NC_000011.9:g.(?_117856768)_(118972385_?)del AND Immunodeficiency 19

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:: RCV001031688.3

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 19 (IMD19)
Synonyms:: CD3-DELTA DEFICIENCY; SEVERE COMBINED IMMUNODEFICIENCY, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE; SCID, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE
Identifiers:: MONDO: MONDO:0014280; MedGen: C3810147; OMIM: 615617

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Golgi SNAP receptor complex member 2 isoform X15 [Homo sapiens]
Golgi SNAP receptor complex member 2 isoform X15 [Homo sapiens]
gi|767996579|ref|XP_011523804.1|

Protein
Taxonomy Links for Nucleotide (Select 1889463823) (1)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001194994	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] 14602880, 15546002, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001194994

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

Effect of CD3delta deficiency on maturation of alpha/beta and gamma/delta T-cell lineages in severe combined immunodeficiency.

Dadi HK, Simon AJ, Roifman CM.

N Engl J Med. 2003 Nov 6;349(19):1821-8. No abstract available. Erratum in: N Engl J Med. 2004 Apr 22;350(17):1803.

PubMed [citation]

PMID:: 14602880

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, SCV001194994.3

#	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 CD3D 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 CD3D-related conditions. Loss-of-function variants in CD3D are known to be pathogenic (PMID: 14602880, 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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