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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 chr17:47,044,492...47,072,232
Ensembl chr17:47,044,495...47,072,245
JBrowse link
G AK2 adenylate kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19043416, PMID:19043417 NCBI chr 6:89,295,164...89,318,169 JBrowse link
G CD3D CD3d molecule ISO 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:14602880, PMID:15546002, PMID:28492532 RGD:1549420 NCBI chr 9:45,640,475...45,644,153
Ensembl chr 9:45,637,129...45,644,221
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 9:45,619,730...45,633,972
Ensembl chr 9:45,619,481...45,635,379
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 chr10:46,820,016...46,863,848
Ensembl chr10:46,820,051...46,868,030
JBrowse link
G EPO erythropoietin ISO Protein: decreased expression:skin RGD PMID:19826948 RGD:2313831 NCBI chr 3:8,620,508...8,622,936
Ensembl chr 3:8,620,508...8,622,936
JBrowse link
G IL2 interleukin 2 ISO mRNA:decreased_expression::no detectable IL2 mRNA RGD PMID:2342538 RGD:1600060 NCBI chr 8:101,640,938...101,645,683
Ensembl chr 8:101,640,944...101,645,609
JBrowse link
G IL2RG interleukin 2 receptor subunit gamma ISO X-linked SCID, OMIM:300400 RGD PMID:7557965 RGD:1600009 NCBI chr  X:57,143,568...57,151,242 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 Immunodeficiency
ClinVar Annotator: match by term: Severe Combined Immune Deficiency
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 chr16:21,300,141...21,330,156
Ensembl chr16:21,300,111...21,329,585
JBrowse link
G JAK3 Janus kinase 3 treatment ISO CTD Direct Evidence: marker/mechanism
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
CTD
ClinVar
RGD
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 chr 2:59,905,901...59,926,504
Ensembl chr 2:59,905,919...59,926,495
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 7:75,650,841...75,672,908
Ensembl chr 7:75,650,445...75,709,232
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 9:114,087,370...114,098,765
Ensembl chr 9:114,087,374...114,098,743
JBrowse link
G PRKDC protein kinase, DNA-activated, catalytic subunit ISO RGD PMID:9122213, PMID:22981234 RGD:1599202, RGD:8696027 NCBI chr 4:79,687,375...79,850,146
Ensembl chr 4:79,687,359...79,847,281
JBrowse link
G PTPRC protein tyrosine phosphatase receptor type C ISO DNA:deletion RGD PMID:11145714 RGD:1599983 NCBI chr10:21,482,984...21,601,627
Ensembl chr10:21,466,373...21,764,560
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 chr 5:10,553,986...10,571,082
Ensembl chr 5:10,553,433...10,573,017
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 disease
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
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 chr 2:24,565,447...24,573,853
Ensembl chr 2:24,565,449...24,602,590
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 chr 2:24,547,605...24,553,944
Ensembl chr 2:24,546,958...24,558,430
JBrowse link
G RFX5 regulatory factor X5 ISO RGD PMID:7744245, PMID:9401005 RGD:1599742, RGD:1599743 NCBI chr 4:97,901,955...97,913,283
Ensembl chr 4:97,888,460...97,913,283
JBrowse link
G RFXANK regulatory factor X associated ankyrin containing protein ISO RGD PMID:12618906 RGD:1599746 NCBI chr 2:58,677,534...58,684,016
Ensembl chr 2:58,677,534...58,683,882
JBrowse link
G TAPBP TAP binding protein ISO type I bare lymphocyte syndrome, OMIM:604571 RGD PMID:12149238 RGD:1599296 NCBI chr 7:29,663,491...29,673,453
Ensembl chr 7:29,663,446...29,676,335
JBrowse link
G TFRC transferrin receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:26642240 NCBI chr13:133,976,765...133,997,554
Ensembl chr13:133,970,594...134,000,278
JBrowse link
G ZAP70 zeta chain of T cell receptor associated protein kinase 70 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Severe Combined Immune Deficiency
ClinVar Annotator: match by term: Severe Combined Immunodeficiency
selective T-cell defect, OMIM:176947
CTD
ClinVar
RGD
PMID:8124727, PMID:8202713 RGD:1599880 NCBI chr 3:56,515,446...56,541,806
Ensembl chr 3:56,515,449...56,541,740
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 chr17:47,044,492...47,072,232
Ensembl chr17:47,044,495...47,072,245
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 7:75,650,841...75,672,908
Ensembl chr 7:75,650,445...75,709,232
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 chr 2:24,565,447...24,573,853
Ensembl chr 2:24,565,449...24,602,590
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 chr 2:24,477,084...24,551,690
Ensembl chr 2:24,477,172...24,551,670
JBrowse link
G RAG1 recombination activating 1 ISO OMIM NCBI chr 2:24,565,447...24,573,853
Ensembl chr 2:24,565,449...24,602,590
JBrowse link
G RAG2 recombination activating 2 ISO OMIM NCBI chr 2:24,547,605...24,553,944
Ensembl chr 2:24,546,958...24,558,430
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 3:18,246,036...18,260,167 JBrowse link
G CORO1A coronin 1A ISO OMIM NCBI chr 3:18,336,813...18,342,381
Ensembl chr 3:18,336,899...18,342,380
JBrowse link
G GDPD3 glycerophosphodiester phosphodiesterase domain containing 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 3:18,282,574...18,291,307
Ensembl chr 3:18,282,889...18,294,196
JBrowse link
G MAPK3 mitogen-activated protein kinase 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 3:18,291,444...18,299,410
Ensembl chr 3:18,291,445...18,299,567
JBrowse link
G PPP4C protein phosphatase 4 catalytic subunit ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 3:18,262,817...18,271,588
Ensembl chr 3:18,262,823...18,271,586
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 8:31,321,005...31,372,366
Ensembl chr 8:31,321,113...31,372,364
JBrowse link
G TBX6 T-box transcription factor 6 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 3:18,271,983...18,277,864
Ensembl chr 3:18,271,984...18,277,573
JBrowse link
G YPEL3 yippee like 3 ISO ClinVar Annotator: match by term: Immunodeficiency 8 ClinVar PMID:18836449, PMID:28492532 NCBI chr 3:18,277,999...18,281,342
Ensembl chr 3:18,277,999...18,281,298
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 chr 9:6,066,612...6,270,090
Ensembl chr 9:6,066,617...6,270,575
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 3:2,145,178...2,266,377
Ensembl chr 3:2,145,177...2,266,356
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 chr17:11,289,607...11,348,557
Ensembl chr17:11,289,690...11,348,553
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 9:45,863,772...45,897,525
Ensembl chr 9:45,863,559...45,897,514
JBrowse link
G ATP5MG ATP synthase membrane subunit g ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,706,449...45,716,541
Ensembl chr 9:45,661,106...45,720,783
JBrowse link
G BCL9L BCL9 like ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,146,519...46,175,052
Ensembl chr 9:46,146,514...46,174,589
JBrowse link
G CD3D CD3d molecule ISO OMIM NCBI chr 9:45,640,475...45,644,153
Ensembl chr 9:45,637,129...45,644,221
JBrowse link
G CD3E CD3e molecule ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,619,730...45,633,972
Ensembl chr 9:45,619,481...45,635,379
JBrowse link
G CD3G CD3g molecule ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,645,243...45,656,779
Ensembl chr 9:45,645,364...45,704,745
JBrowse link
G CENATAC centrosomal AT-AC splicing factor ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,230,365...46,239,433
Ensembl chr 9:46,229,729...46,239,433
JBrowse link
G CXCR5 C-X-C motif chemokine receptor 5 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,134,243...46,146,638
Ensembl chr 9:46,127,488...46,146,637
JBrowse link
G DDX6 DEAD-box helicase 6 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,025,616...46,063,836
Ensembl chr 9:46,025,445...46,063,814
JBrowse link
G DPAGT1 dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,308,824...46,316,905
Ensembl chr 9:46,310,870...46,316,848
JBrowse link
G FOXR1 forkhead box R1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,208,750...46,220,076
Ensembl chr 9:46,208,963...46,220,073
JBrowse link
G HMBS hydroxymethylbilane synthase ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,300,039...46,308,681
Ensembl chr 9:46,300,050...46,313,936
JBrowse link
G HYOU1 hypoxia up-regulated 1 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,264,929...46,277,056
Ensembl chr 9:46,264,929...46,276,996
JBrowse link
G IFT46 intraflagellar transport 46 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,844,636...45,861,918
Ensembl chr 9:45,844,619...45,861,870
JBrowse link
G IL10RA interleukin 10 receptor subunit alpha ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,310,527...45,324,557
Ensembl chr 9:45,310,553...45,389,323
JBrowse link
G JAML junction adhesion molecule like ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,506,496...45,537,304
Ensembl chr 9:45,484,999...45,534,863
JBrowse link
G KMT2A lysine methyltransferase 2A ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,743,566...45,828,559 JBrowse link
G LOC100522201 histone H2AX ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,308,824...46,310,494
Ensembl chr 9:46,309,653...46,310,084
JBrowse link
G MPZL2 myelin protein zero like 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,566,365...45,578,168
Ensembl chr 9:45,565,511...45,578,185
JBrowse link
G MPZL3 myelin protein zero like 3 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,536,024...45,564,210
Ensembl chr 9:45,536,026...45,564,195
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 9:45,902,099...45,949,415
Ensembl chr 9:45,902,105...45,949,417
JBrowse link
G RPS25 ribosomal protein S25 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,237,911...46,242,174
Ensembl chr 9:46,235,727...46,242,432
JBrowse link
G SCN2B sodium voltage-gated channel beta subunit 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,484,994...45,502,578
Ensembl chr 9:45,484,998...45,498,465
JBrowse link
G SCN4B sodium voltage-gated channel beta subunit 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,451,473...45,475,606 JBrowse link
G SLC37A4 solute carrier family 37 member 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,247,278...46,254,068
Ensembl chr 9:46,247,282...46,254,017
JBrowse link
G TMEM25 transmembrane protein 25 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,834,197...45,838,978
Ensembl chr 9:45,829,176...45,838,975
JBrowse link
G TMPRSS4 transmembrane serine protease 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,400,263...45,436,936
Ensembl chr 9:45,400,464...45,435,916
JBrowse link
G TRAPPC4 trafficking protein particle complex 4 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,242,196...46,246,344
Ensembl chr 9:46,242,170...46,246,344
JBrowse link
G TREH trehalase ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,949,891...45,965,372
Ensembl chr 9:45,949,894...45,965,341
JBrowse link
G TTC36 tetratricopeptide repeat domain 36 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,829,014...45,838,978
Ensembl chr 9:45,829,191...45,838,979
JBrowse link
G UBE4A ubiquitination factor E4A ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:45,661,090...45,701,911
Ensembl chr 9:45,645,292...45,704,745
JBrowse link
G UPK2 uroplakin 2 ISO ClinVar Annotator: match by term: Immunodeficiency 19 ClinVar PMID:28492532 NCBI chr 9:46,200,465...46,202,754
Ensembl chr 9:46,200,489...46,202,753
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 9:46,285,718...46,297,465
Ensembl chr 9:46,285,729...46,297,465
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 6:88,719,886...88,745,922
Ensembl chr 6:88,720,176...88,745,917
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 chr 6:170,201,749...170,233,105
Ensembl chr 6:170,201,748...170,233,054
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 chr 4:79,687,375...79,850,146
Ensembl chr 4:79,687,359...79,847,281
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 chr 3:56,515,446...56,541,806
Ensembl chr 3:56,515,449...56,541,740
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 chr14:31,012,212...31,028,008
Ensembl chr14:31,011,644...31,028,639
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 chr14:12,437,551...12,563,548
Ensembl chr14:12,437,515...12,563,544
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 chr 7:25,062,772...25,071,989
Ensembl chr 7:25,062,773...25,071,862
JBrowse link
G TAP2 transporter 2, ATP binding cassette subfamily B member ISO OMIM NCBI chr 7:25,045,085...25,056,915 JBrowse link
G TAPBP TAP binding protein ISO OMIM NCBI chr 7:29,663,491...29,673,453
Ensembl chr 7:29,663,446...29,676,335
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 3:32,171,706...32,230,775
Ensembl chr 3:32,172,214...32,230,780
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 chr 2:58,675,987...58,678,025
Ensembl chr 2:58,675,990...58,678,026
JBrowse link
G RFX5 regulatory factor X5 ISO OMIM NCBI chr 4:97,901,955...97,913,283
Ensembl chr 4:97,888,460...97,913,283
JBrowse link
G RFXANK regulatory factor X associated ankyrin containing protein ISO OMIM NCBI chr 2:58,677,534...58,684,016
Ensembl chr 2:58,677,534...58,683,882
JBrowse link
G RFXAP regulatory factor X associated protein ISO OMIM NCBI chr11:12,660,306...12,695,137 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 chr10:46,820,016...46,863,848
Ensembl chr10:46,820,051...46,868,030
JBrowse link
G RAG1 recombination activating 1 ISO OMIM NCBI chr 2:24,565,447...24,573,853
Ensembl chr 2:24,565,449...24,602,590
JBrowse link
G RAG2 recombination activating 2 ISO OMIM NCBI chr 2:24,547,605...24,553,944
Ensembl chr 2:24,546,958...24,558,430
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 chr 2:24,547,605...24,553,944
Ensembl chr 2:24,546,958...24,558,430
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 6:89,295,164...89,318,169 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 chr15:121,100,624...121,190,086
Ensembl chr15:121,100,611...121,190,062
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 chr10:46,820,016...46,863,848
Ensembl chr10:46,820,051...46,868,030
JBrowse link
G LIG4 DNA ligase 4 ISO ClinVar Annotator: match by term: Severe combined immunodeficiency due to DCLRE1C deficiency
ClinVar Annotator: match by term: Severe combined immunodeficiency with sensitivity to ionizing radiation
ClinVar PMID:12471202, PMID:24033266, PMID:25741868, PMID:28492532 NCBI chr11:75,537,027...75,547,711
Ensembl chr11:75,537,032...75,547,691
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 chr10:46,771,820...46,800,955 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 chr10:46,874,606...46,900,058
Ensembl chr10:46,862,584...46,900,040
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 chr17:47,044,492...47,072,232
Ensembl chr17:47,044,495...47,072,245
JBrowse link
G DCLRE1C DNA cross-link repair 1C IEA Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation OMIA PMID:17998435, PMID:22903400, PMID:25454085, PMID:26320255 NCBI chr10:46,820,016...46,863,848
Ensembl chr10:46,820,051...46,868,030
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 chr 2:24,477,084...24,551,690
Ensembl chr 2:24,477,172...24,551,670
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 combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive
ClinVar Annotator: match by term: Severe 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 chr 2:59,905,901...59,926,504
Ensembl chr 2:59,905,919...59,926,495
JBrowse link
G RAG1 recombination activating 1 ISO OMIM NCBI chr 2:24,565,447...24,573,853
Ensembl chr 2:24,565,449...24,602,590
JBrowse link
G RAG2 recombination activating 2 ISO OMIM NCBI chr 2:24,547,605...24,553,944
Ensembl chr 2:24,546,958...24,558,430
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 chr 2:59,905,901...59,926,504
Ensembl chr 2:59,905,919...59,926,495
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 9:45,640,475...45,644,153
Ensembl chr 9:45,637,129...45,644,221
JBrowse link
G IL7R interleukin 7 receptor ISO OMIM NCBI chr16:21,300,141...21,330,156
Ensembl chr16:21,300,111...21,329,585
JBrowse link
G PTPRC protein tyrosine phosphatase receptor type C ISO OMIM NCBI chr10:21,482,984...21,601,627
Ensembl chr10:21,466,373...21,764,560
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 chr12:44,764,427...44,796,138
Ensembl chr12:44,765,260...44,795,286
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 chr17:47,387,594...47,475,705
Ensembl chr17:47,376,115...47,475,718
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:57,143,568...57,151,242 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 12615
    syndrome 6096
      primary immunodeficiency disease 1915
        combined immunodeficiency 134
          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 6
            severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive 3
Path 2
Term Annotations click to browse term
  disease 12615
    disease of anatomical entity 12148
      Immune & Inflammatory Diseases 2900
        immune system disease 2441
          primary immunodeficiency disease 1915
            combined immunodeficiency 134
              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 6
                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.