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NM_000733.4(CD3E):c.472A>T (p.Lys158Ter) AND Immunodeficiency 18

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 14, 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:
RCV003743222.2

Allele description [Variation Report for NM_000733.4(CD3E):c.472A>T (p.Lys158Ter)]

NM_000733.4(CD3E):c.472A>T (p.Lys158Ter)

Gene:
CD3E:CD3 epsilon subunit of T-cell receptor complex [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.3
Genomic location:
Preferred name:
NM_000733.4(CD3E):c.472A>T (p.Lys158Ter)
HGVS:
  • NC_000011.10:g.118313826A>T
  • NG_007383.1:g.14247A>T
  • NM_000733.4:c.472A>TMANE SELECT
  • NP_000724.1:p.Lys158Ter
  • NP_000724.1:p.Lys158Ter
  • LRG_38t1:c.472A>T
  • LRG_38:g.14247A>T
  • LRG_38p1:p.Lys158Ter
  • NC_000011.9:g.118184541A>T
  • NM_000733.3:c.472A>T
Protein change:
K158*
Molecular consequence:
  • NM_000733.4:c.472A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Immunodeficiency 18 (IMD18)
Synonyms:
CD3-EPSILON DEFICIENCY; CD3epsilon deficiency
Identifiers:
MONDO: MONDO:0014278; MedGen: C3810127; OMIM: 615615

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004464779Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(May 14, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Independent mutations of the human CD3-epsilon gene resulting in a T cell receptor/CD3 complex immunodeficiency.

Soudais C, de Villartay JP, Le Deist F, Fischer A, Lisowska-Grospierre B.

Nat Genet. 1993 Jan;3(1):77-81.

PubMed [citation]
PMID:
8490660

Severe combined immunodeficiency caused by deficiency in either the delta or the epsilon subunit of CD3.

de Saint Basile G, Geissmann F, Flori E, Uring-Lambert B, Soudais C, Cavazzana-Calvo M, Durandy A, Jabado N, Fischer A, Le Deist F.

J Clin Invest. 2004 Nov;114(10):1512-7.

PubMed [citation]
PMID:
15546002
PMCID:
PMC525745
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004464779.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CD3E-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys158*) in the CD3E gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CD3E are known to be pathogenic (PMID: 8490660, 15546002).

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

Last Updated: Sep 29, 2024