IMD25
MCID: IMM085
MIFTS: 38

Immunodeficiency 25 (IMD25)

Categories: Genetic diseases, Immune diseases

Aliases & Classifications for Immunodeficiency 25

MalaCards integrated aliases for Immunodeficiency 25:

Name: Immunodeficiency 25 57 12 72 15
Immunodeficiency Due to Defect in Cd3-Zeta 57 12 72 29 13 6 44 39 70
Imd25 57 12 72

Characteristics:

OMIM®:

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

Miscellaneous:
onset in infancy
one patient has been reported (last curated june 2016)


HPO:

31
immunodeficiency 25:
Inheritance autosomal recessive inheritance
Onset and clinical course infantile onset


Classifications:



External Ids:

Disease Ontology 12 DOID:0111942
OMIM® 57 610163
OMIM Phenotypic Series 57 PS300755
MedGen 41 C1857798
UMLS 70 C1857798

Summaries for Immunodeficiency 25

Disease Ontology : 12 A T cell deficiency characterized by decreased T cell counts, normal B cell counts, and eosinophilia that has material basis in homozygous or compound heterozygous mutation in CD247 on chromosome 1q24.2.

MalaCards based summary : Immunodeficiency 25, also known as immunodeficiency due to defect in cd3-zeta, is related to spermatogenic failure 3 and xeroderma pigmentosum, variant type. An important gene associated with Immunodeficiency 25 is CD247 (CD247 Molecule), and among its related pathways/superpathways are DNA Double-Strand Break Repair and TCR Signaling (Qiagen). Affiliated tissues include t cells and smooth muscle, and related phenotypes are recurrent pneumonia and erythroderma

UniProtKB/Swiss-Prot : 72 Immunodeficiency 25: An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.

More information from OMIM: 610163 PS300755

Related Diseases for Immunodeficiency 25

Diseases related to Immunodeficiency 25 via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 spermatogenic failure 3 9.8 MSH5 MSH4
2 xeroderma pigmentosum, variant type 9.0 UNG RRM1 RAD51 POLI

Symptoms & Phenotypes for Immunodeficiency 25

Human phenotypes related to Immunodeficiency 25:

31 (show all 17)
# Description HPO Frequency HPO Source Accession
1 recurrent pneumonia 31 very rare (1%) HP:0006532
2 erythroderma 31 very rare (1%) HP:0001019
3 eosinophilia 31 very rare (1%) HP:0001880
4 autoimmune hemolytic anemia 31 very rare (1%) HP:0001890
5 increased circulating iga level 31 very rare (1%) HP:0003261
6 increased circulating igm level 31 very rare (1%) HP:0003496
7 recurrent candida infections 31 very rare (1%) HP:0005401
8 recurrent herpes 31 very rare (1%) HP:0005353
9 increased circulating igg level 31 very rare (1%) HP:0003237
10 protracted diarrhea 31 very rare (1%) HP:0004385
11 smooth muscle antibody positivity 31 very rare (1%) HP:0003262
12 complete or near-complete absence of specific antibody response to tetanus vaccine 31 very rare (1%) HP:0410295
13 antimitochondrial antibody positivity 31 very rare (1%) HP:0030167
14 t lymphocytopenia 31 very rare (1%) HP:0005403
15 increased circulating ige level 31 very rare (1%) HP:0003212
16 decreased circulating igg2 level 31 very rare (1%) HP:0008348
17 immunodeficiency 31 HP:0002721

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Immunology:
eosinophilia
recurrent infections
bacterial infections
fungal infections
viral infections
more

Clinical features from OMIM®:

610163 (Updated 05-Apr-2021)

GenomeRNAi Phenotypes related to Immunodeficiency 25 according to GeneCards Suite gene sharing:

26
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased HIV-1 infection GR00226-A 9.13 EXOSC10 POLR2C POLR2J
2 Synthetic lethal with MLN4924 (a NAE inhibitor) GR00250-A-3 8.8 MSH5 RRM1 UNG

Drugs & Therapeutics for Immunodeficiency 25

Search Clinical Trials , NIH Clinical Center for Immunodeficiency 25

Cochrane evidence based reviews: immunodeficiency due to defect in cd3-zeta

Genetic Tests for Immunodeficiency 25

Genetic tests related to Immunodeficiency 25:

# Genetic test Affiliating Genes
1 Immunodeficiency Due to Defect in Cd3-Zeta 29 CD247

Anatomical Context for Immunodeficiency 25

MalaCards organs/tissues related to Immunodeficiency 25:

40
T Cells, Smooth Muscle

Publications for Immunodeficiency 25

Articles related to Immunodeficiency 25:

# Title Authors PMID Year
1
Inherited and somatic CD3zeta mutations in a patient with T-cell deficiency. 6 57
16672702 2006
2
Brief report: primary immunodeficiency caused by mutations in the gene encoding the CD3-gamma subunit of the T-lymphocyte receptor. 57
1635567 1992
3
Biochemical basis of a novel T lymphocyte receptor immunodeficiency by immunohistochemistry. A possible CD3 gamma abnormality. 57
1709425 1991
4
Familial defect in the surface expression of the T-cell receptor-CD3 complex. 57
3262828 1988
5
A founder RAB27A variant causes Griscelli syndrome type 2 with phenotypic heterogeneity in Qatari families. 61
32856792 2020
6
[Risk factors of invasive fungal infections in patients admitted to non- hematological oncology department and pediatric intensive care unit]. 61
24225291 2013
7
Distribution, infections, treatments and molecular analysis in a large cohort of patients with primary immunodeficiency diseases (PIDs) in Taiwan. 61
16783466 2006
8
Lamivudine reduces healthcare resource use when added to zidovudine-containing regimens in patients with HIV infection. 61
10537439 1999

Variations for Immunodeficiency 25

ClinVar genetic disease variations for Immunodeficiency 25:

6 (show top 50) (show all 53)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 CD247 NM_000734.4(CD247):c.208C>T (p.Gln70Ter) SNV Pathogenic 12749 rs74315290 GRCh37: 1:167408592-167408592
GRCh38: 1:167439355-167439355
2 CD247 NM_000734.4(CD247):c.208_209inv (p.Gln70Trp) Inversion Pathogenic 12750 GRCh37: 1:167408591-167408592
GRCh38: 1:167439354-167439355
3 CD247 NM_000734.4(CD247):c.209A>T (p.Gln70Leu) SNV Pathogenic 12751 rs193922740 GRCh37: 1:167408591-167408591
GRCh38: 1:167439354-167439354
4 CD247 NM_000734.4(CD247):c.208_210delinsTAT (p.Gln70Tyr) Indel Pathogenic 12752 rs193922741 GRCh37: 1:167408590-167408592
GRCh38: 1:167439353-167439355
5 CD247 NM_000734.4(CD247):c.2T>C (p.Met1Thr) SNV Pathogenic 162005 rs672601318 GRCh37: 1:167487701-167487701
GRCh38: 1:167518464-167518464
6 CD247 NM_000734.4(CD247):c.51dup (p.Ile18fs) Duplication Pathogenic 534695 rs1553238837 GRCh37: 1:167487651-167487652
GRCh38: 1:167518414-167518415
7 CD247 NM_198053.2(CD247):c.301C>T (p.Gln101Ter) SNV Pathogenic/Likely pathogenic 419227 rs55729925 GRCh37: 1:167404671-167404671
GRCh38: 1:167435434-167435434
8 CD247 NM_198053.3(CD247):c.37C>A (p.Gln13Lys) SNV Uncertain significance 863731 GRCh37: 1:167487666-167487666
GRCh38: 1:167518429-167518429
9 CD247 NM_198053.3(CD247):c.370A>T (p.Ser124Cys) SNV Uncertain significance 935817 GRCh37: 1:167403280-167403280
GRCh38: 1:167434043-167434043
10 CD247 NM_198053.3(CD247):c.495A>C (p.Ter165Tyr) SNV Uncertain significance 939907 GRCh37: 1:167400918-167400918
GRCh38: 1:167431681-167431681
11 CD247 NM_198053.3(CD247):c.187G>C (p.Ala63Pro) SNV Uncertain significance 944598 GRCh37: 1:167408613-167408613
GRCh38: 1:167439376-167439376
12 CD247 NM_198053.3(CD247):c.490C>T (p.Arg164Cys) SNV Uncertain significance 947935 GRCh37: 1:167400923-167400923
GRCh38: 1:167431686-167431686
13 CD247 NM_198053.3(CD247):c.359C>T (p.Ala120Val) SNV Uncertain significance 951502 GRCh37: 1:167403291-167403291
GRCh38: 1:167434054-167434054
14 CD247 NM_198053.3(CD247):c.398G>A (p.Arg133Gln) SNV Uncertain significance 992558 GRCh37: 1:167402292-167402292
GRCh38: 1:167433055-167433055
15 CD247 NM_198053.3(CD247):c.148T>C (p.Phe50Leu) SNV Uncertain significance 1005445 GRCh37: 1:167409915-167409915
GRCh38: 1:167440678-167440678
16 CD247 NM_198053.3(CD247):c.112A>G (p.Ile38Val) SNV Uncertain significance 835176 GRCh37: 1:167409951-167409951
GRCh38: 1:167440714-167440714
17 CD247 NM_198053.3(CD247):c.111A>T (p.Gly37=) SNV Uncertain significance 935732 GRCh37: 1:167409952-167409952
GRCh38: 1:167440715-167440715
18 CD247 NM_198053.3(CD247):c.463G>A (p.Ala155Thr) SNV Uncertain significance 937736 GRCh37: 1:167400950-167400950
GRCh38: 1:167431713-167431713
19 CD247 NM_198053.3(CD247):c.268C>T (p.Arg90Cys) SNV Uncertain significance 947324 GRCh37: 1:167407839-167407839
GRCh38: 1:167438602-167438602
20 CD247 NM_198053.3(CD247):c.235C>G (p.Arg79Gly) SNV Uncertain significance 948788 GRCh37: 1:167407872-167407872
GRCh38: 1:167438635-167438635
21 CD247 NM_000734.4(CD247):c.488G>A (p.Arg163His) SNV Uncertain significance 626075 rs201937405 GRCh37: 1:167400922-167400922
GRCh38: 1:167431685-167431685
22 CD247 NM_198053.3(CD247):c.220-3T>C SNV Uncertain significance 1025806 GRCh37: 1:167407890-167407890
GRCh38: 1:167438653-167438653
23 CD247 NM_198053.3(CD247):c.300+3A>G SNV Uncertain significance 953720 GRCh37: 1:167407804-167407804
GRCh38: 1:167438567-167438567
24 CD247 NM_198053.3(CD247):c.310A>G (p.Lys104Glu) SNV Uncertain significance 1035756 GRCh37: 1:167404662-167404662
GRCh38: 1:167435425-167435425
25 CD247 NM_198053.3(CD247):c.250G>T (p.Asp84Tyr) SNV Uncertain significance 1038153 GRCh37: 1:167407857-167407857
GRCh38: 1:167438620-167438620
26 CD247 NM_198053.3(CD247):c.274C>T (p.Arg92Trp) SNV Uncertain significance 1040612 GRCh37: 1:167407833-167407833
GRCh38: 1:167438596-167438596
27 CD247 NM_198053.2(CD247):c.27G>A (p.Ala9=) SNV Uncertain significance 466355 rs757294201 GRCh37: 1:167487676-167487676
GRCh38: 1:167518439-167518439
28 CD247 NM_198053.3(CD247):c.337-6C>A SNV Uncertain significance 845328 GRCh37: 1:167403319-167403319
GRCh38: 1:167434082-167434082
29 CD247 NM_198053.2(CD247):c.263A>G (p.Lys88Arg) SNV Uncertain significance 643887 rs143180729 GRCh37: 1:167407844-167407844
GRCh38: 1:167438607-167438607
30 CD247 NM_198053.2(CD247):c.162+8C>A SNV Uncertain significance 665272 rs1571515476 GRCh37: 1:167409893-167409893
GRCh38: 1:167440656-167440656
31 CD247 NM_198053.2(CD247):c.427C>T (p.Gln143Ter) SNV Uncertain significance 466358 rs759213998 GRCh37: 1:167402263-167402263
GRCh38: 1:167433026-167433026
32 CD247 NM_198053.2(CD247):c.250G>C (p.Asp84His) SNV Uncertain significance 581037 rs753572867 GRCh37: 1:167407857-167407857
GRCh38: 1:167438620-167438620
33 CD247 NM_198053.2(CD247):c.275G>A (p.Arg92Gln) SNV Uncertain significance 644174 rs367690333 GRCh37: 1:167407832-167407832
GRCh38: 1:167438595-167438595
34 CD247 NM_198053.3(CD247):c.386A>G (p.Lys129Arg) SNV Uncertain significance 937259 GRCh37: 1:167403264-167403264
GRCh38: 1:167434027-167434027
35 CD247 NM_198053.3(CD247):c.288G>T (p.Met96Ile) SNV Uncertain significance 946910 GRCh37: 1:167407819-167407819
GRCh38: 1:167438582-167438582
36 CD247 NM_198053.3(CD247):c.300G>A (p.Pro100=) SNV Uncertain significance 952188 GRCh37: 1:167407807-167407807
GRCh38: 1:167438570-167438570
37 CD247 NM_198053.2(CD247):c.128G>T (p.Gly43Val) SNV Uncertain significance 575487 rs1557996000 GRCh37: 1:167409935-167409935
GRCh38: 1:167440698-167440698
38 CD247 NM_198053.2(CD247):c.394C>T (p.Arg132Cys) SNV Uncertain significance 575904 rs781510519 GRCh37: 1:167402296-167402296
GRCh38: 1:167433059-167433059
39 CD247 NM_198053.2(CD247):c.39G>A (p.Gln13=) SNV Likely benign 466357 rs760945719 GRCh37: 1:167487664-167487664
GRCh38: 1:167518427-167518427
40 CD247 NM_198053.2(CD247):c.294A>G (p.Gly98=) SNV Likely benign 534697 rs1453205554 GRCh37: 1:167407813-167407813
GRCh38: 1:167438576-167438576
41 CD247 NM_198053.2(CD247):c.414C>T (p.His138=) SNV Likely benign 757680 rs184894260 GRCh37: 1:167402276-167402276
GRCh38: 1:167433039-167433039
42 CD247 NM_198053.2(CD247):c.251A>G (p.Asp84Gly) SNV Likely benign 762586 rs181746205 GRCh37: 1:167407856-167407856
GRCh38: 1:167438619-167438619
43 CD247 NM_198053.2(CD247):c.394-8_394-5del Deletion Likely benign 799755 rs769263658 GRCh37: 1:167402301-167402304
GRCh38: 1:167433064-167433067
44 CD247 NM_198053.2(CD247):c.462C>T (p.Asp154=) SNV Likely benign 534696 rs181656780 GRCh37: 1:167400951-167400951
GRCh38: 1:167431714-167431714
45 CD247 NM_198053.2(CD247):c.15G>A (p.Ala5=) SNV Likely benign 534698 rs746701386 GRCh37: 1:167487688-167487688
GRCh38: 1:167518451-167518451
46 CD247 NM_198053.2(CD247):c.430-6C>T SNV Likely benign 703238 rs200103990 GRCh37: 1:167400989-167400989
GRCh38: 1:167431752-167431752
47 CD247 NM_198053.2(CD247):c.360G>A (p.Ala120=) SNV Likely benign 704386 rs568106106 GRCh37: 1:167403290-167403290
GRCh38: 1:167434053-167434053
48 CD247 NM_198053.2(CD247):c.337-7T>C SNV Benign 705623 rs36056000 GRCh37: 1:167403320-167403320
GRCh38: 1:167434083-167434083
49 CD247 NM_198053.2(CD247):c.100C>T (p.Leu34=) SNV Benign 723755 rs181342622 GRCh37: 1:167409963-167409963
GRCh38: 1:167440726-167440726
50 CD247 NM_198053.2(CD247):c.177A>G (p.Ala59=) SNV Benign 466352 rs373031213 GRCh37: 1:167408623-167408623
GRCh38: 1:167439386-167439386

Expression for Immunodeficiency 25

Search GEO for disease gene expression data for Immunodeficiency 25.

Pathways for Immunodeficiency 25

GO Terms for Immunodeficiency 25

Cellular components related to Immunodeficiency 25 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 nuclear chromosome GO:0000228 9.26 RAD51 MSH5
2 condensed nuclear chromosome GO:0000794 9.16 RAD51 MSH4
3 condensed chromosome GO:0000793 8.96 RAD51 MSH4
4 RNA polymerase II, core complex GO:0005665 8.62 POLR2J POLR2C

Biological processes related to Immunodeficiency 25 according to GeneCards Suite gene sharing:

(show all 11)
# Name GO ID Score Top Affiliating Genes
1 cellular response to DNA damage stimulus GO:0006974 9.67 UNG RAD51 POLI MSH5
2 DNA repair GO:0006281 9.56 UNG RAD51 POLI MSH5
3 response to ionizing radiation GO:0010212 9.49 RRM1 RAD51
4 RNA metabolic process GO:0016070 9.48 POLR2J POLR2C
5 7-methylguanosine mRNA capping GO:0006370 9.46 POLR2J POLR2C
6 mismatch repair GO:0006298 9.43 MSH5 MSH4
7 positive regulation of viral transcription GO:0050434 9.4 POLR2J POLR2C
8 resolution of meiotic recombination intermediates GO:0000712 9.32 MSH4 HFM1
9 meiotic mismatch repair GO:0000710 9.16 MSH5 MSH4
10 reciprocal meiotic recombination GO:0007131 9.13 RAD51 MSH5 MSH4
11 meiotic cell cycle GO:0051321 8.92 RAD51 MSH5 MSH4 HFM1

Molecular functions related to Immunodeficiency 25 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 DNA binding GO:0003677 9.8 RAD51 POLR2J POLR2C POLI MSH5 MSH4
2 nucleotide binding GO:0000166 9.63 RRM1 RAD51 MSH5 MSH4 HFM1 EXOSC10
3 DNA-directed 5'-3' RNA polymerase activity GO:0003899 9.26 POLR2J POLR2C
4 mismatched DNA binding GO:0030983 8.96 MSH5 MSH4
5 DNA-dependent ATPase activity GO:0008094 8.8 RAD51 MSH5 MSH4

Sources for Immunodeficiency 25

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-Apr-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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