NC_000011.9:g.(?_117856768)_(118972385_?)del AND Immunodeficiency 18

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 7, 2019
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:: RCV001389243.3

Allele description

NC_000011.9:g.(?_117856768)_(118972385_?)del

Genes:

ATP5MG:ATP synthase membrane subunit g [Gene - OMIM - HGNC]
BCL9L:BCL9 like [Gene - OMIM - HGNC]
CXCR5:C-X-C motif chemokine receptor 5 [Gene - OMIM - HGNC]
CD3D:CD3 delta subunit of T-cell receptor complex [Gene - OMIM - HGNC]
CD3E:CD3 epsilon subunit of T-cell receptor complex [Gene - OMIM - HGNC]
CD3G:CD3 gamma subunit of T-cell receptor complex [Gene - OMIM - HGNC]
DDX6:DEAD-box helicase 6 [Gene - OMIM - HGNC]
H2AX:H2A.X variant histone [Gene - OMIM - HGNC]
VPS11:VPS11 core subunit of CORVET and HOPS complexes [Gene - OMIM - HGNC]
ARCN1:archain 1 [Gene - OMIM - HGNC]
CENATAC:centrosomal AT-AC splicing factor [Gene - OMIM - HGNC]
DPAGT1:dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 [Gene - OMIM - HGNC]
FOXR1:forkhead box R1 [Gene - OMIM - HGNC]
HMBS:hydroxymethylbilane synthase [Gene - OMIM - HGNC]
HYOU1:hypoxia up-regulated 1 [Gene - OMIM - HGNC]
IL10RA:interleukin 10 receptor subunit alpha [Gene - OMIM - HGNC]
IFT46:intraflagellar transport 46 [Gene - HGNC]
JAML:junction adhesion molecule like [Gene - OMIM - HGNC]
KMT2A:lysine methyltransferase 2A [Gene - OMIM - HGNC]
MPZL2:myelin protein zero like 2 [Gene - OMIM - HGNC]
MPZL3:myelin protein zero like 3 [Gene - OMIM - HGNC]
PHLDB1:pleckstrin homology like domain family B member 1 [Gene - OMIM - HGNC]
RPS25:ribosomal protein S25 [Gene - OMIM - HGNC]
SCN2B:sodium voltage-gated channel beta subunit 2 [Gene - OMIM - HGNC]
SCN4B:sodium voltage-gated channel beta subunit 4 [Gene - OMIM - HGNC]
SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]
TTC36:tetratricopeptide repeat domain 36 [Gene - HGNC]
TRAPPC4:trafficking protein particle complex subunit 4 [Gene - OMIM - HGNC]
TMEM25:transmembrane protein 25 [Gene - OMIM - HGNC]
TMPRSS4:transmembrane serine protease 4 [Gene - OMIM - HGNC]
TREH:trehalase [Gene - OMIM - HGNC]
UBE4A:ubiquitination factor E4A [Gene - OMIM - HGNC]
UPK2:uroplakin 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q23.3

Genomic location:

Chr11: 117856768 - 118972385 (on Assembly GRCh37)

Preferred name:

NC_000011.9:g.(?_117856768)_(118972385_?)del

HGVS:

NC_000011.9:g.(?_117856768)_(118972385_?)del

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001590519	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 7, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 8490660, 15546002, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001590519

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 7, 2019)

germline

clinical testing

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

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

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 Invitae, SCV001590519.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the CD3E gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with CD3E-related conditions. Loss-of-function variants in CD3E are known to be pathogenic (PMID: 8490660, 15546002). For these reasons, this variant has been classified as Pathogenic.

#	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: Feb 13, 2023

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