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,...

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Sources:
12diseasecard, 26GTR, 30ICD10 via Orphanet, 36MedGen, 38MeSH, 51OMIM, 53Orphanet, 67UMLS, 69UniProtKB/Swiss-Prot
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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 51 12
Alpha/beta T-Cell Lymphopenia, with Gamma/delta T-Cell Expansion, Severe Cytomegalovirus Infection and Autoimmunity 69 26
Combined Immunodeficiency with Expansion of Gamma Delta T Cells 53
Combined Immunodeficiency Due to Partial Rag1 Deficiency 53
Cid with Expansion of Gamma Delta T Cells 53
 
Cid Due to Partial Rag1 Deficiency 53
Autoimmune Diseases 67
Autoimmune State 67
Autoimmunity 38
T-Cmva 69

Characteristics:

Orphanet epidemiological data:

53
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:

OMIM51 609889
Orphanet53 ORPHA231154
ICD10 via Orphanet30 D81.8
MedGen36 C1835931

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

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UniProtKB/Swiss-Prot:69 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:51 609889

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

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

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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:

 63 53 (show all 13)
id Description HPO Frequency Orphanet Frequency HPO Source Accession
1 splenomegaly63 53 hallmark (90%) Very frequent (99-80%) HP:0001744
2 severe combined immunodeficiency63 53 hallmark (90%) Very frequent (99-80%) HP:0004430
3 cellular immunodeficiency63 hallmark (90%) HP:0005374
4 sepsis63 53 hallmark (90%) Very frequent (99-80%) HP:0100806
5 abnormality of neutrophils63 typical (50%) HP:0001874
6 hemolytic anemia63 typical (50%) HP:0001878
7 autoimmunity63 53 occasional (7.5%) Occasional (29-5%) HP:0002960
8 autoimmune hemolytic anemia53 Frequent (79-30%)
9 autoimmune neutropenia53 Frequent (79-30%)
10 immunodeficiency53 Very frequent (99-80%)
11 t lymphocytopenia53 Very frequent (99-80%)
12 interstitial pneumonitis53 Very frequent (99-80%)
13 b lymphocytopenia53 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

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

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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 UMLS67/NDF-RT45:


Cochrane evidence based reviews: autoimmunity

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

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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 Autoimmunity26

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

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

35
T cells, Neutrophil

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

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

40 (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

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

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

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

69
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,...

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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,...

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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,...

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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:006120210.1GAD1, GAD2
2perinuclear region of cytoplasmGO:00484718.7CTLA4, GAD2, PTPN22, TG, TNFSF13B
3extracellular spaceGO:00056157.0HSPD1, 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
1glutamate decarboxylation to succinateGO:000654010.5GAD1, GAD2
2positive regulation of interleukin-6 secretionGO:200077810.3HSPD1, IL17A
3neurotransmitter biosynthetic processGO:004213610.3GAD1, GAD2
4positive regulation of osteoclast differentiationGO:004567210.3IFNG, IL17A
5positive regulation of interleukin-23 productionGO:003274710.3IFNG, IL17A
6hormone biosynthetic processGO:004244610.2TG, TPO
7thyroid hormone generationGO:000659010.2TG, TPO
8negative regulation of immune responseGO:005077710.1CTLA4, FOXP3
9negative regulation of interleukin-17 productionGO:003270010.0FOXP3, IFNG
10negative regulation of B cell proliferationGO:00308899.9CTLA4, IL10
11positive regulation of macrophage activationGO:00430329.8HSPD1, IL10
12positive regulation of MHC class II biosynthetic processGO:00453489.8IFNG, IL10
13defense response to protozoanGO:00428329.8IFNG, IL10
14negative regulation of growth of symbiont in hostGO:00441309.6IFNG, IL10
15B cell differentiationGO:00301839.5IL10, RAG1, TSHR
16negative regulation of tumor necrosis factor productionGO:00327209.3FOXP3, IL10, PTPN22
17negative regulation of T cell proliferationGO:00421309.1CTLA4, FOXP3, IL10
18response to lipopolysaccharideGO:00324968.9HSPD1, IL10, PTPN22, TG
19cell-cell signalingGO:00072678.7IL10, IL17A, INS, TSHR
20positive regulation of gene expressionGO:00106288.6FOXP3, IFNG, INS, PTPN22
21immune responseGO:00069558.5AIRE, CTLA4, IL10, IL17A, RAG1, TNFSF13B
22response to drugGO:00424938.0GAD1, 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 decarboxylase activityGO:000435110.4GAD1, GAD2
2glutamate bindingGO:001659510.2GAD1, GAD2
3cytokine activityGO:00051258.6IFNG, IL10, IL17A, TNFSF13B

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

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2CDC
6CNVD
10DGIdb
15ExPASy
16FDA
17FMA
26GTR
27HGMD
28HMDB
29ICD10
30ICD10 via Orphanet
31ICD9CM
32IUPHAR
33KEGG
36MedGen
38MeSH
39MESH via Orphanet
40MGI
43NCI
44NCIt
45NDF-RT
48NINDS
49Novoseek
51OMIM
52OMIM via Orphanet
56PubMed
57QIAGEN
62SNOMED-CT via Orphanet
66Tumor Gene Family of Databases
67UMLS
68UMLS via Orphanet