NM_020964.3(EPG5):c.67AAG[2] (p.Lys25del) AND Vici syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 22, 2022
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:: RCV002575394.3

Allele description [Variation Report for NM_020964.3(EPG5):c.67AAG[2] (p.Lys25del)]

NM_020964.3(EPG5):c.67AAG[2] (p.Lys25del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

18q21.1

Genomic location:

Preferred name:

NM_020964.3(EPG5):c.67AAG[2] (p.Lys25del)

HGVS:

NC_000018.10:g.45955327CTT[2]
NG_042838.1:g.17005AAG[2]
NM_001410858.1:c.67_69AAG[2]
NM_001410859.1:c.67_69AAG[2]
NM_020964.3:c.67AAG[2]MANE SELECT
NP_001397787.1:p.Lys25del
NP_001397788.1:p.Lys25del
NP_066015.2:p.Lys25del
LRG_1234t1:c.67AAG[2]
LRG_1234:g.17005AAG[2]
LRG_1234p1:p.Lys25del
NC_000018.9:g.43535293CTT[2]
NC_000018.9:g.43535293_43535295del
NM_020964.2:c.73_75delAAG

Protein change:

K25del

Molecular consequence:

NM_020964.3:c.67AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001410858.1:c.67_69AAG[2] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001410859.1:c.67_69AAG[2] - inframe_indel - [Sequence Ontology: SO:0001820]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002935844	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 22, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002935844

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 22, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002935844.2

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

Description

This variant, c.73_75del, results in the deletion of 1 amino acid(s) of the EPG5 protein (p.Lys25del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs773704123, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with EPG5-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

ClinVar

Relating variation to medicine