c.7156G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001216161	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 23, 2020)	germline	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

SCV001216161

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 23, 2020)

germline

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	germline	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, SCV001216161.3

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

Description

This sequence change creates a premature translational stop signal (p.Glu2386*) in the EPG5 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with EPG5-related conditions. Loss-of-function variants in EPG5 are known to be pathogenic (PMID: 23222957, 23674064). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

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