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NM_020964.3(EPG5):c.25C>A (p.Arg9Ser) AND Vici syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 4, 2021
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:
RCV002210920.2

Allele description [Variation Report for NM_020964.3(EPG5):c.25C>A (p.Arg9Ser)]

NM_020964.3(EPG5):c.25C>A (p.Arg9Ser)

Gene:
EPG5:ectopic P-granules 5 autophagy tethering factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q21.1
Genomic location:
Preferred name:
NM_020964.3(EPG5):c.25C>A (p.Arg9Ser)
HGVS:
  • NC_000018.10:g.45967215G>T
  • NG_042838.1:g.5125C>A
  • NM_020964.3:c.25C>AMANE SELECT
  • NP_066015.2:p.Arg9Ser
  • LRG_1234t1:c.25C>A
  • LRG_1234:g.5125C>A
  • LRG_1234p1:p.Arg9Ser
  • NC_000018.9:g.43547181G>T
Protein change:
R9S
Links:
dbSNP: rs368321414
NCBI 1000 Genomes Browser:
rs368321414
Molecular consequence:
  • NM_020964.3:c.25C>A - 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
SCV002496108Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 4, 2021) 		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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV002496108.1

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

Description

EPG5 NM_020964.2 exon 1 p.Arg9Ser (c.25C>A): This variant has not been reported in the literature but is present in 0.002% (2/68048) of European alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/18-45967215-G-T?dataset=gnomad_r3). Evolutionary conservation for this variant is limited; computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Dec 24, 2023