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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:Reduction in the number of lymphocytes.
Synonyms:exact_synonym: Lymphocytopenia;   Lymphocytopenias;   Lymphopenias
 primary_id: MESH:D008231
 alt_id: RDO:0002473
 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 3:160,115,840...160,139,947
Ensembl chr 3:160,115,842...160,139,947
JBrowse link
G Atg5 autophagy related 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26568842 NCBI chr20:49,301,783...49,393,147
Ensembl chr20:49,318,308...49,393,140
JBrowse link
G Atg7 autophagy related 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26568842 NCBI chr 4:146,570,113...146,777,093
Ensembl chr 4:146,598,413...146,777,124
JBrowse link
G Cbl Cbl proto-oncogene onset ISO RGD PMID:20404156 RGD:11038797 NCBI chr 8:48,481,256...48,564,775
Ensembl chr 8:48,489,036...48,564,722
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 2:52,379,341...52,403,979
Ensembl chr 2:52,379,341...52,404,246
JBrowse link
G Cd28 Cd28 molecule IMP RGD PMID:12750179 RGD:2307205 NCBI chr 9:67,546,408...67,573,858
Ensembl chr 9:67,546,408...67,571,871
JBrowse link
G Csf1r colony stimulating factor 1 receptor IMP RGD PMID:30249809 RGD:41404725 NCBI chr18:56,414,493...56,458,300
Ensembl chr18:56,414,488...56,458,300
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 NCBI chr  X:155,844,914...155,862,363
Ensembl chr  X:155,844,857...155,862,475
JBrowse link
G Ednrb endothelin receptor type B IAGP RGD PMID:22975636 RGD:7207471 NCBI chr15:88,004,775...88,036,354
Ensembl chr15:88,006,977...88,036,354
JBrowse link
G Ednrbsl endothelin receptor type B, spotting lethal IAGP RGD PMID:22975636 RGD:7207471
G Fcgr2a Fc fragment of IgG receptor IIa susceptibility ISO associated with Lupus Erythematosus, Systemic;DNA:SNP:cds:p.R131H (human) RGD PMID:17596285 RGD:5508454 NCBI chr13:91,146,878...91,163,691
Ensembl chr13:91,168,973...91,198,036
Ensembl chr13:91,168,973...91,198,036
JBrowse link
G Fcgr3a Fc fragment of IgG receptor IIIa susceptibility ISO associated with Lupus Erythematosus, Systemic;DNA:SNP:cds:p.V158F (human) RGD PMID:17596285 RGD:5508454 NCBI chr13:89,385,775...89,396,047
Ensembl chr13:89,385,859...89,396,051
JBrowse link
G Gimap5 GTPase, IMAP family member 5 IAGP DNA:frameshift deletion RGD PMID:12097339 RGD:619544 NCBI chr 4:78,377,228...78,386,683
Ensembl chr 4:78,378,144...78,385,577
JBrowse link
G Hoxd13 homeo box D13 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27725143 NCBI chr 3:61,590,376...61,593,692
Ensembl chr 3:61,590,376...61,593,692
JBrowse link
G Il1b interleukin 1 beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:1884014 NCBI chr 3:121,876,256...121,882,637
Ensembl chr 3:121,876,263...121,882,726
JBrowse link
G Il2ra interleukin 2 receptor subunit alpha ISO IL2RA/CD25 Deficiency, OMIM:606367 RGD PMID:9096364 RGD:1600117 NCBI chr17:70,500,672...70,547,929
Ensembl chr17:70,499,083...70,548,071
JBrowse link
G Il7 interleukin 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17151827 NCBI chr 2:96,427,884...96,474,979
Ensembl chr 2:96,439,286...96,474,977
JBrowse link
G Lbr lamin B receptor ISO DNA:point mutation RGD PMID:22105998 RGD:11062006 NCBI chr13:100,431,390...100,450,209 JBrowse link
G Myh7 myosin heavy chain 7 ISO ClinVar Annotator: match by term: Lymphocytopenia 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 chr15:33,605,769...33,657,761
Ensembl chr15:33,634,422...33,656,089
JBrowse link
G Mysm1 myb-like, SWIRM and MPN domains 1 ISO RGD PMID:22184403 RGD:9589161 NCBI chr 5:113,902,115...113,939,083
Ensembl chr 5:113,906,803...113,939,127
JBrowse link
G Nek1 NIMA-related kinase 1 ISO ClinVar Annotator: match by term: Lymphocytopenia ClinVar PMID:25741868 PMID:28089114 PMID:28492532 NCBI chr16:32,321,010...32,439,421
Ensembl chr16:32,321,010...32,439,421
JBrowse link
G Nup98 nucleoporin 98 and 96 precursor ISO CTD Direct Evidence: marker/mechanism CTD PMID:27725143 NCBI chr 1:167,213,866...167,308,851
Ensembl chr 1:167,213,866...167,308,851
JBrowse link
G Tnf tumor necrosis factor ISO associated with HIV Infections;protein:increased expression:serum RGD PMID:2324681 RGD:10450888 NCBI chr20:5,189,382...5,192,000
Ensembl chr20:5,189,390...5,192,000
Ensembl chr20:5,189,390...5,192,000
JBrowse link
G Vav1 vav guanine nucleotide exchange factor 1 IEP mRNA, protein:increased expression:thymus RGD PMID:10433093 RGD:2306005 NCBI chr 9:9,617,551...9,675,167
Ensembl chr 9:9,617,786...9,675,110
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
ClinVar Annotator: match by null
ClinVar Annotator: match by OMIM:609889
OMIM
ClinVar
PMID:9630231 PMID:11121059 PMID:11133745 PMID:11313270 PMID:16276422 PMID:17890453 PMID:18592361 PMID:19246248 PMID:21664875 PMID:24144642 PMID:24290284 PMID:24406074 PMID:25741868 PMID:25976673 PMID:26476733 PMID:26596586 PMID:28492532 PMID:28769923 PMID:28783691 PMID:30290665 PMID:30307608 NCBI chr 3:91,206,394...91,217,491
Ensembl chr 3:91,206,394...91,217,491
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 CTD NCBI chr10:65,606,919...65,612,324
Ensembl chr10:65,606,898...65,612,324
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
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 PMID:20864124 PMID:20978268 PMID:21507891 PMID:28492532 PMID:28636882 PMID:31447097 PMID:31566583 NCBI chr10:65,621,142...65,634,666
Ensembl chr10:65,621,257...65,634,666
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 chr10:88,686,207...88,712,313
Ensembl chr10:88,686,207...88,754,829
JBrowse link
G Themis thymocyte selection associated IAGP DNA:frameshift mutation: RGD PMID:22275874 RGD:38599149 NCBI chr 1:17,152,973...17,378,225
Ensembl chr 1:17,171,631...17,378,047
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:15,753,175...15,768,648
Ensembl chr  X:15,753,175...15,768,522
JBrowse link
G Was WASP actin nucleation promoting factor ISO ClinVar Annotator: match by null
ClinVar Annotator: match by term: Wiskott-Aldrich syndrome, attenuated
CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Aldrich syndrome
OMIM
ClinVar
CTD
PMID:2906042 PMID:7579329 PMID:7579347 PMID:7735919 PMID:8069912 PMID:8528198 PMID:8528199 PMID:8595430 PMID:8673127 PMID:8682510 PMID:8743175 PMID:9126958 PMID:9326235 PMID:9536098 PMID:9657775 PMID:10202051 PMID:10447259 PMID:10653325 PMID:10691337 PMID:10737997 PMID:11298372 PMID:11442475 PMID:11598004 PMID:12073025 PMID:12199801 PMID:12351383 PMID:12437929 PMID:12727931 PMID:12969986 PMID:14504083 PMID:14566484 PMID:14612666 PMID:15284122 PMID:15497008 PMID:16091449 PMID:16511828 PMID:16638962 PMID:17065640 PMID:17213309 PMID:17250667 PMID:17390083 PMID:17400488 PMID:17576681 PMID:17703096 PMID:18162713 PMID:19308710 PMID:19817875 PMID:20173115 PMID:20232122 PMID:20959042 PMID:21185603 PMID:21710275 PMID:21771083 PMID:22523910 PMID:23033889 PMID:24210885 PMID:24728327 PMID:25091438 PMID:25741868 PMID:25931402 PMID:27993330 PMID:28492532 PMID:30981783, PMID:8069912 RGD:1599803 NCBI chr  X:15,155,246...15,164,099
Ensembl chr  X:15,155,230...15,164,105
JBrowse link
G Wipf1 WAS/WASL interacting protein family, member 1 ISO CTD Direct Evidence: marker/mechanism CTD NCBI chr 3:60,150,001...60,207,125
Ensembl chr 3:60,150,021...60,166,013
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
ClinVar Annotator: match by This custom term has been created by RGD curators.
OMIM
ClinVar
PMID:9536098 PMID:17576681 PMID:22231303 PMID:24033266 PMID:27742395 PMID:28492532 NCBI chr 3:60,150,001...60,207,125
Ensembl chr 3:60,150,021...60,166,013
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: Immunodeficiency, X-Linked, with magnesium defect, Epstein-Barr virus infection, and neoplasia ClinVar PMID:28492532 NCBI chr  X:77,076,085...77,193,644
Ensembl chr  X:77,076,106...77,193,644
JBrowse link
G Cox7b cytochrome c oxidase subunit 7B ISO ClinVar Annotator: match by term: Immunodeficiency, X-Linked, with magnesium defect, Epstein-Barr virus infection, and neoplasia ClinVar PMID:28492532 NCBI chr  X:77,065,427...77,071,676
Ensembl chr  X:77,065,397...77,071,676
JBrowse link
G Magt1 magnesium transporter 1 ISO ClinVar Annotator: match by term: Immunodeficiency, X-Linked, with magnesium defect, Epstein-Barr virus infection, and neoplasia
ClinVar Annotator: match by OMIM:300853
OMIM
ClinVar
PMID:16199547 PMID:21796205 PMID:24550228 PMID:25135935 PMID:25504528 PMID:25741868 PMID:25956530 PMID:26422833 PMID:27770395 PMID:28492532 PMID:31036665 NCBI chr  X:77,023,423...77,061,603
Ensembl chr  X:77,020,402...77,061,667
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 17129
    syndrome 8018
      primary immunodeficiency disease 2694
        lymphopenia 59
          T-Lymphocytopenia + 8
          Wiskott-Aldrich syndrome + 3
          X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia 3
Path 2
Term Annotations click to browse term
  disease 17129
    disease of anatomical entity 16476
      Hemic and Lymphatic Diseases 2218
        hematopoietic system disease 1797
          leukocyte disease 519
            leukopenia 126
              lymphopenia 59
                T-Lymphocytopenia + 8
                Wiskott-Aldrich syndrome + 3
                X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia 3
paths to the root