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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:lymphopenia
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Accession:DOID:614 term browser browse the term
Definition:A leukopenia that is the condition of having an abnormally low level of lymphocytes in the blood. (DO)
Synonyms:exact_synonym: lymphocytopenia;   lymphocytopenias;   lymphopenias
 primary_id: MESH:D008231
 xref: ICD10CM:D72.810;   ICD9CM:288.51
For additional species annotation, visit the Alliance of Genome Resources.



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lymphopenia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ada adenosine deaminase ISO RGD PMID:9478961 RGD:1300251 NCBI chr 3:152,398,745...152,422,854
Ensembl chr 3:152,398,747...152,447,088
JBrowse link
G Atg5 autophagy related 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26568842 NCBI chr20:47,798,222...47,889,216
Ensembl chr20:47,798,290...47,889,209
JBrowse link
G Atg7 autophagy related 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26568842 NCBI chr 4:147,718,663...147,925,656
Ensembl chr 4:147,718,752...147,925,593
JBrowse link
G Cbl Cbl proto-oncogene onset ISO RGD PMID:20404156 RGD:11038797 NCBI chr 8:44,487,824...44,571,620
Ensembl chr 8:44,489,410...44,571,176
JBrowse link
G Ccl28 C-C motif chemokine ligand 28 IEP protein:decreased expression:small intestine villus (rat) RGD PMID:19393265 RGD:4892224 NCBI chr 2:51,601,354...51,625,999
Ensembl chr 2:51,601,331...51,625,997
JBrowse link
G Cd28 Cd28 molecule IMP RGD PMID:12750179 RGD:2307205 NCBI chr 9:62,166,324...62,194,674
Ensembl chr 9:62,166,192...62,194,685
JBrowse link
G Csf1r colony stimulating factor 1 receptor IMP RGD PMID:30249809 RGD:41404725 NCBI chr18:54,546,673...54,590,418
Ensembl chr18:54,546,659...54,590,415
JBrowse link
G Csf1rtm(EGFP)Tset colony stimulating factor 1 receptor; target mutant, Tset IMP RGD PMID:30249809 RGD:41404725
G Dkc1 dyskerin pseudouridine synthase 1 ISO RGD PMID:12522253 RGD:11251731
G Ednrb endothelin receptor type B IAGP RGD PMID:22975636 RGD:7207471 NCBI chr15:80,640,839...80,672,115
Ensembl chr15:80,643,043...80,672,115
JBrowse link
G Ednrbsl endothelin receptor type B, spotting lethal IAGP RGD PMID:22975636 RGD:7207471
G Fcgr2a Fc gamma receptor 2A susceptibility ISO associated with Lupus Erythematosus, Systemic;DNA:SNP:cds:p.R131H (human) RGD PMID:17596285 RGD:5508454 NCBI chr13:83,280,782...83,297,535
Ensembl chr13:83,280,784...83,295,967
JBrowse link
G Fcgr3a Fc gamma receptor 3A susceptibility ISO associated with Lupus Erythematosus, Systemic;DNA:SNP:cds:p.V158F (human) RGD PMID:17596285 RGD:5508454 NCBI chr13:83,249,905...83,259,921
Ensembl chr13:83,249,872...83,259,921
JBrowse link
G Gimap5 GTPase, IMAP family member 5 IAGP DNA:frameshift deletion RGD PMID:12097339 RGD:619544 NCBI chr 4:77,693,417...77,701,025
Ensembl chr 4:77,687,564...77,703,086
JBrowse link
G Hoxd13 homeo box D13 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27725143 NCBI chr 3:59,570,647...59,573,963
Ensembl chr 3:59,570,646...59,573,963
JBrowse link
G Il1b interleukin 1 beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:1884014 NCBI chr 3:116,577,005...116,583,386
Ensembl chr 3:116,577,010...116,583,415
JBrowse link
G Il2ra interleukin 2 receptor subunit alpha ISO IL2RA/CD25 Deficiency, OMIM:606367 RGD PMID:9096364 RGD:1600117 NCBI chr17:66,849,974...66,898,665
Ensembl chr17:66,849,974...66,898,697
JBrowse link
G Il7 interleukin 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17151827 NCBI chr 2:94,235,219...94,280,075
Ensembl chr 2:94,234,766...94,280,075
JBrowse link
G Jak3 Janus kinase 3 ISO ClinVar Annotator: match by term: Lymphopenia ClinVar PMID:25741868 PMID:28492532 NCBI chr16:18,386,330...18,398,542
Ensembl chr16:18,386,405...18,398,536
JBrowse link
G Lbr lamin B receptor ISO DNA:point mutation RGD PMID:22105998 RGD:11062006 NCBI chr13:93,539,360...93,564,065
Ensembl chr13:93,538,920...93,564,017
JBrowse link
G Myh7 myosin heavy chain 7 ISO ClinVar Annotator: match by term: Lymphopenia ClinVar PMID:7581410 PMID:10521296 PMID:11186938 PMID:11447480 PMID:15358028 More... NCBI chr15:28,446,550...28,469,888
Ensembl chr15:28,446,550...28,468,217
JBrowse link
G Mysm1 myb-like, SWIRM and MPN domains 1 ISO RGD PMID:22184403 RGD:9589161 NCBI chr 5:109,761,345...109,826,652
Ensembl chr 5:109,776,286...109,819,967
JBrowse link
G Nek1 NIMA-related kinase 1 ISO ClinVar Annotator: match by term: Lymphopenia ClinVar PMID:25741868 PMID:28089114 PMID:28492532 NCBI chr16:28,998,229...29,125,426
Ensembl chr16:28,998,231...29,117,723
JBrowse link
G Nup98 nucleoporin 98 and 96 precursor ISO CTD Direct Evidence: marker/mechanism CTD PMID:27725143 NCBI chr 1:156,494,423...156,591,415
Ensembl chr 1:156,494,423...156,591,415
JBrowse link
G Tnf tumor necrosis factor ISO associated with HIV Infections;protein:increased expression:serum RGD PMID:2324681 RGD:10450888 NCBI chr20:3,622,011...3,624,629
Ensembl chr20:3,622,011...3,624,629
JBrowse link
G Vav1 vav guanine nucleotide exchange factor 1 IEP mRNA, protein:increased expression:thymus RGD PMID:10433093 RGD:2306005 NCBI chr 9:2,161,985...2,209,951
Ensembl chr 9:2,157,900...2,208,937
JBrowse link
Alpha/Beta T-Cell Lymphopenia with Gamma/Delta T-Cell Expansion, Severe Cytomegalovirus Infection, and Autoimmunity term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Rag1 recombination activating 1 ISO ClinVar Annotator: match by term: Alpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severe cytomegalovirus infection, and autoimmunity OMIM
ClinVar
PMID:9630231 PMID:11121059 PMID:11133745 PMID:11213808 PMID:11313270 More... NCBI chr 3:87,917,061...87,928,158
Ensembl chr 3:87,917,004...87,928,291
JBrowse link
idiopathic CD4-positive T-lymphocytopenia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Unc119 unc-119 lipid binding chaperone ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: IDIOPATHIC CD4 LYMPHOPENIA
CTD
ClinVar
PMID:22184408 PMID:24033266 PMID:25741868 PMID:28492532 NCBI chr10:63,237,862...63,243,339
Ensembl chr10:63,237,903...63,243,339
JBrowse link
T-CELL LYMPHOPENIA, INFANTILE, WITH OR WITHOUT NAIL DYSTROPHY, AUTOSOMAL DOMINANT term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Foxn1 forkhead box N1 ISO ClinVar Annotator: match by term: T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant OMIM
ClinVar
PMID:8911612 PMID:10206641 PMID:15180707 PMID:15897400 PMID:18339010 More... NCBI chr10:63,251,400...63,273,710
Ensembl chr10:63,251,400...63,273,710
JBrowse link
T-Lymphocytopenia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Stat5b signal transducer and activator of transcription 5B ISO CTD Direct Evidence: marker/mechanism CTD PMID:17030597 NCBI chr10:85,704,841...85,775,856
Ensembl chr10:85,705,670...85,775,668
JBrowse link
G Themis thymocyte selection associated IAGP DNA:frameshift mutation: RGD PMID:22275874 RGD:38599149 NCBI chr 1:16,433,906...16,623,889
Ensembl chr 1:16,432,631...16,664,329
JBrowse link
G Themism1Adej thymocyte selection associated; mutant1, Adej IAGP RGD PMID:22275874 RGD:38599149
Wiskott-Aldrich syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Foxp3 forkhead box P3 ISS OMIM:301000 | OMIM:614493 MouseDO NCBI chr  X:14,908,494...14,924,994
Ensembl chr  X:14,908,494...14,923,838
JBrowse link
G Was WASP actin nucleation promoting factor ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Wiskott-Aldrich syndrome | ClinVar Annotator: match by term: Wiskott-Aldrich syndrome, attenuated
OMIM
CTD
ClinVar
RGD
PMID:2906042 PMID:7579329 PMID:7579347 PMID:7735919 PMID:7753869 More... RGD:1599803 NCBI chr  X:14,405,096...14,413,850
Ensembl chr  X:14,405,124...14,413,849
JBrowse link
G Washc4 WASH complex subunit 4 ISS OMIM:301000 MouseDO NCBI chr 7:20,187,905...20,240,228
Ensembl chr 7:20,187,922...20,240,226
JBrowse link
G Wipf1 WAS/WASL interacting protein family, member 1 ISO CTD Direct Evidence: marker/mechanism CTD NCBI chr 3:58,314,521...58,416,668
Ensembl chr 3:58,314,542...58,372,742
JBrowse link
Wiskott-Aldrich Syndrome 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Wipf1 WAS/WASL interacting protein family, member 1 ISO ClinVar Annotator: match by term: Wiskott-Aldrich syndrome 2 OMIM
ClinVar
PMID:9536098 PMID:17576681 PMID:22231303 PMID:24033266 PMID:25741868 More... NCBI chr 3:58,314,521...58,416,668
Ensembl chr 3:58,314,542...58,372,742
JBrowse link
X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Atp7a ATPase copper transporting alpha ISO ClinVar Annotator: match by term: X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia ClinVar PMID:28492532 NCBI chr  X:71,094,144...71,201,550
Ensembl chr  X:71,094,202...71,198,354
JBrowse link
G Cox7b cytochrome c oxidase subunit 7B ISO ClinVar Annotator: match by term: X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia ClinVar PMID:28492532 NCBI chr  X:71,083,486...71,089,733
Ensembl chr  X:71,083,456...71,089,732
JBrowse link
G Magt1 magnesium transporter 1 ISO ClinVar Annotator: match by term: X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia OMIM
ClinVar
PMID:9536098 PMID:16199547 PMID:17576681 PMID:21796205 PMID:24550228 More... NCBI chr  X:71,038,489...71,079,704
Ensembl chr  X:71,038,489...71,079,699
JBrowse link
G Pgk1 phosphoglycerate kinase 1 ISO ClinVar Annotator: match by term: X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia ClinVar PMID:28492532 NCBI chr  X:71,271,454...71,287,429
Ensembl chr  X:71,271,440...71,287,418
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18133
    syndrome 9686
      primary immunodeficiency disease 3831
        lymphopenia 62
          T-Lymphocytopenia + 8
          Wiskott-Aldrich syndrome + 4
          X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia 4
Path 2
Term Annotations click to browse term
  disease 18133
    disease of anatomical entity 17503
      Hemic and Lymphatic Diseases 3292
        hematopoietic system disease 2831
          leukocyte disease 881
            leukopenia 383
              lymphopenia 62
                T-Lymphocytopenia + 8
                Wiskott-Aldrich syndrome + 4
                X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia 4
paths to the root