MCID: ALP042
MIFTS: 49

Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity malady

Categories: Genetic diseases, Blood diseases, Rare diseases, Immune diseases

Aliases & Classifications for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section
Sources:
12diseasecard, 27GTR, 31ICD10 via Orphanet, 37MedGen, 39MeSH, 52OMIM, 54Orphanet, 68UMLS, 70UniProtKB/Swiss-Prot
See all MalaCards sources

Aliases & Descriptions for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:

Name: Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity 52 12
Alpha/beta T-Cell Lymphopenia, with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection and Autoimmunity 70 27
Combined Immunodeficiency with Expansion of Gamma Delta T Cells 54
Combined Immunodeficiency Due to Partial Rag1 Deficiency 54
Cid with Expansion of Gamma Delta T Cells 54
 
Cid Due to Partial Rag1 Deficiency 54
Autoimmune Diseases 68
Autoimmune State 68
Autoimmunity 39
T-Cmva 70

Characteristics:

Orphanet epidemiological data:

54
combined immunodeficiency with expansion of gamma delta t cells:
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal; Age of death: early childhood

Classifications:



External Ids:

OMIM52 609889
Orphanet54 ORPHA231154
ICD10 via Orphanet31 D81.8
MedGen37 C1835931

Summaries for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section
UniProtKB/Swiss-Prot:70 Alpha/beta T-cell lymphopenia, with gamma/delta T-cell expansion, severe cytomegalovirus infection and autoimmunity: An immunological disorder characterized by oligoclonal expansion of TCR gamma/delta T-cells, TCR alpha/beta T-cell lymphopenia, severe, disseminated cytomegalovirus infection and autoimmune cytopenia.

MalaCards based summary: Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity, also known as alpha/beta t-cell lymphopenia, with gamma/delta t-cell expansion, severe cytomegalovirus infection and autoimmunity, is related to autoimmune myocarditis and hashimoto thyroiditis, and has symptoms including splenomegaly, severe combined immunodeficiency and cellular immunodeficiency. An important gene associated with Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity is RAG1 (Recombination Activating 1), and among its related pathways are Synaptic Neurotransmission Pathways: GABAergic Inhibition and Alanine and aspartate metabolism. The drugs methylprednisolone sodium succinate and prednisone have been mentioned in the context of this disorder. Affiliated tissues include t cells and neutrophil, and related mouse phenotypes are renal/urinary system and craniofacial.

Description from OMIM:52 609889

Related Diseases for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

Diseases related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50)    (show all 1185)
idRelated DiseaseScoreTop Affiliating Genes
1autoimmune myocarditis32.9FOXP3, IL17A
2hashimoto thyroiditis31.9CTLA4, IFNG, PTPN22, TG, TPO, TSHR
3addison's disease31.5IFNG, IL10
4autoimmune thyroid disease 431.0AIRE, FOXP3, IFNG, IL10, RAG1
5lupus erythematosus30.9IL10, INS
6systemic lupus erythematosus30.6CTLA4, IFNG, IL10, PTPN22, TNFSF13B
7goodpasture syndrome30.1CTLA4, HSPD1, IFNG, IL10, IL17A
8demyelinating polyneuropathy30.1TG, TSHR
9churg-strauss syndrome30.1FOXP3, IFNG, IL10, IL17A
10nodular goiter29.9TG, TPO
11rheumatoid arthritis29.6CTLA4, FOXP3, IFNG, IL10, IL17A, PTPN22
12multicentric castleman disease29.5IFNG, PTPN22, TNFSF13B
13multiple sclerosis, disease progression, modifier of29.4CTLA4, FOXP3, IFNG, IL10, IL17A, TNFSF13B
14hepatitis b29.2CTLA4, IFNG, IL10
15hemophagocytic lymphohistiocytosis29.0CTLA4, IFNG, IL10
16epididymo-orchitis28.8IL10, IL17A
17myelofibrosis28.8CTLA4, FOXP3, IL10, PTPN22
18atherosclerosis28.8CTLA4, IFNG, IL10, IL17A, PTPN22
19gastric ulcer28.7CTLA4, IFNG, IL10
20chronic rhinitis28.4IFNG, IL10, IL17A
21malaria27.7CTLA4, FOXP3, IFNG, IL10, IL17A
22autoimmune hepatitis12.3
23autoimmune lymphoproliferative syndrome12.3
24autoimmune polyendocrinopathy syndrome , type i, with or without reversible metaphyseal dysplasia12.3
25autoimmune polyendocrine syndrome, type ii12.3
26autoimmune polyendocrine syndrome12.2
27autoimmune hemolytic anemia12.2
28ras-associated autoimmune leukoproliferative disorder12.1
29autoimmune lymphoproliferative syndrome, type ii12.1
30autoimmune lymphoproliferative syndrome, type iii12.1
31vitiligo-associated multiple autoimmune disease susceptibility 112.0
32thrombocytopenic purpura, autoimmune12.0
33autoimmune pancreatitis12.0
34autoimmune hemolytic anemia, warm type12.0
35autoimmune lymphoproliferative syndrome, type v12.0
36drug-induced autoimmune hemolytic anemia12.0
37autoimmune encephalitis12.0
38autoimmune addison disease12.0
39autoimmune enteropathy12.0
40autoimmune disease 112.0
41autoimmune disease, multisystem, infantile-onset12.0
42autoimmune inner ear disease12.0
43immunodeficiency, common variable, 8, with autoimmunity11.9
44autoimmune progesterone dermatitis11.9
45t-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations11.9
46autoimmune lymphoproliferative syndrome, type iib11.9
47autoimmune neuropathy11.9
48autoimmune retinopathy11.9
49autoimmune interstitial lung, joint, and kidney disease11.9
50autoimmune autonomic ganglionopathy11.9

Graphical network of the top 20 diseases related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:



Diseases related to alpha/beta t-cell lymphopenia with gamma/delta t-cell expansion, severe cytomegalovirus infection, and autoimmunity

Symptoms & Phenotypes for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section


Clinical features from OMIM:

609889

Human phenotypes related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:

 64 54 (show all 13)
id Description HPO Frequency Orphanet Frequency HPO Source Accession
1 splenomegaly64 54 hallmark (90%) Very frequent (99-80%) HP:0001744
2 severe combined immunodeficiency64 54 hallmark (90%) Very frequent (99-80%) HP:0004430
3 cellular immunodeficiency64 hallmark (90%) HP:0005374
4 sepsis64 54 hallmark (90%) Very frequent (99-80%) HP:0100806
5 abnormality of neutrophils64 typical (50%) HP:0001874
6 hemolytic anemia64 typical (50%) HP:0001878
7 autoimmunity64 54 occasional (7.5%) Occasional (29-5%) HP:0002960
8 autoimmune hemolytic anemia54 Frequent (79-30%)
9 autoimmune neutropenia54 Frequent (79-30%)
10 immunodeficiency54 Very frequent (99-80%)
11 t lymphocytopenia54 Very frequent (99-80%)
12 interstitial pneumonitis54 Very frequent (99-80%)
13 b lymphocytopenia54 Very frequent (99-80%)

UMLS symptoms related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:


xerostomia due to autoimmune disease

MGI Mouse Phenotypes related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity according to GeneCards Suite gene sharing:

41 (show all 19)
idDescriptionMGI Source AccessionScoreTop Affiliating Genes
1MP:00053678.1FOXP3, IFNG, IL17A, INS, PTPN22, RAG1
2MP:00053827.9FOXP3, GAD1, GAD2, IFNG, IL10, IL17A
3MP:00053707.4AIRE, CTLA4, FOXP3, IFNG, IL10, INS
4MP:00053907.3CTLA4, GAD1, IFNG, IL10, IL17A, INS
5MP:00030127.2AIRE, FOXP3, GAD1, GAD2, IFNG, IL10
6MP:00053917.2AIRE, FOXP3, IFNG, IL10, INS, RAG1
7MP:00053887.0AIRE, CTLA4, FOXP3, GAD1, GAD2, IFNG
8MP:00053896.9AIRE, FOXP3, GAD2, HSPD1, IFNG, IL10
9MP:00028736.9AIRE, CTLA4, FOXP3, GAD1, GAD2, IFNG
10MP:00053846.7AIRE, FOXP3, GAD1, HSPD1, IFNG, IL10
11MP:00036316.3AIRE, GAD1, GAD2, HSPD1, IFNG, IL10
12MP:00053866.1AIRE, FOXP3, GAD1, GAD2, HSPD1, IFNG
13MP:00053815.8AIRE, CTLA4, FOXP3, GAD1, GAD2, IFNG
14MP:00053795.8AIRE, CTLA4, FOXP3, GAD1, GAD2, IFNG
15MP:00053875.7AIRE, CTLA4, FOXP3, GAD2, IFNG, IL10
16MP:00053975.6AIRE, CTLA4, FOXP3, IFNG, IL10, IL17A
17MP:00107685.1AIRE, CTLA4, FOXP3, GAD1, GAD2, HSPD1
18MP:00053765.1AIRE, CTLA4, FOXP3, GAD1, GAD2, IFNG
19MP:00053784.9AIRE, FOXP3, GAD1, GAD2, HSPD1, IFNG

Drugs & Therapeutics for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

Interventional clinical trials:

Search ClinicalTrials, NIH Clinical Center for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity

Inferred drug relations via UMLS68/NDF-RT46:


Cochrane evidence based reviews: autoimmunity

Genetic Tests for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

Genetic tests related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:

id Genetic test Affiliating Genes
1 Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity27

Anatomical Context for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

MalaCards organs/tissues related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:

36
T cells, Neutrophil

Publications for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

Variations for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

UniProtKB/Swiss-Prot genetic disease variations for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:

70
id Symbol AA change Variation ID SNP ID
1RAG1p.Arg841TrpVAR_025985rs104894287
2RAG1p.Gln981ProVAR_025988rs104894288

Clinvar genetic disease variations for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity:

5
id Gene Variation Type Significance SNP ID Assembly Location
1RAG1RAG1, 2-BP DEL, 368AAdeletionPathogenicChr na, -1: -1
2RAG1RAG1, 1-BP DEL, 631TdeletionPathogenicChr na, -1: -1
3RAG1NM_000448.2(RAG1): c.2521C> T (p.Arg841Trp)SNVPathogenicrs104894287GRCh37Chr 11, 36597375: 36597375
4RAG1NM_000448.2(RAG1): c.2942A> C (p.Gln981Pro)SNVPathogenicrs104894288GRCh37Chr 11, 36597796: 36597796

Expression for genes affiliated with Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section
Search GEO for disease gene expression data for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity.

Pathways for genes affiliated with Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

Pathways related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity according to GeneCards Suite gene sharing:

(show all 18)
idSuper pathwaysScoreTop Affiliating Genes
19.8GAD1, GAD2
2
Show member pathways
9.8GAD1, GAD2
39.8GAD1, GAD2
4
Show member pathways
9.8GAD1, GAD2
5
Show member pathways
9.8GAD1, GAD2
69.5TG, TPO, TSHR
7
Show member pathways
9.2CTLA4, FOXP3, IFNG
89.2CTLA4, IFNG, IL17A, TNFSF13B
9
Show member pathways
9.0INS, TG, TPO, TSHR
10
Show member pathways
8.9IFNG, IL10, IL17A
11
Show member pathways
8.9IFNG, IL10, IL17A
128.9IFNG, IL10, IL17A
13
Show member pathways
8.7CTLA4, IFNG, IL10, IL17A
14
Show member pathways
8.6FOXP3, IFNG, IL10
158.6FOXP3, IFNG, IL10
168.4CTLA4, FOXP3, IL10, TNFSF13B
177.5CTLA4, FOXP3, IFNG, IL10, PTPN22, RAG1
18
Show member pathways
5.1CTLA4, FOXP3, GAD1, GAD2, HSPD1, IFNG

GO Terms for genes affiliated with Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section

Cellular components related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity according to GeneCards Suite gene sharing:

idNameGO IDScoreTop Affiliating Genes
1clathrin-sculpted gamma-aminobutyric acid transport vesicle membraneGO:006120210.6GAD1, GAD2
2perinuclear region of cytoplasmGO:00484719.0CTLA4, GAD2, PTPN22, TG, TNFSF13B
3extracellular spaceGO:00056157.6HSPD1, IFNG, IL10, IL17A, INS, TG

Biological processes related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity according to GeneCards Suite gene sharing:

(show all 22)
idNameGO IDScoreTop Affiliating Genes
1hormone biosynthetic processGO:004244610.6TG, TPO
2glutamate decarboxylation to succinateGO:000654010.6GAD1, GAD2
3neurotransmitter biosynthetic processGO:004213610.5GAD1, GAD2
4positive regulation of interleukin-23 productionGO:003274710.4IFNG, IL17A
5positive regulation of osteoclast differentiationGO:004567210.4IFNG, IL17A
6positive regulation of interleukin-6 secretionGO:200077810.3HSPD1, IL17A
7negative regulation of immune responseGO:005077710.3CTLA4, FOXP3
8negative regulation of B cell proliferationGO:003088910.1CTLA4, IL10
9negative regulation of interleukin-17 productionGO:003270010.1FOXP3, IFNG
10thyroid hormone generationGO:00065909.9TG, TPO
11defense response to protozoanGO:00428329.9IFNG, IL10
12negative regulation of growth of symbiont in hostGO:00441309.9IFNG, IL10
13positive regulation of MHC class II biosynthetic processGO:00453489.9IFNG, IL10
14positive regulation of macrophage activationGO:00430329.8HSPD1, IL10
15B cell differentiationGO:00301839.8IL10, RAG1, TSHR
16negative regulation of T cell proliferationGO:00421309.5CTLA4, FOXP3, IL10
17negative regulation of tumor necrosis factor productionGO:00327209.5FOXP3, IL10, PTPN22
18positive regulation of gene expressionGO:00106289.3FOXP3, IFNG, INS, PTPN22
19cell-cell signalingGO:00072679.2IL10, IL17A, INS, TSHR
20immune responseGO:00069559.0AIRE, CTLA4, IL10, IL17A, RAG1, TNFSF13B
21response to lipopolysaccharideGO:00324968.8HSPD1, IL10, PTPN22, TG
22response to drugGO:00424938.6GAD1, GAD2, HSPD1, IFNG, IL10

Molecular functions related to Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity according to GeneCards Suite gene sharing:

idNameGO IDScoreTop Affiliating Genes
1glutamate bindingGO:00165959.9GAD1, GAD2
2glutamate decarboxylase activityGO:00043519.8GAD1, GAD2
3cytokine activityGO:00051258.8IFNG, IL10, IL17A, TNFSF13B

Sources for Alpha/beta T-Cell Lymphopenia with Gamma/delta T-Cell Expansion,...

About this section
2CDC
6CNVD
10DGIdb
15ExPASy
16FDA
17FMA
27GTR
28HGMD
29HMDB
30ICD10
31ICD10 via Orphanet
32ICD9CM
33IUPHAR
34KEGG
37MedGen
39MeSH
40MESH via Orphanet
41MGI
44NCI
45NCIt
46NDF-RT
49NINDS
50Novoseek
52OMIM
53OMIM via Orphanet
57PubMed
58QIAGEN
63SNOMED-CT via Orphanet
67Tumor Gene Family of Databases
68UMLS
69UMLS via Orphanet