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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:lupus nephritis
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Accession:DOID:0080162 term browser browse the term
Definition:A glomerulonephritis that is characterized by inflammation of the kidneys resulting from systemic lupus erythematosus. (DO)
Synonyms:exact_synonym: Lupus Glomerulonephritides;   Lupus Glomerulonephritis;   Lupus Nephritides;   SLE nephritis;   Systemic Lupus Erythematosus with Nephritis
 related_synonym: SLEN1;   SLEN2;   SLEN3;   Systemic Lupus Erythematosus with Nephritis, Susceptibility To, 1;   Systemic Lupus Erythematosus with Nephritis, Susceptibility To, 2;   Systemic Lupus Erythematosus with Nephritis, Susceptibility To, 3;   lupus nephritis, susceptibility to
 primary_id: MESH:D008181
 alt_id: DOID:9004124
 xref: EFO:0005761;   GARD:10747;   MIM:607965;   MIM:607966;   MIM:607967


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lupus nephritis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ager advanced glycosylation end product-specific receptor ISO DNA:polymorphisms:promoter, intron:g.-429T>C rs1800625, g.-374T>A rs1800624, g.2184A>G rs3134940 (human) RGD PMID:22513366 RGD:6767309 NCBI chr20:4,152,758...4,155,956
Ensembl chr20:4,147,890...4,151,078 		JBrowse link
G Apoc3 apolipoprotein C3 ISO protein:increased expression:serum RGD PMID:17957542 RGD:7207211 NCBI chr 8:55,428,172...55,430,352
Ensembl chr 8:46,531,478...46,533,583 		JBrowse link
G C3 complement C3 ISO protein:decreased expression:serum
CTD Direct Evidence: marker/mechanism		 CTD
RGD		 PMID:31182691 PMID:21888025 RGD:7175544 NCBI chr 9:2,174,412...2,201,339
Ensembl chr 9:2,087,437...2,114,429 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 severity
susceptibility		 ISO protein:increased expression:urine (human)
DNA:snp:promoter:g.-2518A>G (human)		 RGD PMID:8558841 PMID:15188361 RGD:8549732, RGD:11528534 NCBI chr10:67,503,077...67,504,875
Ensembl chr10:67,005,424...67,007,226 		JBrowse link
G Ccl3 C-C motif chemokine ligand 3 ISO RGD PMID:18187931 RGD:7241814 NCBI chr10:68,948,889...68,950,439
Ensembl chr10:68,451,388...68,452,938 		JBrowse link
G Ccr1 C-C motif chemokine receptor 1 disease_progression ISO RGD PMID:15153561 RGD:5688164 NCBI chr 8:132,433,711...132,439,266 JBrowse link
G Cd40 CD40 molecule treatment ISO RGD PMID:23799000 PMID:19265127 PMID:18566369 RGD:7248418, RGD:7248425, RGD:7248429 NCBI chr 3:174,209,113...174,224,592
Ensembl chr 3:153,790,449...153,805,534 		JBrowse link
G Cd40lg CD40 ligand treatment ISO protein:increased expression:serum RGD PMID:20726330 PMID:15693003 PMID:13130474 PMID:12632425 PMID:11751940 RGD:7248426, RGD:7248439, RGD:7248600, RGD:7248710, RGD:7248714 NCBI chr  X:140,164,341...140,176,057
Ensembl chr  X:135,126,969...135,138,306 		JBrowse link
G Cfb complement factor B ISO RGD PMID:10623824 PMID:21893562 PMID:3183062 RGD:7242736, RGD:7242755, RGD:7242763 NCBI chr20:3,975,271...3,981,138
Ensembl chr20:3,951,474...3,976,505 		JBrowse link
G Cfh complement factor H ISO RGD PMID:22171659 RGD:5684551 NCBI chr13:54,063,079...54,164,523
Ensembl chr13:51,511,828...51,613,838 		JBrowse link
G Clu clusterin ISO mRNA:increased expression: epithelial cell of renal tubule RGD PMID:9546356 RGD:8890679 NCBI chr15:44,336,619...44,375,861
Ensembl chr15:40,174,617...40,200,315 		JBrowse link
G Col1a1 collagen type I alpha 1 chain ISO mRNA, protein:increased expression:kidney cortex
associated with Graft vs Host Disease		 RGD PMID:21354048 PMID:7723234 PMID:7700025 RGD:5688301, RGD:5688332, RGD:5688333 NCBI chr10:80,380,458...80,397,461
Ensembl chr10:79,883,622...79,900,624 		JBrowse link
G Crp C-reactive protein no_association ISO DNA:SNP RGD PMID:18852001 PMID:15692982 PMID:20039408 PMID:17596285 RGD:6907400, RGD:6909145, RGD:6909146, RGD:5508454 NCBI chr13:87,694,062...87,695,978
Ensembl chr13:85,124,977...85,175,178 		JBrowse link
G Csf1 colony stimulating factor 1 ISO RGD PMID:21885670 PMID:17659436 RGD:7257567, RGD:7257589 NCBI chr 2:198,065,400...198,084,774
Ensembl chr 2:195,377,215...195,411,704 		JBrowse link
G Ctla4 cytotoxic T-lymphocyte-associated protein 4 ISO RGD PMID:15146424 RGD:7204726 NCBI chr 9:69,812,859...69,819,959
Ensembl chr 9:62,319,312...62,324,963 		JBrowse link
G Egf epidermal growth factor ISO RGD PMID:21354048 RGD:5688301 NCBI chr 2:220,893,660...220,976,331
Ensembl chr 2:218,219,415...218,302,064 		JBrowse link
G Fas Fas cell surface death receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:33632240 PMID:38555047 NCBI chr 1:241,212,155...241,245,774
Ensembl chr 1:231,798,960...231,832,591 		JBrowse link
G Fcgr2a Fc gamma receptor 2A ISO DNA:missense mutation:cds:p.H131R (human)
ClinVar Annotator: match by term: Lupus nephritis, susceptibility to		 ClinVar
RGD		 PMID:8636449 PMID:9843982 PMID:10675363 PMID:15367919 PMID:19915573 More... RGD:5147975 NCBI chr13:85,813,516...85,830,269
Ensembl chr13:83,280,784...83,295,967 		JBrowse link
G Fcgr2b Fc gamma receptor 2B ISO RGD PMID:15681388 RGD:7240529 NCBI chr13:85,725,897...85,740,517
Ensembl chr13:83,193,163...83,207,778 		JBrowse link
G Fcgr3a Fc gamma receptor 3A susceptibility ISO DNA:SNP:cds:p.V158F (human) RGD PMID:17596285 RGD:5508454 NCBI chr13:85,782,636...85,792,656
Ensembl chr13:83,249,872...83,259,921 		JBrowse link
G Ifng interferon gamma ISO protein:increased expression:serum,urine
protein:increased processing:kidney
CTD Direct Evidence: marker/mechanism		 CTD
RGD		 PMID:31182691 PMID:22764573 PMID:29925830 RGD:6893369, RGD:14974252 NCBI chr 7:55,789,180...55,793,216
Ensembl chr 7:53,903,337...53,907,375 		JBrowse link
G Il17a interleukin 17A treatment ISO RGD PMID:25129462 RGD:9244623 NCBI chr 9:30,640,844...30,644,331
Ensembl chr 9:23,144,402...23,147,889 		JBrowse link
G Il18 interleukin 18 ISO RGD PMID:20980973 RGD:6893449 NCBI chr 8:59,802,072...59,829,275
Ensembl chr 8:50,906,960...50,932,887 		JBrowse link
G Il1b interleukin 1 beta ISO mRNA:increased expression:renal glomerulus (mouse) RGD PMID:21641991 PMID:20410215 RGD:7175315, RGD:7175344 NCBI chr 3:137,030,200...137,036,581
Ensembl chr 3:116,577,010...116,583,415 		JBrowse link
G Il1rn interleukin 1 receptor antagonist resistance ISO associated with Lupus Erythematosus, Systemic; protein:increased expression:serum (human) RGD PMID:20538031 RGD:6907068 NCBI chr 3:27,509,836...27,525,738
Ensembl chr 3:7,111,550...7,127,445 		JBrowse link
G Itgam integrin subunit alpha M ISO RGD PMID:21719445 RGD:5147916 NCBI chr 1:192,089,496...192,139,947
Ensembl chr 1:182,659,000...182,709,503 		JBrowse link
G Jak1 Janus kinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31182691 NCBI chr 5:120,895,606...121,004,207
Ensembl chr 5:115,780,248...115,888,926 		JBrowse link
G Klkb1 kallikrein B1 susceptibility ISO DNA:SNPs:promoter: RGD PMID:19307730 RGD:7327150 NCBI chr16:53,690,180...53,714,570
Ensembl chr16:46,958,707...46,982,053 		JBrowse link
G Mbl2 mannose binding lectin 2 disease_progression ISO DNA:polymorphism:exon: RGD PMID:24850777 RGD:12910847 NCBI chr 1:237,429,873...237,465,567 JBrowse link
G Mir125a microRNA 125a IEP RNA:decreased expression:kidney RGD PMID:30972208 RGD:26884458 NCBI chr 1:58,677,626...58,677,710
Ensembl chr 1:58,677,626...58,677,710 		JBrowse link
G Mmp2 matrix metallopeptidase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22479529 NCBI chr19:30,327,643...30,355,856
Ensembl chr19:14,154,657...14,182,870 		JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22479529 NCBI chr 3:174,103,474...174,111,434
Ensembl chr 3:153,683,858...153,692,120 		JBrowse link
G Mpo myeloperoxidase susceptibility ISO DNA:polymorphism: :−463G > A (human) RGD PMID:17896805 RGD:7174701 NCBI chr10:73,092,124...73,102,057
Ensembl chr10:72,594,661...72,604,819 		JBrowse link
G Mtor mechanistic target of rapamycin kinase ISO RGD PMID:17283580 RGD:7245502 NCBI chr 5:164,167,985...164,277,438
Ensembl chr 5:158,884,804...158,994,311 		JBrowse link
G Muc20 mucin 20, cell surface associated ISO RGD PMID:14565953 RGD:7364790 NCBI chr11:67,987,816...68,001,496
Ensembl chr11:67,987,800...68,001,495 		JBrowse link
G Nr3c1 nuclear receptor subfamily 3, group C, member 1 ISO RGD PMID:21509671 PMID:17880936 RGD:7174713, RGD:7174734 NCBI chr18:31,522,783...31,644,508
Ensembl chr18:31,271,681...31,393,375 		JBrowse link
G Otub1 OTU deubiquitinase, ubiquitin aldehyde binding 1 ISO protein:increased expression:kidney RGD PMID:22279542 RGD:7175260 NCBI chr 1:204,387,215...204,395,495
Ensembl chr 1:204,387,215...204,395,483 		JBrowse link
G Pdcd1 programmed cell death 1 onset ISO DNA:polymorphism: :
DNA:polymorphism:intron:6867 C>T (human)		 RGD PMID:15934088 PMID:15352422 PMID:21041733 RGD:7248675, RGD:7248676, RGD:7248678 NCBI chr 9:101,866,124...101,879,278
Ensembl chr 9:94,418,791...94,431,937 		JBrowse link
G RT1-Ba RT1 class II, locus Ba susceptibility ISO DNA:polymorphisms:cds:HLA-DQA1*0101 (human)
DNA:polymorphisms:cds:HLA-DQA1*0102 (human)		 RGD PMID:12651073 RGD:40902999 NCBI chr20:4,577,057...4,581,650
Ensembl chr20:4,575,134...4,579,744 		JBrowse link
G RT1-Db1 RT1 class II, locus Db1 susceptibility ISO DNA:polymorphisms:cds:HLA-DRB1*1501 (human) RGD PMID:12651073 RGD:40902999 NCBI chr20:4,550,594...4,560,182
Ensembl chr20:4,548,666...4,558,258 		JBrowse link
G Sell selectin L ISO RGD PMID:20512127 RGD:7175284 NCBI chr13:78,950,100...78,969,604
Ensembl chr13:76,416,915...76,436,456 		JBrowse link
G Serping1 serpin family G member 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:4014294 NCBI chr 3:69,842,726...69,852,583
Ensembl chr 3:69,842,739...69,852,034 		JBrowse link
G Snrpe small nuclear ribonucleoprotein polypeptide E treatment IDA mouse model RGD PMID:15494537 RGD:10760401 NCBI chr13:45,050,986...45,057,231
Ensembl chr13:45,050,986...45,057,310
Ensembl chr 8:45,050,986...45,057,310 		JBrowse link
G Stat1 signal transducer and activator of transcription 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31182691 NCBI chr 9:56,911,522...56,951,926
Ensembl chr 9:49,419,340...49,588,540 		JBrowse link
G Stat4 signal transducer and activator of transcription 4 ISO RGD PMID:20980973 RGD:6893449 NCBI chr 9:56,964,617...57,080,523
Ensembl chr 9:49,419,340...49,588,540 		JBrowse link
G Stat6 signal transducer and activator of transcription 6 disease_progression ISO RGD PMID:12874250 RGD:7244140 NCBI chr 7:63,480,229...63,497,551
Ensembl chr 7:63,479,642...63,498,495 		JBrowse link
G Tlr7 toll-like receptor 7 ISO RGD PMID:19944565 RGD:7246905 NCBI chr  X:30,644,324...30,670,796
Ensembl chr  X:27,027,425...27,054,754 		JBrowse link
G Tlr9 toll-like receptor 9 no_association
treatment
severity		 ISO DNA:snps:intron, exon:g.+1174G>A, g.+1635C>T (rs352139, rs352140) (human, Chinese)
associated with Lupus Erythematosus, Systemic; DNA:snps:promoter, intron:g.-1486T>C, g.+1174A>G (rs187084, rs352139) (human, North Indian)
protein:increased expression:renal glomerulus (human)
associated with Graft vs Host Disease
mRNA, protein:increased expression:kidney (mouse) 		RGD PMID:23467932 PMID:20497632 PMID:22787315 PMID:19578108 PMID:21127878 More... RGD:7245987, RGD:7246884, RGD:7245989, RGD:7246896, RGD:7246897, RGD:7246911 NCBI chr 8:115,743,407...115,747,523
Ensembl chr 8:106,864,680...106,868,796 		JBrowse link
G Tnf tumor necrosis factor ISO protein:increased expression:glomerular mesangial cell RGD PMID:7750940 RGD:7394786 NCBI chr20:3,626,685...3,629,303
Ensembl chr20:3,622,011...3,624,629 		JBrowse link
G Tnfrsf11b TNF receptor superfamily member 11B ISO associated with Lupus Erythematosus, Systemic;protein:increased expression:urine RGD PMID:21691937 RGD:7205483 NCBI chr 7:87,456,318...87,484,324
Ensembl chr 7:85,566,520...85,594,538 		JBrowse link
G Tnfrsf1a TNF receptor superfamily member 1A severity ISO RGD PMID:19201910 PMID:10906156 RGD:7245569, RGD:7245572 NCBI chr 4:159,837,119...159,849,817
Ensembl chr 4:158,150,820...158,163,591 		JBrowse link
G Tnfrsf1b TNF receptor superfamily member 1B treatment ISO RGD PMID:22846145 PMID:22674120 RGD:7245541, RGD:7245544 NCBI chr 5:162,356,250...162,387,411
Ensembl chr 5:157,070,642...157,104,206 		JBrowse link
G Vcam1 vascular cell adhesion molecule 1 severity ISO protein:increased expression:urine RGD PMID:22788914 RGD:7241032 NCBI chr 2:206,723,050...206,742,783
Ensembl chr 2:204,038,114...204,057,958 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19134
    disease of anatomical entity 18447
      Immune & Inflammatory Diseases 5751
        Inflammation 2841
          nephritis 495
            lupus nephritis 53
Path 2
Term Annotations click to browse term
  disease 19134
    disease of anatomical entity 18447
      Immune & Inflammatory Diseases 5751
        immune system disease 5070
          primary immunodeficiency disease 4476
            autoimmune disease 2376
              autoimmune disease of musculoskeletal system 1002
                lupus erythematosus 216
                  systemic lupus erythematosus 210
                    lupus nephritis 53
paths to the root