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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.


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severe combined immunodeficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ak2 adenylate kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19043416, PMID:19043417 NCBI chrNW_004936474:15,887,014...15,908,522 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 chrNW_004936542:3,400,129...3,403,628 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 chrNW_004936542:3,379,361...3,390,677 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 chrNW_004936613:1,467,797...1,501,107 JBrowse link
G Epo erythropoietin ISO Protein: decreased expression:skin RGD PMID:19826948 RGD:2313831 NCBI chrNW_004936543:742,722...745,332 JBrowse link
G Il2 interleukin 2 ISO mRNA:decreased_expression::no detectable IL2 mRNA RGD PMID:2342538 RGD:1600060 NCBI chrNW_004936662:1,594,953...1,599,625 JBrowse link
G Il2rg interleukin 2 receptor subunit gamma ISO X-linked SCID, OMIM:300400 RGD PMID:7557965 RGD:1600009 NCBI chrNW_004936762:487,414...491,028 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 Immune Deficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency
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 chrNW_004936518:5,815,820...5,842,571 JBrowse link
G Jak3 Janus kinase 3 treatment ISO 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 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 chrNW_004936596:3,212,593...3,224,426 JBrowse link
G LOC101971458 tyrosine-protein kinase ZAP-70 ISO selective T-cell defect, OMIM:176947
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
ClinVar Annotator: match by term: Severe Combined Immune Deficiency
CTD Direct Evidence: marker/mechanism
RGD
ClinVar
CTD
PMID:8124727, PMID:8202713 RGD:1599880 NCBI chrNW_004936744:1,000,105...1,012,712 JBrowse link
G LOC101972165 myosin-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 chrNW_004936722:967,443...991,530 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 chrNW_004936481:15,544,733...15,556,813 JBrowse link
G Prkdc protein kinase, DNA-activated, catalytic subunit ISO RGD PMID:9122213, PMID:22981234 RGD:1599202, RGD:8696027 NCBI chrNW_004936590:4,722,914...4,887,615 JBrowse link
G Ptprc protein tyrosine phosphatase receptor type C ISO DNA:deletion RGD PMID:11145714 RGD:1599983 NCBI chrNW_004936567:5,266,653...5,378,464 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 chrNW_004936492:3,726,375...3,737,961 JBrowse link
G Rag1 recombination activating 1 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
ClinVar Annotator: match by term: Severe combined immunodeficiency disease
missense mutations in both genes Omenn syndrome, OMIM:179615 , OMIM:179616
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 chrNW_004936533:1,817,135...1,827,393 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 chrNW_004936533:1,801,207...1,807,431 JBrowse link
G Rfx5 regulatory factor X5 ISO RGD PMID:7744245, PMID:9401005 RGD:1599742, RGD:1599743 NCBI chrNW_004936580:1,532,806...1,540,353 JBrowse link
G Rfxank regulatory factor X associated ankyrin containing protein ISO RGD PMID:12618906 RGD:1599746 NCBI chrNW_004936596:2,225,423...2,231,504 JBrowse link
G Tapbp TAP binding protein ISO type I bare lymphocyte syndrome, OMIM:604571 RGD PMID:12149238 RGD:1599296 NCBI chrNW_004936476:25,554,186...25,566,634 JBrowse link
G Tfrc transferrin receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:26642240 NCBI chrNW_004936784:696,738...728,385 JBrowse link
adenosine deaminase deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101972165 myosin-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 chrNW_004936722:967,443...991,530 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 chrNW_004936533:1,817,135...1,827,393 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 chrNW_004936533:1,746,762...1,805,191 JBrowse link
G Rag1 recombination activating 1 ISO OMIM NCBI chrNW_004936533:1,817,135...1,827,393 JBrowse link
G Rag2 recombination activating 2 ISO OMIM NCBI chrNW_004936533:1,801,207...1,807,431 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 chrNW_004936501:12,418,090...12,423,959 JBrowse link
G Coro1a coronin 1A ISO OMIM NCBI chrNW_004936501:12,338,542...12,344,236 JBrowse link
G Gdpd3 glycerophosphodiester phosphodiesterase domain containing 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chrNW_004936501:12,391,204...12,397,877 JBrowse link
G Mapk3 mitogen-activated protein kinase 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chrNW_004936501:12,342,670...12,390,650 JBrowse link
G Ppp4c protein phosphatase 4 catalytic subunit ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chrNW_004936501:12,407,968...12,416,057 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 chrNW_004936482:7,721,815...7,723,395 JBrowse link
G Tbx6 T-box transcription factor 6 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chrNW_004936501:12,402,709...12,407,571 JBrowse link
G Ypel3 yippee like 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chrNW_004936501:12,399,323...12,402,349 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 chrNW_004936498:849,775...1,063,552 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 chrNW_004936823:580,438...621,298 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 chrNW_004936785:358,128...406,751 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 chrNW_004936542:3,605,553...3,634,889 JBrowse link
G Atp5mg ATP synthase membrane subunit g ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,453,287...3,461,125 JBrowse link
G Bcl9l BCL9 like ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,873,530...3,902,871 JBrowse link
G Cd3d CD3d molecule ISO OMIM NCBI chrNW_004936542:3,400,129...3,403,628 JBrowse link
G Cd3e CD3e molecule ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,379,361...3,390,677 JBrowse link
G Cd3g CD3g molecule ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,405,084...3,412,104 JBrowse link
G Cenatac centrosomal AT-AC splicing factor ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,965,259...3,974,736 JBrowse link
G Cxcr5 C-X-C motif chemokine receptor 5 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,860,536...3,872,528 JBrowse link
G Ddx6 DEAD-box helicase 6 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,748,599...3,781,405 JBrowse link
G Dpagt1 dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:4,049,107...4,054,100 JBrowse link
G Foxr1 forkhead box R1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,943,174...3,951,473 JBrowse link
G Hmbs hydroxymethylbilane synthase ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:4,037,888...4,046,089 JBrowse link
G Hyou1 hypoxia up-regulated 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:4,005,616...4,018,135 JBrowse link
G Ift46 intraflagellar transport 46 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,577,387...3,597,954 JBrowse link
G Il10ra interleukin 10 receptor subunit alpha ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,099,484...3,113,159 JBrowse link
G Jaml junction adhesion molecule like ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,284,445...3,312,190 JBrowse link
G Kmt2a lysine methyltransferase 2A ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,480,071...3,566,823 JBrowse link
G LOC101966907 histone H2AX ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:4,046,930...4,049,017 JBrowse link
G Mpzl2 myelin protein zero like 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,332,822...3,344,663 JBrowse link
G Mpzl3 myelin protein zero like 3 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,314,921...3,332,785 JBrowse link
G Phldb1 pleckstrin homology like domain family B member 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,639,992...3,688,000 JBrowse link
G Rps25 ribosomal protein S25 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,974,796...3,977,155 JBrowse link
G Scn2b sodium voltage-gated channel beta subunit 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,262,161...3,274,545 JBrowse link
G Scn4b sodium voltage-gated channel beta subunit 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,236,238...3,252,550 JBrowse link
G Slc37a4 solute carrier family 37 member 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,980,538...3,987,039 JBrowse link
G Tmem25 transmembrane protein 25 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,569,735...3,575,987 JBrowse link
G Tmprss4 transmembrane serine protease 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,180,260...3,216,208 JBrowse link
G Trappc4 trafficking protein particle complex 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,977,223...3,980,168 JBrowse link
G Treh trehalase ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,688,086...3,702,067 JBrowse link
G Ttc36 tetratricopeptide repeat domain 36 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,567,469...3,571,393 JBrowse link
G Upk2 uroplakin 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:3,929,555...3,931,754 JBrowse link
G Vps11 VPS11 core subunit of CORVET and HOPS complexes ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chrNW_004936542:4,022,928...4,035,577 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 chrNW_004936474:15,293,115...15,314,072 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 chrNW_004936474:22,611,037...22,633,208 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 chrNW_004936590:4,722,914...4,887,615 JBrowse link
immunodeficiency 48 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101971458 tyrosine-protein kinase ZAP-70 ISO OMIM NCBI chrNW_004936744:1,000,105...1,012,712 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 chrNW_004936558:2,730,098...2,743,062 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 chrNW_004936675:1,448,381...1,479,735 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 chrNW_004936476:25,899,514...25,907,690 JBrowse link
G Tap2 transporter 2, ATP binding cassette subfamily B member ISO OMIM NCBI chrNW_004936476:25,913,699...25,923,419 JBrowse link
G Tapbp TAP binding protein ISO OMIM NCBI chrNW_004936476:25,554,186...25,566,634 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 chrNW_004936530:9,033,510...9,073,341 JBrowse link
G Nr2c2ap nuclear receptor 2C2 associated protein ISO ClinVar Annotator: match by term: MHC Class II Deficiency
ClinVar Annotator: match by term: Bare lymphocyte syndrome 2
ClinVar PMID:28492532 NCBI chrNW_004936596:2,223,907...2,225,434 JBrowse link
G Rfx5 regulatory factor X5 ISO OMIM NCBI chrNW_004936580:1,532,806...1,540,353 JBrowse link
G Rfxank regulatory factor X associated ankyrin containing protein ISO OMIM NCBI chrNW_004936596:2,225,423...2,231,504 JBrowse link
G Rfxap regulatory factor X associated protein ISO OMIM NCBI chrNW_004936472:30,959,399...30,964,863 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 chrNW_004936613:1,467,797...1,501,107 JBrowse link
G Rag1 recombination activating 1 ISO OMIM NCBI chrNW_004936533:1,817,135...1,827,393 JBrowse link
G Rag2 recombination activating 2 ISO OMIM NCBI chrNW_004936533:1,801,207...1,807,431 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 chrNW_004936533:1,801,207...1,807,431 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 chrNW_004936474:15,887,014...15,908,522 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 chrNW_004936569:1,494,783...1,578,587 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 chrNW_004936613:1,467,797...1,501,107 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 chrNW_004936472:3,861,833...3,867,943 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 chrNW_004936613:1,508,975...1,513,769 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 chrNW_004936613:1,443,663...1,467,776 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 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 chrNW_004936533:1,746,762...1,805,191 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 chrNW_004936596:3,212,593...3,224,426 JBrowse link
G Rag1 recombination activating 1 ISO OMIM NCBI chrNW_004936533:1,817,135...1,827,393 JBrowse link
G Rag2 recombination activating 2 ISO OMIM NCBI chrNW_004936533:1,801,207...1,807,431 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 chrNW_004936596:3,212,593...3,224,426 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 chrNW_004936542:3,400,129...3,403,628 JBrowse link
G Il7r interleukin 7 receptor ISO OMIM NCBI chrNW_004936518:5,815,820...5,842,571 JBrowse link
G Ptprc protein tyrosine phosphatase receptor type C ISO OMIM NCBI chrNW_004936567:5,266,653...5,378,464 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 chrNW_004936538:4,717,509...4,745,504 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 chrNW_004936514:7,686,760...7,784,948 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 chrNW_004936762:487,414...491,028 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 11940
    syndrome 5830
      primary immunodeficiency disease 1834
        combined immunodeficiency 131
          severe combined immunodeficiency 78
            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 2
            coronin-1A deficiency 8
            immunodeficiency 10 1
            immunodeficiency 11A 1
            immunodeficiency 15B 1
            immunodeficiency 19 32
            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 4
            severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive 3
Path 2
Term Annotations click to browse term
  disease 11940
    disease of anatomical entity 11502
      Immune & Inflammatory Diseases 2743
        immune system disease 2338
          primary immunodeficiency disease 1834
            combined immunodeficiency 131
              severe combined immunodeficiency 78
                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 2
                coronin-1A deficiency 8
                immunodeficiency 10 1
                immunodeficiency 11A 1
                immunodeficiency 15B 1
                immunodeficiency 19 32
                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 4
                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.