IMD19
MCID: IMM081
MIFTS: 44

Immunodeficiency 19 (IMD19)

Categories: Genetic diseases, Immune diseases, Infectious diseases, Respiratory diseases

Aliases & Classifications for Immunodeficiency 19

MalaCards integrated aliases for Immunodeficiency 19:

Name: Immunodeficiency 19 57 12 73 29 6 71
Cd3-Delta Deficiency 57 12 73
Imd19 57 12 73
Severe Combined Immunodeficiency, T Cell-Negative, B Cell-Positive, Nk Cell-Positive 57 12
Cd3delta Deficiency 12 15
T Cell-Negative, B Cell-Positive, Nk Cell-Positive Severe Combined Immunodeficiency 73
Scid, T Cell-Negative, B Cell-Positive, Nk Cell-Positive 57
Scid T Cell-Negative, B Cell-Positive, Nk Cell-Positive 12
T Cell-Negative, B Cell-Positive, Nk Cell-Positive Scid 73
Immunodeficiency, Type 19 39
Cd3d 12

Characteristics:

OMIM®:

57 (Updated 05-Mar-2021)
Inheritance:
autosomal recessive

Miscellaneous:
onset in infancy
death in infancy without bone marrow transplantation


HPO:

31
immunodeficiency 19:
Inheritance autosomal recessive inheritance
Onset and clinical course infantile onset


Classifications:



External Ids:

Disease Ontology 12 DOID:0060016 DOID:0111972
OMIM® 57 615617
OMIM Phenotypic Series 57 PS300755
MeSH 44 D007153
UMLS 71 C3810147

Summaries for Immunodeficiency 19

OMIM® : 57 Immunodeficiency-19 (IMD19) is an autosomal recessive form of severe combined immunodeficiency (SCID) characterized by onset in early infancy of recurrent bacterial, viral, and fungal infections. Patients usually have chronic diarrhea, recurrent respiratory infections, and failure to thrive. Immunologic work-up shows a T cell-negative, B cell-positive, natural killer (NK) cell-positive phenotype. The disorder is lethal in early childhood without bone marrow transplantation (summary by Yu et al., 2011). (615617) (Updated 05-Mar-2021)

MalaCards based summary : Immunodeficiency 19, also known as cd3-delta deficiency, is related to granulomatous disease, chronic, autosomal recessive, 3 and immunodeficiency 17, and has symptoms including diarrhea An important gene associated with Immunodeficiency 19 is CD3D (CD3d Molecule), and among its related pathways/superpathways are Phospholipase-C Pathway and TCR Signaling (Qiagen). Affiliated tissues include bone marrow, bone and t cells, and related phenotypes are failure to thrive and recurrent respiratory infections

Disease Ontology : 12 A severe combined immunodeficiency characterized by onset in early infancy of recurrent bacterial, viral, and fungal infections with a T cell-negative, B cell-positive, natural killer cell-positive immune cell phenotype that has material basis in homozygous or compound heterozygous mutation in CD3D on chromosome 11q23.3.

UniProtKB/Swiss-Prot : 73 Immunodeficiency 19: An autosomal recessive form of severe combined immunodeficiency characterized by onset in early infancy of recurrent bacterial, viral, and fungal infections. Patients usually have chronic diarrhea, recurrent respiratory infections, and failure to thrive. Immunologic work-up shows a T-cell negative, B-cell positive, NK-cell positive phenotype.

Related Diseases for Immunodeficiency 19

Diseases related to Immunodeficiency 19 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 38)
# Related Disease Score Top Affiliating Genes
1 granulomatous disease, chronic, autosomal recessive, 3 31.4 CD3G CD3D
2 immunodeficiency 17 31.2 ZAP70 CD3G CD3D
3 cd3zeta deficiency 31.2 CD3G CD3D CD247
4 immunodeficiency 18 31.1 CD3G CD3D CD247
5 coronin-1a deficiency 31.1 DOCK2 CORO1A CD3D
6 reticular dysgenesis 30.6 PNP CD3D ADA
7 adenosine deaminase deficiency 30.6 PNP CD3D ADA
8 omenn syndrome 29.7 ZAP70 PNP CORO1A CD3G CD3D ADA
9 leukemia, acute lymphoblastic 28.8 ZAP70 PNP CD247 ADA
10 immune deficiency disease 28.8 ZAP70 PNP CD247 ADA
11 severe combined immunodeficiency 28.0 ZAP70 PNP CORO1A CD3G CD3D CD247
12 combined immunodeficiency 27.6 ZAP70 PNP DOCK2 CORO1A CD3G CD3D
13 immunodeficiency 49 12.1
14 severe combined immunodeficiency, autosomal recessive, t cell-negative, b cell-positive, nk cell-positive 11.0
15 aplastic anemia 11.0
16 immunodeficiency 11b with atopic dermatitis 10.9
17 t-b+ severe combined immunodeficiency due to cd3delta/cd3epsilon/cd3zeta 10.0 CD3D CD247
18 immunodeficiency 40 10.0 DOCK2 CORO1A
19 melioidosis 9.9
20 cutaneous leishmaniasis 9.9
21 bladder cancer 9.9
22 breast cancer 9.9
23 type 1 diabetes mellitus 9.9
24 leukemia, acute myeloid 9.9
25 leukemia 9.9
26 acute leukemia 9.9
27 colon adenocarcinoma 9.9
28 t-cell acute lymphoblastic leukemia 9.9
29 myeloid leukemia 9.9
30 prolymphocytic leukemia 9.8 ZAP70 ADA
31 t cell deficiency 9.8 ZAP70 CORO1A CD247
32 lesch-nyhan syndrome 9.5 PNP ADA
33 lymphopenia 9.5 DOCK2 CORO1A CD3G ADA
34 bare lymphocyte syndrome, type ii 9.5 ZAP70 PNP
35 purine nucleoside phosphorylase deficiency 9.5 ZAP70 PNP ADA
36 common variable immunodeficiency 9.2 ZAP70 PNP CD247 ADA
37 t-cell lymphoblastic leukemia/lymphoma 9.1 ZAP70 PTCRA PNP CD3G ADA
38 leukemia, chronic lymphocytic 9.1 ZAP70 PNP CD247 ADA

Graphical network of the top 20 diseases related to Immunodeficiency 19:



Diseases related to Immunodeficiency 19

Symptoms & Phenotypes for Immunodeficiency 19

Human phenotypes related to Immunodeficiency 19:

31 (show all 6)
# Description HPO Frequency HPO Source Accession
1 failure to thrive 31 HP:0001508
2 recurrent respiratory infections 31 HP:0002205
3 immunodeficiency 31 HP:0002721
4 recurrent otitis media 31 HP:0000403
5 lymphopenia 31 HP:0001888
6 diarrhea 31 HP:0002014

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Mar-2021)
Growth Other:
failure to thrive

Abdomen Gastrointestinal:
diarrhea
gastroenteritis

Head And Neck Ears:
otitis media, recurrent

Immunology:
lymphopenia
primary immunodeficiency
normal b cells
normal nk cells
recurrent infections, bacterial, viral, and fungal
more
Respiratory:
respiratory infections, recurrent

Head And Neck Mouth:
thrush

Clinical features from OMIM®:

615617 (Updated 05-Mar-2021)

UMLS symptoms related to Immunodeficiency 19:


diarrhea

MGI Mouse Phenotypes related to Immunodeficiency 19:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 cellular MP:0005384 9.8 ADA CD247 CD3G CORO1A DOCK2 PNP
2 endocrine/exocrine gland MP:0005379 9.7 ADA CD247 CD3G CORO1A PNP PTCRA
3 hematopoietic system MP:0005397 9.65 ADA ATP5MG CD247 CD3D CD3G CORO1A
4 immune system MP:0005387 9.32 ADA ATP5MG CD247 CD3D CD3G CORO1A

Drugs & Therapeutics for Immunodeficiency 19

Search Clinical Trials , NIH Clinical Center for Immunodeficiency 19

Genetic Tests for Immunodeficiency 19

Genetic tests related to Immunodeficiency 19:

# Genetic test Affiliating Genes
1 Immunodeficiency 19 29 CD3D

Anatomical Context for Immunodeficiency 19

MalaCards organs/tissues related to Immunodeficiency 19:

40
Bone Marrow, Bone, T Cells, Nk Cells, B Cells

Publications for Immunodeficiency 19

Articles related to Immunodeficiency 19:

# Title Authors PMID Year
1
Genotype, phenotype, and outcomes of nine patients with T-B+NK+ SCID. 6 57
21883749 2011
2
A leaky mutation in CD3D differentially affects αβ and γδ T cells and leads to a Tαβ-Tγδ+B+NK+ human SCID. 57 6
21926461 2011
3
Effect of CD3delta deficiency on maturation of alpha/beta and gamma/delta T-cell lineages in severe combined immunodeficiency. 6 57
14602880 2003
4
Severe combined immunodeficiency caused by deficiency in either the delta or the epsilon subunit of CD3. 57
15546002 2004
5
CD3delta couples T-cell receptor signalling to ERK activation and thymocyte positive selection. 6
10935641 2000
6
Acute hypoxemic respiratory failure in children following bone marrow transplantation: an outcome and pathologic study. 61
7712767 1995

Variations for Immunodeficiency 19

ClinVar genetic disease variations for Immunodeficiency 19:

6 (show all 43)
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 CD3D NM_000732.4(CD3D):c.202C>T (p.Arg68Ter) SNV Pathogenic 12747 rs111033580 11:118211162-118211162 11:118340447-118340447
2 CD3D NM_001040651.2(CD3D):c.275-408C>A SNV Pathogenic 12748 rs111033581 11:118210617-118210617 11:118339902-118339902
3 CD3D NM_000732.4(CD3D):c.274+5G>A SNV Pathogenic 180674 rs730880296 11:118211085-118211085 11:118340370-118340370
4 CD3D NM_000732.4(CD3D):c.128G>A (p.Trp43Ter) SNV Pathogenic 643120 rs1591278347 11:118211236-118211236 11:118340521-118340521
5 ATP5MG NC_000011.9:g.(?_117856768)_(118972385_?)del Deletion Pathogenic 831101 11:117856768-118972385
6 CD3D NM_000732.6(CD3D):c.317G>A (p.Gly106Asp) SNV Uncertain significance 840028 11:118210579-118210579 11:118339864-118339864
7 CD3D NM_000732.6(CD3D):c.247G>A (p.Glu83Lys) SNV Uncertain significance 842296 11:118211117-118211117 11:118340402-118340402
8 CD3D NM_000732.4(CD3D):c.274+4C>T SNV Uncertain significance 302671 rs201299420 11:118211086-118211086 11:118340371-118340371
9 CD3D NM_000732.6(CD3D):c.262G>A (p.Val88Ile) SNV Uncertain significance 844932 11:118211102-118211102 11:118340387-118340387
10 CD3D NM_000732.6(CD3D):c.114T>A (p.Asn38Lys) SNV Uncertain significance 845145 11:118211250-118211250 11:118340535-118340535
11 CD3D NM_000732.6(CD3D):c.403G>A (p.Gly135Arg) SNV Uncertain significance 846720 11:118210493-118210493 11:118339778-118339778
12 CD3D NM_000732.6(CD3D):c.112A>G (p.Asn38Asp) SNV Uncertain significance 848861 11:118211252-118211252 11:118340537-118340537
13 CD3D NM_000732.6(CD3D):c.455T>C (p.Leu152Pro) SNV Uncertain significance 849523 11:118209938-118209938 11:118339223-118339223
14 CD3D NM_000732.4(CD3D):c.416C>T (p.Thr139Ile) SNV Uncertain significance 420806 rs527584796 11:118210200-118210200 11:118339485-118339485
15 CD3D NM_000732.6(CD3D):c.-8G>A SNV Uncertain significance 877885 11:118213330-118213330 11:118342615-118342615
16 CD3D NM_000732.6(CD3D):c.-77G>A SNV Uncertain significance 877886 11:118213399-118213399 11:118342684-118342684
17 CD3D NM_000732.6(CD3D):c.450+7G>T SNV Uncertain significance 879824 11:118210159-118210159 11:118339444-118339444
18 CD3D NM_000732.6(CD3D):c.457C>T (p.Arg153Ter) SNV Uncertain significance 940758 11:118209936-118209936 11:118339221-118339221
19 CD3D NM_000732.6(CD3D):c.356C>T (p.Ala119Val) SNV Uncertain significance 952605 11:118210540-118210540 11:118339825-118339825
20 CD3D NM_000732.6(CD3D):c.505C>T (p.Arg169Trp) SNV Uncertain significance 962292 11:118209888-118209888 11:118339173-118339173
21 CD3D NM_000732.6(CD3D):c.382C>A (p.His128Asn) SNV Uncertain significance 970636 11:118210514-118210514 11:118339799-118339799
22 CD3D NM_000732.4(CD3D):c.440A>G (p.Gln147Arg) SNV Uncertain significance 645619 rs45510201 11:118210176-118210176 11:118339461-118339461
23 CD3D NM_000732.4(CD3D):c.457C>G (p.Arg153Gly) SNV Uncertain significance 653087 rs201994476 11:118209936-118209936 11:118339221-118339221
24 CD3D NM_000732.4(CD3D):c.211T>C (p.Tyr71His) SNV Uncertain significance 656796 rs377725940 11:118211153-118211153 11:118340438-118340438
25 CD3D NM_000732.4(CD3D):c.60C>G (p.Ser20Arg) SNV Uncertain significance 658379 rs529268621 11:118211304-118211304 11:118340589-118340589
26 CD3D NM_000732.4(CD3D):c.-46T>C SNV Uncertain significance 302675 rs886047740 11:118213368-118213368 11:118342653-118342653
27 CD3D NM_000732.4(CD3D):c.121A>G (p.Ile41Val) SNV Uncertain significance 302672 rs886047737 11:118211243-118211243 11:118340528-118340528
28 CD3D NM_000732.4(CD3D):c.510C>T (p.Asn170=) SNV Uncertain significance 302670 rs146997233 11:118209883-118209883 11:118339168-118339168
29 CD3D NM_000732.4(CD3D):c.-93C>T SNV Uncertain significance 302676 rs772705529 11:118213415-118213415 11:118342700-118342700
30 CD3D NM_000732.4(CD3D):c.-44G>A SNV Uncertain significance 302674 rs886047739 11:118213366-118213366 11:118342651-118342651
31 CD3D NM_000732.4(CD3D):c.-128G>T SNV Uncertain significance 302677 rs200171722 11:118213450-118213450 11:118342735-118342735
32 CD3D NM_000732.4(CD3D):c.76A>G (p.Ile26Val) SNV Uncertain significance 541672 rs201374139 11:118211288-118211288 11:118340573-118340573
33 CD3D NM_000732.4(CD3D):c.418C>A (p.Gln140Lys) SNV Uncertain significance 541673 rs201126605 11:118210198-118210198 11:118339483-118339483
34 CD3D NM_000732.4(CD3D):c.244A>G (p.Lys82Glu) SNV Uncertain significance 541674 rs1555119773 11:118211120-118211120 11:118340405-118340405
35 CD3D NM_000732.4(CD3D):c.450+6C>T SNV Uncertain significance 35805 rs193922617 11:118210160-118210160 11:118339445-118339445
36 CD3D NM_000732.4(CD3D):c.485A>T (p.His162Leu) SNV Uncertain significance 639952 rs1246867427 11:118209908-118209908 11:118339193-118339193
37 CD3D NM_000732.4(CD3D):c.463C>T (p.Arg155Ter) SNV Uncertain significance 474829 rs777721098 11:118209930-118209930 11:118339215-118339215
38 CD3D NM_000732.4(CD3D):c.52C>A (p.Gln18Lys) SNV Likely benign 541671 rs141902449 11:118213271-118213271 11:118342556-118342556
39 CD3D NM_000732.4(CD3D):c.275-5C>T SNV Likely benign 742068 rs188697778 11:118210626-118210626 11:118339911-118339911
40 CD3D NM_000732.4(CD3D):c.309C>T (p.Thr103=) SNV Likely benign 755525 rs777386322 11:118210587-118210587 11:118339872-118339872
41 CD3D NM_000732.4(CD3D):c.202C>A (p.Arg68=) SNV Likely benign 761076 rs111033580 11:118211162-118211162 11:118340447-118340447
42 CD3D NM_000732.4(CD3D):c.360G>A (p.Leu120=) SNV Likely benign 763721 rs150570955 11:118210536-118210536 11:118339821-118339821
43 CD3D NM_000732.4(CD3D):c.*59C>T SNV Benign 302669 rs113271462 11:118209818-118209818 11:118339103-118339103

Expression for Immunodeficiency 19

Search GEO for disease gene expression data for Immunodeficiency 19.

Pathways for Immunodeficiency 19

Pathways related to Immunodeficiency 19 according to GeneCards Suite gene sharing:

(show all 31)
# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.84 ZAP70 CD3G CD3D CD247
2
Show member pathways
12.71 ZAP70 CD3G CD3D CD247
3
Show member pathways
12.69 DOCK2 CD3G CD3D CD247
4
Show member pathways
12.65 ZAP70 CD3G CD3D CD247
5
Show member pathways
12.46 ZAP70 CD3G CD3D CD247
6
Show member pathways
12.42 ZAP70 CD3G CD3D CD247
7
Show member pathways
12.41 ZAP70 CD3G CD3D CD247
8
Show member pathways
12.27 CD3G CD3D CD247
9
Show member pathways
12.24 ZAP70 CD3G CD3D
10
Show member pathways
12.22 ZAP70 CD3G CD3D CD247
11
Show member pathways
12.17 ZAP70 CD3G CD3D CD247
12
Show member pathways
12.04 CD3G CD3D CD247
13 11.92 CD3G CD3D CD247
14
Show member pathways
11.9 PNP ATP5MG ADA
15
Show member pathways
11.82 CD3G CD3D CD247
16 11.74 ZAP70 CD3G CD3D CD247
17 11.74 ZAP70 CD3G CD3D CD247
18
Show member pathways
11.71 ZAP70 CD3G CD3D CD247
19
Show member pathways
11.71 ZAP70 CD3G CD3D CD247
20
Show member pathways
11.66 ZAP70 CD3G CD3D CD247
21
Show member pathways
11.63 CD3G CD3D CD247
22 11.61 CD3G CD3D CD247
23
Show member pathways
11.51 CD3G CD3D CD247
24
Show member pathways
11.47 CD3G CD3D CD247
25
Show member pathways
11.41 CD3G CD247
26 11.33 ZAP70 CD3G CD3D CD247
27 11.27 ZAP70 CD3D ADA
28 11.2 CD3G CD3D CD247
29 11.11 ZAP70 CD3G CD3D CD247
30 11.03 CD3G CD3D CD247
31 10.62 ZAP70 CD3G CD3D CD247

GO Terms for Immunodeficiency 19

Cellular components related to Immunodeficiency 19 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 membrane GO:0016020 9.97 ZAP70 PTCRA DOCK2 CORO1A CD3G CD3D
2 clathrin-coated vesicle membrane GO:0030665 9.26 CD3G CD3D
3 T cell receptor complex GO:0042101 9.26 ZAP70 CD3G CD3D CD247
4 immunological synapse GO:0001772 9.16 ZAP70 CORO1A
5 alpha-beta T cell receptor complex GO:0042105 8.8 CD3G CD3D CD247

Biological processes related to Immunodeficiency 19 according to GeneCards Suite gene sharing:

(show all 17)
# Name GO ID Score Top Affiliating Genes
1 immune system process GO:0002376 9.85 ZAP70 CD3G CD3D CD247
2 adaptive immune response GO:0002250 9.78 ZAP70 CD3G CD3D CD247
3 cell surface receptor signaling pathway GO:0007166 9.73 CD3G CD3D CD247
4 regulation of immune response GO:0050776 9.71 CD3G CD3D CD247
5 positive regulation of T cell proliferation GO:0042102 9.57 PNP CORO1A
6 T cell receptor signaling pathway GO:0050852 9.56 ZAP70 CD3G CD3D CD247
7 regulation of defense response to virus by virus GO:0050690 9.52 DOCK2 CD247
8 positive regulation of T cell activation GO:0050870 9.51 CORO1A ADA
9 positive regulation of T cell differentiation GO:0045582 9.49 ZAP70 ADA
10 positive regulation of calcium-mediated signaling GO:0050850 9.46 ZAP70 ADA
11 purine-containing compound salvage GO:0043101 9.43 PNP ADA
12 immunological synapse formation GO:0001771 9.4 DOCK2 CORO1A
13 negative thymic T cell selection GO:0045060 9.37 ZAP70 DOCK2
14 positive regulation of alpha-beta T cell differentiation GO:0046638 9.33 ZAP70 PNP ADA
15 negative regulation of thymocyte apoptotic process GO:0070244 9.32 PTCRA ADA
16 T cell activation GO:0042110 9.26 ZAP70 DOCK2 CD3G ADA
17 positive thymic T cell selection GO:0045059 8.92 ZAP70 DOCK2 CD3G CD3D

Molecular functions related to Immunodeficiency 19 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 identical protein binding GO:0042802 9.55 PNP CORO1A CD3G CD3D CD247
2 transmembrane signaling receptor activity GO:0004888 9.13 CD3G CD3D CD247
3 T cell receptor binding GO:0042608 8.62 DOCK2 CD3G

Sources for Immunodeficiency 19

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Mar-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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