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NM_020964.3(EPG5):c.4184_4205+5del AND Vici syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 8, 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:
RCV003655929.2

Allele description [Variation Report for NM_020964.3(EPG5):c.4184_4205+5del]

NM_020964.3(EPG5):c.4184_4205+5del

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.4184_4205+5del
HGVS:
  • NC_000018.10:g.45910518_45910544del
  • NG_042838.1:g.61798_61824del
  • NM_001410858.1:c.4184_4205+5del
  • NM_001410859.1:c.4184_4205+5del
  • NM_020964.3:c.4184_4205+5delMANE SELECT
  • LRG_1234t1:c.4184_4205+5del
  • LRG_1234:g.61798_61824del
  • NC_000018.9:g.43490481_43490507del
  • NC_000018.9:g.43490483_43490509del
Molecular consequence:
  • NM_001410858.1:c.4184_4205+5del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001410859.1:c.4184_4205+5del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_020964.3:c.4184_4205+5del - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV004500610Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Mar 8, 2023)
germlineclinical testing

PubMed (4)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

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
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004500610.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with EPG5-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant results in the deletion of part of exon 23 (c.4184_4205+5del) of the EPG5 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EPG5 are known to be pathogenic (PMID: 23222957, 23674064).

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

Last Updated: Sep 29, 2024