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NM_020964.3(EPG5):c.6595A>G (p.Ile2199Val) AND Vici syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 14, 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:
RCV000642210.3

Allele description [Variation Report for NM_020964.3(EPG5):c.6595A>G (p.Ile2199Val)]

NM_020964.3(EPG5):c.6595A>G (p.Ile2199Val)

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.6595A>G (p.Ile2199Val)
HGVS:
  • NC_000018.10:g.45866824T>C
  • NG_042838.1:g.105516A>G
  • NM_020964.3:c.6595A>GMANE SELECT
  • NP_066015.2:p.Ile2199Val
  • LRG_1234t1:c.6595A>G
  • LRG_1234:g.105516A>G
  • LRG_1234p1:p.Ile2199Val
  • NC_000018.9:g.43446789T>C
  • NM_020964.2:c.6595A>G
Protein change:
I2199V
Links:
dbSNP: rs1555662276
NCBI 1000 Genomes Browser:
rs1555662276
Molecular consequence:
  • NM_020964.3:c.6595A>G - missense variant - [Sequence Ontology: SO:0001583]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000763864Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 14, 2017) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV000763864.1

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

Description

This sequence change replaces isoleucine with valine at codon 2199 of the EPG5 protein (p.Ile2199Val). The isoleucine residue is weakly conserved and there is a small physicochemical difference between isoleucine and valine. 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 disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

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

Last Updated: Sep 29, 2024