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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:severe combined immunodeficiency
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Accession:DOID:627 term browser browse the term
Definition:A combined T cell and B cell immunodeficiency that is caused by a defect in infection-fighting immune cells resulting in individuals with non-functional immune systems. (DO)
Synonyms:exact_synonym: Bare Lymphocyte Syndrome;   Familial Reticuloendothelioses;   Familial Reticuloendotheliosis;   SCID;   Severe Combined Immune Deficiency;   Severe Combined Immunodeficiencies;   Severe Combined Immunodeficiency Syndrome;   bare lymphocyte syndromes;   combined T and B cell inborn immunodeficiency;   severe combined immunodeficiency disease;   severe combined immunologic deficiency
 narrow_synonym: Severe combined immunodeficiency disease, autosomal
 primary_id: MESH:D016511
 alt_id: OMIA:000220
 xref: GARD:7628;   NCI:C3472
For additional species annotation, visit the Alliance of Genome Resources.


show annotations for term's descendants           Sort by:
 
severe combined immunodeficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADA adenosine deaminase ISO ClinVar Annotator: match by term: Severe Combined Immune Deficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency disease
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
RGD
ClinVar
PMID:498598, PMID:980079, PMID:1284479, PMID:2166947, PMID:2651461, PMID:2758612, PMID:2783588, PMID:3839802, PMID:6208479, PMID:7599635, PMID:8023852, PMID:8178821, PMID:8227344, PMID:8589684, PMID:8673127, PMID:9225964, PMID:9361033, PMID:9758612, PMID:9806422, PMID:14499267, PMID:16825284, PMID:18952502, PMID:19179314, PMID:19830125, PMID:21664875, PMID:21865538, PMID:22409989, PMID:22447032, PMID:22764473, PMID:22968453, PMID:24033266, PMID:25525159, PMID:25741868, PMID:25875700, PMID:26255240, PMID:26376800, PMID:27129325, PMID:28492532, PMID:29744787, PMID:30290665 RGD:1300353 NCBI chr24:32,083,786...32,119,810
Ensembl chr24:32,083,931...32,111,160
JBrowse link
G AK2 adenylate kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19043416, PMID:19043417 NCBI chr 2:68,342,769...68,371,769
Ensembl chr 2:68,350,057...68,371,090
JBrowse link
G CD3D CD3d molecule ISO ClinVar Annotator: match by term: Severe Combined Immune Deficiency
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
CTD Direct Evidence: marker/mechanism
RGD
ClinVar
CTD
PMID:14602880, PMID:15546002, PMID:28492532 RGD:1549420 NCBI chr 5:15,392,841...15,396,745
Ensembl chr 5:15,389,243...15,396,750
JBrowse link
G CD3E CD3e molecule ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
CTD
ClinVar
PMID:15546002, PMID:28492532 NCBI chr 5:15,403,724...15,415,259
Ensembl chr 5:15,403,710...15,415,260
JBrowse link
G DCLRE1C DNA cross-link repair 1C susceptibility ISO DNA:deletion:exon
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
RGD
ClinVar
PMID:11336668, PMID:24033266, PMID:25741868 RGD:1601049 NCBI chr 2:21,688,822...21,725,021
Ensembl chr 2:21,688,766...21,724,248
JBrowse link
G EPO erythropoietin ISO Protein: decreased expression:skin RGD PMID:19826948 RGD:2313831 NCBI chr 6:8,994,211...8,995,954
Ensembl chr 6:8,994,211...8,996,144
JBrowse link
G IL2 interleukin 2 ISO mRNA:decreased_expression::no detectable IL2 mRNA RGD PMID:2342538 RGD:1600060 NCBI chr19:17,750,780...17,756,394
Ensembl chr19:17,750,780...17,756,394
JBrowse link
G IL2RG interleukin 2 receptor subunit gamma ISO X-linked SCID, OMIM:300400 RGD PMID:7557965 RGD:1600009 NCBI chr  X:55,480,846...55,488,485
Ensembl chr  X:55,481,092...55,484,751
JBrowse link
G IL7R interleukin 7 receptor ISO autosomal recessive T cell(-), B cell(+), NK cell(+) severe combined immunodeficiency, OMIM:608971 DNA:point_mutation:CDS:C->T, amino acid T66I
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
ClinVar Annotator: match by term: Severe Combined Immune Deficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency disease
RGD
ClinVar
PMID:9843216, PMID:15661025, PMID:16492442, PMID:17827065, PMID:18255337, PMID:18403192, PMID:18641513, PMID:24759676, PMID:25741868, PMID:27833609, PMID:28492532 RGD:1600151 NCBI chr 4:72,633,528...72,668,242
Ensembl chr 4:72,636,325...72,668,300
JBrowse link
G JAK3 Janus kinase 3 treatment ISO ClinVar Annotator: match by term: Severe Combined Immune Deficiency
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency disease
CTD Direct Evidence: marker/mechanism
RGD
ClinVar
CTD
PMID:9354668, PMID:9427607, PMID:9753072, PMID:10900158, PMID:10982185, PMID:11213805, PMID:11668610, PMID:14615376, PMID:15220007, PMID:15661026, PMID:17433830, PMID:17644747, PMID:18559588, PMID:19203666, PMID:21184155, PMID:24033266, PMID:24728327, PMID:25146434, PMID:25741868, PMID:28492532 RGD:11531109 NCBI chr20:45,051,135...45,068,445
Ensembl chr20:45,050,526...45,072,805
JBrowse link
G MYH7 myosin heavy chain 7 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency disease ClinVar PMID:7581410, PMID:10521296, PMID:11186938, PMID:11447480, PMID:15358028, PMID:16858239, PMID:17125710, PMID:18029407, PMID:19880069, PMID:20031618, PMID:22857948, PMID:23233322, PMID:23283745, PMID:24033266, PMID:24093860, PMID:24111713, PMID:24793961, PMID:25031304, PMID:25351510, PMID:25637381, PMID:25741868, PMID:26743238, PMID:26969327, PMID:27247418, PMID:27532257, PMID:27737317, PMID:27831900, PMID:28138913, PMID:28420666, PMID:28492532, PMID:28615295, PMID:28790153 NCBI chr 8:3,660,155...3,677,650
Ensembl chr 8:3,629,585...3,792,725
JBrowse link
G MYOC myocilin ISO ClinVar Annotator: match by term: Severe combined immunodeficiency disease ClinVar PMID:9005853, PMID:9639450, PMID:10815160, PMID:11292420, PMID:11535458, PMID:11803488, PMID:11815346, PMID:12189160, PMID:12522550, PMID:12872267, PMID:17562996, PMID:17615537, PMID:19023451, PMID:20021252, PMID:22933836, PMID:23304066, PMID:24732711, PMID:25741868, PMID:30311386 NCBI chr 7:27,335,314...27,346,821
Ensembl chr 7:27,335,314...27,346,820
JBrowse link
G PRKDC protein kinase, DNA-activated, catalytic subunit IEA Severe combined immunodeficiency disease, autosomal OMIA PMID:11489998, PMID:11867233, PMID:12033674, PMID:19635917 NCBI chr29:24,904...243,926
Ensembl chr29:35,007...243,895
JBrowse link
G PTPRC protein tyrosine phosphatase receptor type C ISO DNA:deletion RGD PMID:11145714 RGD:1599983 NCBI chr 7:4,155,876...4,282,151
Ensembl chr 7:4,137,728...4,282,124
JBrowse link
G RAC2 Rac family small GTPase 2 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency disease ClinVar PMID:25741868, PMID:28492532, PMID:30723080 NCBI chr10:27,295,597...27,311,864
Ensembl chr10:27,295,640...27,311,397
JBrowse link
G RAG1 recombination activating 1 ISO missense mutations in both genes Omenn syndrome, OMIM:179615 , OMIM:179616
ClinVar Annotator: match by term: Severe Combined Immune Deficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency disease
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
RGD
ClinVar
PMID:8810255, PMID:9630231, PMID:11133745, PMID:11213808, PMID:11520796, PMID:11908269, PMID:11971977, PMID:17075247, PMID:17572155, PMID:18463379, PMID:18768869, PMID:20956421, PMID:21664875, PMID:23136839, PMID:24144642, PMID:24290284, PMID:24406074, PMID:25516070, PMID:25741868, PMID:25869295, PMID:26186701, PMID:26476733, PMID:26596586, PMID:27484032, PMID:28492532, PMID:30290665 RGD:1599402, RGD:1599403, RGD:7204131 NCBI chr18:31,628,231...31,639,980
Ensembl chr18:31,630,737...31,641,660
JBrowse link
G RAG2 recombination activating 2 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency disease
ClinVar Annotator: match by term: Severe Combined Immune Deficiency
RGD
ClinVar
PMID:8810255, PMID:15025726, PMID:20603253, PMID:21131235, PMID:24174341, PMID:24481607, PMID:25741868, PMID:26457731, PMID:26476733, PMID:26515615, PMID:28492532, PMID:28747913, PMID:28769923, PMID:29051008, PMID:29772310, PMID:30206106, PMID:30307608 RGD:1599402, RGD:38508903 NCBI chr18:31,614,143...31,621,489
Ensembl chr18:31,618,481...31,620,064
JBrowse link
G RFX5 regulatory factor X5 ISO RGD PMID:7744245, PMID:9401005 RGD:1599742, RGD:1599743 NCBI chr17:60,393,773...60,400,150
Ensembl chr17:60,395,321...60,400,009
JBrowse link
G RFXANK regulatory factor X associated ankyrin containing protein ISO RGD PMID:12618906 RGD:1599746 NCBI chr20:43,977,860...43,984,063
Ensembl chr20:43,977,867...43,983,273
JBrowse link
G TAPBP TAP binding protein ISO type I bare lymphocyte syndrome, OMIM:604571 RGD PMID:12149238 RGD:1599296 NCBI chr12:2,740,276...2,751,808
Ensembl chr12:2,740,276...2,751,808
JBrowse link
G TFRC transferrin receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:26642240 NCBI chr33:29,206,024...29,237,221
Ensembl chr33:29,208,609...29,238,242
JBrowse link
G ZAP70 zeta chain of T cell receptor associated protein kinase 70 ISO selective T-cell defect, OMIM:176947
ClinVar Annotator: match by term: Severe Combined Immune Deficiency
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
CTD Direct Evidence: marker/mechanism
RGD
ClinVar
CTD
PMID:8124727, PMID:8202713 RGD:1599880 NCBI chr10:44,887,416...44,913,845
Ensembl chr10:44,887,433...44,900,071
JBrowse link
adenosine deaminase deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADA adenosine deaminase ISO OMIM NCBI chr24:32,083,786...32,119,810
Ensembl chr24:32,083,931...32,111,160
JBrowse link
G MYH7 myosin heavy chain 7 ISO ClinVar Annotator: match by term: Bubble boy disease ClinVar PMID:7581410, PMID:10521296, PMID:11186938, PMID:11447480, PMID:15358028, PMID:16858239, PMID:17125710, PMID:18029407, PMID:19880069, PMID:20031618, PMID:22857948, PMID:23233322, PMID:23283745, PMID:24033266, PMID:24093860, PMID:24111713, PMID:24793961, PMID:25031304, PMID:25351510, PMID:25637381, PMID:25741868, PMID:26743238, PMID:26969327, PMID:27247418, PMID:27532257, PMID:27737317, PMID:27831900, PMID:28138913, PMID:28420666, PMID:28492532, PMID:28615295, PMID:28790153 NCBI chr 8:3,660,155...3,677,650
Ensembl chr 8:3,629,585...3,792,725
JBrowse link
G RAG1 recombination activating 1 ISO ClinVar Annotator: match by term: Bubble boy disease ClinVar PMID:11133745, PMID:21664875, PMID:24290284, PMID:24406074, PMID:26476733, PMID:26596586, PMID:28492532, PMID:30290665 NCBI chr18:31,628,231...31,639,980
Ensembl chr18:31,630,737...31,641,660
JBrowse link
Combined Cellular and Humoral Immune Defects with Granulomas term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G IFTAP intraflagellar transport associated protein ISO ClinVar Annotator: match by term: Combined cellular and humoral immune defects with granulomas ClinVar PMID:8810255, PMID:25739914, PMID:28492532 NCBI chr18:31,553,965...31,618,147
Ensembl chr18:31,556,023...31,618,123
JBrowse link
G RAG1 recombination activating 1 ISO OMIM NCBI chr18:31,628,231...31,639,980
Ensembl chr18:31,630,737...31,641,660
JBrowse link
G RAG2 recombination activating 2 ISO OMIM NCBI chr18:31,614,143...31,621,489
Ensembl chr18:31,618,481...31,620,064
JBrowse link
coronin-1A deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ALDOA aldolase, fructose-bisphosphate A ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 6:18,077,241...18,083,053 JBrowse link
G CORO1A coronin 1A ISO OMIM NCBI chr 6:18,161,850...18,167,915
Ensembl chr 6:18,160,601...18,167,818
JBrowse link
G GDPD3 glycerophosphodiester phosphodiesterase domain containing 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 6:18,103,273...18,108,818
Ensembl chr 6:18,103,267...18,108,533
JBrowse link
G MAPK3 mitogen-activated protein kinase 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 6:18,109,184...18,115,728
Ensembl chr 6:18,109,222...18,114,425
JBrowse link
G PPP4C protein phosphatase 4 catalytic subunit ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 6:18,085,048...18,092,861
Ensembl chr 6:18,085,116...18,092,854
JBrowse link
G RHOH ras homolog family member H ISO ClinVar Annotator: match by term: T-cell immunodeficiency with epidermodysplasia verruciformis ClinVar PMID:28492532 NCBI chr 3:72,272,446...72,277,015
Ensembl chr 3:72,276,418...72,276,993
JBrowse link
G TBX6 T-box transcription factor 6 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 6:18,093,201...18,098,592
Ensembl chr 6:18,093,189...18,097,636
JBrowse link
G YPEL3 yippee like 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 6:18,098,761...18,102,062
Ensembl chr 6:18,098,788...18,102,068
JBrowse link
immunodeficiency 10 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G STIM1 stromal interaction molecule 1 ISO OMIM NCBI chr21:26,394,592...26,594,764
Ensembl chr21:26,394,811...26,593,375
JBrowse link
immunodeficiency 11A term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CARD11 caspase recruitment domain family member 11 ISO OMIM NCBI chr 6:14,273,115...14,331,029
Ensembl chr 6:14,210,114...14,332,094
JBrowse link
immunodeficiency 15B term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G IKBKB inhibitor of nuclear factor kappa B kinase subunit beta ISO OMIM NCBI chr16:23,359,551...23,419,114
Ensembl chr16:23,359,813...23,419,075
JBrowse link
immunodeficiency 19 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ARCN1 archain 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,141,861...15,171,642
Ensembl chr 5:15,143,499...15,171,586
JBrowse link
G ATP5MG ATP synthase membrane subunit g ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,329,060...15,336,344 JBrowse link
G BCL9L BCL9 like ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,893,548...14,919,121
Ensembl chr 5:14,900,208...14,919,193
JBrowse link
G CD3D CD3d molecule ISO OMIM NCBI chr 5:15,392,841...15,396,745
Ensembl chr 5:15,389,243...15,396,750
JBrowse link
G CD3E CD3e molecule ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,403,724...15,415,259
Ensembl chr 5:15,403,710...15,415,260
JBrowse link
G CD3G CD3g molecule ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,379,788...15,391,271
Ensembl chr 5:15,380,633...15,391,214
JBrowse link
G CENATAC centrosomal AT-AC splicing factor ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,836,293...14,843,731
Ensembl chr 5:14,836,291...14,843,875
JBrowse link
G CXCR5 C-X-C motif chemokine receptor 5 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,921,447...14,932,937
Ensembl chr 5:14,923,089...14,932,762
JBrowse link
G DDX6 DEAD-box helicase 6 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,001,988...15,034,128
Ensembl chr 5:15,002,246...15,032,348
JBrowse link
G DPAGT1 dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,760,518...14,765,306
Ensembl chr 5:14,760,784...14,764,967
JBrowse link
G FOXR1 forkhead box R1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,852,381...14,861,364
Ensembl chr 5:14,852,205...14,861,728
JBrowse link
G H2AX H2A.X variant histone ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,765,625...14,766,590
Ensembl chr 5:14,766,126...14,766,557
JBrowse link
G HMBS hydroxymethylbilane synthase ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,767,306...14,775,205
Ensembl chr 5:14,767,666...14,775,082
JBrowse link
G HYOU1 hypoxia up-regulated 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,795,750...14,808,203
Ensembl chr 5:14,795,750...14,807,262
JBrowse link
G IFT46 intraflagellar transport 46 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,179,287...15,197,737
Ensembl chr 5:15,170,854...15,197,736
JBrowse link
G IL10RA interleukin 10 receptor subunit alpha ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,675,775...15,688,935
Ensembl chr 5:15,677,547...15,682,163
JBrowse link
G JAML junction adhesion molecule like ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,485,378...15,513,457
Ensembl chr 5:15,476,582...15,513,075
JBrowse link
G KMT2A lysine methyltransferase 2A ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,212,559...15,302,825
Ensembl chr 5:15,217,348...15,270,971
JBrowse link
G MPZL2 myelin protein zero like 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,446,803...15,458,667
Ensembl chr 5:15,447,104...15,458,515
JBrowse link
G MPZL3 myelin protein zero like 3 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,460,147...15,485,274
Ensembl chr 5:15,460,211...15,484,202
JBrowse link
G PHLDB1 pleckstrin homology like domain family B member 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,090,823...15,138,397
Ensembl chr 5:15,090,813...15,134,784
JBrowse link
G RPS25 ribosomal protein S25 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,833,804...14,836,376
Ensembl chr 5:14,833,918...14,836,749
JBrowse link
G SCN2B sodium voltage-gated channel beta subunit 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,514,760...15,534,179
Ensembl chr 5:15,521,481...15,534,179
JBrowse link
G SCN4B sodium voltage-gated channel beta subunit 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,552,347...15,564,085
Ensembl chr 5:15,543,632...15,563,486
JBrowse link
G SLC37A4 solute carrier family 37 member 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,823,485...14,830,007
Ensembl chr 5:14,823,499...14,830,004
JBrowse link
G TMEM25 transmembrane protein 25 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,202,726...15,207,252
Ensembl chr 5:15,203,974...15,206,704
JBrowse link
G TMPRSS4 transmembrane serine protease 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,575,068...15,609,819
Ensembl chr 5:15,575,338...15,610,190
JBrowse link
G TRAPPC4 trafficking protein particle complex 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,830,604...14,833,444
Ensembl chr 5:14,830,611...14,833,447
JBrowse link
G TREH trehalase ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,085,038...15,090,667
Ensembl chr 5:15,071,802...15,090,522
JBrowse link
G TTC36 tetratricopeptide repeat domain 36 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,207,400...15,211,905
Ensembl chr 5:15,207,403...15,211,853
JBrowse link
G UBE4A ubiquitination factor E4A ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:15,338,279...15,375,722
Ensembl chr 5:15,341,141...15,370,294
JBrowse link
G UPK2 uroplakin 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,868,064...14,872,527
Ensembl chr 5:14,868,051...14,871,153
JBrowse link
G VPS11 VPS11 core subunit of CORVET and HOPS complexes ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 5:14,776,975...14,786,736
Ensembl chr 5:14,776,976...14,786,692
JBrowse link
immunodeficiency 22 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LCK LCK proto-oncogene, Src family tyrosine kinase ISO OMIM NCBI chr 2:68,940,816...68,964,585
Ensembl chr 2:68,941,249...68,964,567
JBrowse link
immunodeficiency 24 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CTPS1 CTP synthase 1 ISO OMIM NCBI chr15:2,067,767...2,093,014
Ensembl chr15:2,067,763...2,093,014
JBrowse link
immunodeficiency 26 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G PRKDC protein kinase, DNA-activated, catalytic subunit ISO OMIM NCBI chr29:24,904...243,926
Ensembl chr29:35,007...243,895
JBrowse link
immunodeficiency 48 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ZAP70 zeta chain of T cell receptor associated protein kinase 70 ISO OMIM NCBI chr10:44,887,416...44,913,845
Ensembl chr10:44,887,433...44,900,071
JBrowse link
immunodeficiency 9 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ORAI1 ORAI calcium release-activated calcium modulator 1 ISO OMIM NCBI chr26:7,584,276...7,599,667
Ensembl chr26:7,584,880...7,599,401
JBrowse link
Immunoskeletal Dysplasia with Neurodevelopmental Abnormalities term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G EXTL3 exostosin like glycosyltransferase 3 ISO OMIM NCBI chr25:28,788,803...28,833,964
Ensembl chr25:28,790,506...28,937,647
JBrowse link
MHC class I deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G TAP1 transporter 1, ATP binding cassette subfamily B member ISO OMIM NCBI chr12:2,424,049...2,432,165
Ensembl chr12:2,378,126...2,432,303
JBrowse link
G TAP2 transporter 2, ATP binding cassette subfamily B member ISO OMIM NCBI chr12:2,407,512...2,417,469
Ensembl chr12:2,378,126...2,432,303
JBrowse link
G TAPBP TAP binding protein ISO OMIM NCBI chr12:2,740,276...2,751,808
Ensembl chr12:2,740,276...2,751,808
JBrowse link
MHC class II deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CIITA class II major histocompatibility complex transactivator severity ISO DNA:mutation:CDS:c.1524T>C, p.L469P associated with mild or asymptomatic disease despite absence of MHC-II expression on immune cells OMIM
RGD
PMID:11466404 RGD:5491200 NCBI chr 6:31,774,486...31,837,025
Ensembl chr 6:31,774,609...31,836,820
JBrowse link
G NR2C2AP nuclear receptor 2C2 associated protein ISO ClinVar Annotator: match by term: Bare lymphocyte syndrome 2
ClinVar Annotator: match by term: MHC Class II Deficiency
ClinVar PMID:28492532 NCBI chr20:43,976,373...43,978,410
Ensembl chr20:43,976,665...43,977,823
JBrowse link
G RFX5 regulatory factor X5 ISO OMIM NCBI chr17:60,393,773...60,400,150
Ensembl chr17:60,395,321...60,400,009
JBrowse link
G RFXANK regulatory factor X associated ankyrin containing protein ISO OMIM NCBI chr20:43,977,860...43,984,063
Ensembl chr20:43,977,867...43,983,273
JBrowse link
G RFXAP regulatory factor X associated protein ISO OMIM NCBI chr25:3,861,927...3,871,854
Ensembl chr25:3,862,069...3,870,994
JBrowse link
Omenn syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G DCLRE1C DNA cross-link repair 1C ISO OMIM NCBI chr 2:21,688,822...21,725,021
Ensembl chr 2:21,688,766...21,724,248
JBrowse link
G RAG1 recombination activating 1 ISO OMIM NCBI chr18:31,628,231...31,639,980
Ensembl chr18:31,630,737...31,641,660
JBrowse link
G RAG2 recombination activating 2 ISO OMIM NCBI chr18:31,614,143...31,621,489
Ensembl chr18:31,618,481...31,620,064
JBrowse link
recombinase activating gene 2 deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G RAG2 recombination activating 2 ISO ClinVar Annotator: match by term: RAG2 deficiency
ClinVar Annotator: match by term: Recombinase activating gene 2 deficiency
ClinVar PMID:25741868, PMID:28492532, PMID:29772310 NCBI chr18:31,614,143...31,621,489
Ensembl chr18:31,618,481...31,620,064
JBrowse link
reticular dysgenesis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AK2 adenylate kinase 2 ISO OMIM NCBI chr 2:68,342,769...68,371,769
Ensembl chr 2:68,350,057...68,371,090
JBrowse link
Severe Combined Immunodeficiency with Microcephaly, Growth Retardation, and Sensitivity to Ionizing Radiation term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G NHEJ1 non-homologous end joining factor 1 ISO OMIM NCBI chr37:25,637,214...25,719,241
Ensembl chr37:25,637,601...25,715,372
JBrowse link
severe combined immunodeficiency with sensitivity to ionizing radiation term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G DCLRE1C DNA cross-link repair 1C ISO OMIM NCBI chr 2:21,688,822...21,725,021
Ensembl chr 2:21,688,766...21,724,248
JBrowse link
G LIG4 DNA ligase 4 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency with sensitivity to ionizing radiation
ClinVar Annotator: match by term: Severe combined immunodeficiency due to DCLRE1C deficiency
ClinVar PMID:12471202, PMID:24033266, PMID:25741868, PMID:28492532 NCBI chr22:56,980,333...56,987,636
Ensembl chr22:56,980,622...56,983,357
JBrowse link
G MEIG1 meiosis/spermiogenesis associated 1 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency with sensitivity to ionizing radiation ClinVar PMID:19912631, PMID:28492532 NCBI chr 2:21,675,003...21,684,020
Ensembl chr 2:21,675,012...21,679,456
JBrowse link
G SUV39H2 suppressor of variegation 3-9 homolog 2 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency due to DCLRE1C deficiency ClinVar PMID:28492532 NCBI chr 2:21,715,677...21,749,732
Ensembl chr 2:21,728,964...21,749,597
JBrowse link
severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADA adenosine deaminase ISO ClinVar Annotator: match by term: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive ClinVar PMID:1346349, PMID:2651461, PMID:2773932, PMID:3182793, PMID:3475710, PMID:8401541, PMID:8614422, PMID:9758612, PMID:25326637, PMID:25741868, PMID:26376800, PMID:28492532 NCBI chr24:32,083,786...32,119,810
Ensembl chr24:32,083,931...32,111,160
JBrowse link
G IFTAP intraflagellar transport associated protein ISO ClinVar Annotator: match by term: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive ClinVar NCBI chr18:31,553,965...31,618,147
Ensembl chr18:31,556,023...31,618,123
JBrowse link
G JAK3 Janus kinase 3 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-negative
ClinVar Annotator: match by term: Severe immunodeficiency, autosomal recessive, T-cell negative, B-cell negative, NK cell-positive
ClinVar Annotator: match by term: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive
ClinVar PMID:7481768, PMID:7659163, PMID:10982185, PMID:11668610, PMID:11668621, PMID:11741532, PMID:11781709, PMID:16843266, PMID:17644747, PMID:18270328, PMID:18397343, PMID:19203666, PMID:19282076, PMID:20132407, PMID:20372971, PMID:20400977, PMID:20417861, PMID:21050946, PMID:21599579, PMID:21821710, PMID:21868263, PMID:24033266, PMID:24728327, PMID:25146434, PMID:25157968, PMID:25193870, PMID:25395141, PMID:25505553, PMID:25672756, PMID:25741868, PMID:25815310, PMID:26915675, PMID:28492532, PMID:28747913, PMID:29375547 NCBI chr20:45,051,135...45,068,445
Ensembl chr20:45,050,526...45,072,805
JBrowse link
G RAG1 recombination activating 1 ISO
IEA
Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive OMIM
OMIA
PMID:24799706, PMID:24973446, PMID:25437445 NCBI chr18:31,628,231...31,639,980
Ensembl chr18:31,630,737...31,641,660
JBrowse link
G RAG2 recombination activating 2 ISO OMIM NCBI chr18:31,614,143...31,621,489
Ensembl chr18:31,618,481...31,620,064
JBrowse link
Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, NK Cell-Negative term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G JAK3 Janus kinase 3 ISO OMIM NCBI chr20:45,051,135...45,068,445
Ensembl chr20:45,050,526...45,072,805
JBrowse link
severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CD3D CD3d molecule ISO ClinVar Annotator: match by term: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive ClinVar NCBI chr 5:15,392,841...15,396,745
Ensembl chr 5:15,389,243...15,396,750
JBrowse link
G IL7R interleukin 7 receptor ISO OMIM NCBI chr 4:72,633,528...72,668,242
Ensembl chr 4:72,636,325...72,668,300
JBrowse link
G PTPRC protein tyrosine phosphatase receptor type C ISO OMIM NCBI chr 7:4,155,876...4,282,151
Ensembl chr 7:4,137,728...4,282,124
JBrowse link
T-cell immunodeficiency, congenital alopecia, and nail dystrophy term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G FOXN1 forkhead box N1 ISO OMIM NCBI chr 9:42,734,228...42,749,856
Ensembl chr 9:42,735,656...42,748,632
JBrowse link
T-Cell Immunodeficiency, Recurrent Infections, and Autoimmunity with or without Cardiac Malformations term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G STK4 serine/threonine kinase 4 ISO OMIM NCBI chr24:32,375,630...32,463,848
Ensembl chr24:32,375,189...32,521,042
JBrowse link
X-linked severe combined immunodeficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G IL2RG interleukin 2 receptor subunit gamma ISO OMIM NCBI chr  X:55,480,846...55,488,485
Ensembl chr  X:55,481,092...55,484,751
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 12675
    syndrome 6127
      primary immunodeficiency disease 1913
        combined immunodeficiency 132
          severe combined immunodeficiency 80
            CD3delta deficiency 0
            CD3epsilon deficiency 0
            CD3gamma deficiency 0
            CD3zeta deficiency 0
            CD45 deficiency 0
            Combined Cellular and Humoral Immune Defects with Granulomas 3
            HLA Class 1 Deficiency 0
            Immunoskeletal Dysplasia with Neurodevelopmental Abnormalities 1
            MHC class I deficiency 3
            MHC class II deficiency 5
            Omenn syndrome 3
            Reticuloendotheliosis, X-Linked 0
            Severe Combined Immunodeficiency with Microcephaly, Growth Retardation, and Sensitivity to Ionizing Radiation 1
            Severe Combined Immunodeficiency, Atypical 0
            Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, NK Cell-Negative 1
            Short-Limb Skeletal Dysplasia with Severe Combined Immunodeficiency 0
            T-Cell Immunodeficiency, Recurrent Infections, and Autoimmunity with or without Cardiac Malformations 1
            T-cell immunodeficiency, congenital alopecia, and nail dystrophy 1
            X-linked severe combined immunodeficiency 1
            adenosine deaminase deficiency 3
            coronin-1A deficiency 8
            immunodeficiency 10 1
            immunodeficiency 11A 1
            immunodeficiency 15B 1
            immunodeficiency 19 33
            immunodeficiency 22 1
            immunodeficiency 24 1
            immunodeficiency 26 1
            immunodeficiency 48 1
            immunodeficiency 9 1
            interleukin-7 receptor alpha deficiency 0
            janus kinase-3 deficiency 0
            recombinase activating gene 1 deficiency 0
            recombinase activating gene 2 deficiency 1
            reticular dysgenesis 1
            severe combined immunodeficiency with sensitivity to ionizing radiation 4
            severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 5
            severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive 3
Path 2
Term Annotations click to browse term
  disease 12675
    disease of anatomical entity 12213
      Immune & Inflammatory Diseases 2906
        immune system disease 2442
          primary immunodeficiency disease 1913
            combined immunodeficiency 132
              severe combined immunodeficiency 80
                CD3delta deficiency 0
                CD3epsilon deficiency 0
                CD3gamma deficiency 0
                CD3zeta deficiency 0
                CD45 deficiency 0
                Combined Cellular and Humoral Immune Defects with Granulomas 3
                HLA Class 1 Deficiency 0
                Immunoskeletal Dysplasia with Neurodevelopmental Abnormalities 1
                MHC class I deficiency 3
                MHC class II deficiency 5
                Omenn syndrome 3
                Reticuloendotheliosis, X-Linked 0
                Severe Combined Immunodeficiency with Microcephaly, Growth Retardation, and Sensitivity to Ionizing Radiation 1
                Severe Combined Immunodeficiency, Atypical 0
                Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, NK Cell-Negative 1
                Short-Limb Skeletal Dysplasia with Severe Combined Immunodeficiency 0
                T-Cell Immunodeficiency, Recurrent Infections, and Autoimmunity with or without Cardiac Malformations 1
                T-cell immunodeficiency, congenital alopecia, and nail dystrophy 1
                X-linked severe combined immunodeficiency 1
                adenosine deaminase deficiency 3
                coronin-1A deficiency 8
                immunodeficiency 10 1
                immunodeficiency 11A 1
                immunodeficiency 15B 1
                immunodeficiency 19 33
                immunodeficiency 22 1
                immunodeficiency 24 1
                immunodeficiency 26 1
                immunodeficiency 48 1
                immunodeficiency 9 1
                interleukin-7 receptor alpha deficiency 0
                janus kinase-3 deficiency 0
                recombinase activating gene 1 deficiency 0
                recombinase activating gene 2 deficiency 1
                reticular dysgenesis 1
                severe combined immunodeficiency with sensitivity to ionizing radiation 4
                severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 5
                severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive 3
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.