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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 chr17:34,816,545...34,819,911
Ensembl chr17:34,816,836...34,819,910 		JBrowse link
G Apoc3 apolipoprotein C-III ISO protein:increased expression:serum RGD PMID:17957542 RGD:7207211 NCBI chr 9:46,144,348...46,146,934
Ensembl chr 9:46,144,231...46,146,934 		JBrowse link
G C3 complement component 3 ISO protein:decreased expression:serum
CTD Direct Evidence: marker/mechanism		 CTD
RGD		 PMID:31182691 PMID:21888025 RGD:7175544 NCBI chr17:57,510,967...57,535,136
Ensembl chr17:57,510,970...57,535,136 		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 chr11:81,926,403...81,928,278
Ensembl chr11:81,926,397...81,928,279 		JBrowse link
G Ccl3 C-C motif chemokine ligand 3 IEP RGD PMID:18187931 RGD:7241814 NCBI chr11:83,538,669...83,540,204
Ensembl chr11:83,538,670...83,540,181 		JBrowse link
G Ccr1 C-C motif chemokine receptor 1 disease_progression IMP RGD PMID:15153561 RGD:5688164 NCBI chr 9:123,762,163...123,768,729
Ensembl chr 9:123,762,161...123,768,729 		JBrowse link
G Cd40 CD40 antigen treatment IMP
IDA		 RGD PMID:23799000 PMID:19265127 PMID:18566369 RGD:7248418, RGD:7248425, RGD:7248429 NCBI chr 2:164,897,535...164,913,574
Ensembl chr 2:164,897,547...164,914,868 		JBrowse link
G Cd40lg CD40 ligand treatment ISO
IMP
IDA		 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:56,257,448...56,269,402
Ensembl chr  X:56,257,503...56,269,402 		JBrowse link
G Cfb complement factor B IMP
ISO
IEP		 RGD PMID:10623824 PMID:21893562 PMID:3183062 RGD:7242736, RGD:7242755, RGD:7242763 NCBI chr17:35,075,350...35,081,492
Ensembl chr17:35,075,350...35,081,494 		JBrowse link
G Cfh complement component factor h ISO RGD PMID:22171659 RGD:5684551 NCBI chr 1:140,013,593...140,111,149
Ensembl chr 1:140,012,446...140,111,502 		JBrowse link
G Clu clusterin IEP mRNA:increased expression: epithelial cell of renal tubule RGD PMID:9546356 RGD:8890679 NCBI chr14:66,206,093...66,218,992
Ensembl chr14:66,205,932...66,218,996 		JBrowse link
G Col1a1 collagen, type I, alpha 1 ISO
IEP
IDA		 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 chr11:94,827,050...94,843,868
Ensembl chr11:94,827,050...94,843,868 		JBrowse link
G Crp C-reactive protein, pentraxin-related no_association ISO DNA:SNP RGD PMID:18852001 PMID:15692982 PMID:20039408 PMID:17596285 RGD:6907400, RGD:6909145, RGD:6909146, RGD:5508454 NCBI chr 1:172,525,623...172,527,533
Ensembl chr 1:172,525,622...172,660,598 		JBrowse link
G Csf1 colony stimulating factor 1 (macrophage) IMP
ISO		 RGD PMID:21885670 PMID:17659436 RGD:7257567, RGD:7257589 NCBI chr 3:107,648,364...107,668,048
Ensembl chr 3:107,648,364...107,667,785 		JBrowse link
G Ctla4 cytotoxic T-lymphocyte-associated protein 4 ISO RGD PMID:15146424 RGD:7204726 NCBI chr 1:60,948,184...60,954,991
Ensembl chr 1:60,926,159...60,954,991 		JBrowse link
G Egf epidermal growth factor ISO RGD PMID:21354048 RGD:5688301 NCBI chr 3:129,471,223...129,548,971
Ensembl chr 3:129,471,214...129,548,965 		JBrowse link
G Fas Fas cell surface death receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:33632240 PMID:38555047 NCBI chr19:34,267,926...34,305,175
Ensembl chr19:34,268,066...34,305,172 		JBrowse link
G Fcgr2b Fc receptor, IgG, low affinity IIb IMP RGD PMID:15681388 RGD:7240529 NCBI chr 1:170,786,186...170,804,141
Ensembl chr 1:170,786,186...170,804,116 		JBrowse link
G Fcgr3 Fc receptor, IgG, low affinity III ISO DNA:missense mutation:cds:p.H131R (human) RGD PMID:15004265 RGD:5147975 NCBI chr 1:170,878,738...170,893,477
Ensembl chr 1:170,878,743...170,892,504 		JBrowse link
G Fcgr4 Fc receptor, IgG, low affinity IV susceptibility ISO DNA:SNP:cds:p.V158F (human) RGD PMID:17596285 RGD:5508454 NCBI chr 1:170,846,495...170,857,330
Ensembl chr 1:170,846,489...170,857,330 		JBrowse link
G H2-Aa histocompatibility 2, class II antigen A, alpha susceptibility ISO DNA:polymorphisms:cds:HLA-DQA1*0101 (human)
DNA:polymorphisms:cds:HLA-DQA1*0102 (human)		 RGD PMID:12651073 RGD:40902999 NCBI chr17:34,501,718...34,506,797
Ensembl chr17:34,501,718...34,506,797 		JBrowse link
G H2-Eb1 histocompatibility 2, class II antigen E beta susceptibility ISO DNA:polymorphisms:cds:HLA-DRB1*1501 (human) RGD PMID:12651073 RGD:40902999 NCBI chr17:34,524,841...34,535,648
Ensembl chr17:34,524,841...34,535,648 		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 chr10:118,276,951...118,281,799
Ensembl chr10:118,276,951...118,281,797 		JBrowse link
G Il17a interleukin 17A treatment IDA RGD PMID:25129462 RGD:9244623 NCBI chr 1:20,801,129...20,804,720
Ensembl chr 1:20,801,129...20,804,720 		JBrowse link
G Il18 interleukin 18 IEP RGD PMID:20980973 RGD:6893449 NCBI chr 9:50,466,000...50,493,141
Ensembl chr 9:50,466,127...50,493,140 		JBrowse link
G Il1b interleukin 1 beta IDA
IEP		 mRNA:increased expression:renal glomerulus (mouse) RGD PMID:21641991 PMID:20410215 RGD:7175315, RGD:7175344 NCBI chr 2:129,206,490...129,213,059
Ensembl chr 2:129,206,490...129,213,059 		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 2:24,226,872...24,241,503
Ensembl chr 2:24,226,865...24,241,506 		JBrowse link
G Itgam integrin alpha M ISO RGD PMID:21719445 RGD:5147916 NCBI chr 7:127,661,812...127,717,663
Ensembl chr 7:127,661,812...127,717,663 		JBrowse link
G Jak1 Janus kinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31182691 NCBI chr 4:101,009,171...101,122,493
Ensembl chr 4:101,009,564...101,122,479 		JBrowse link
G Klkb1 kallikrein B, plasma 1 susceptibility ISO DNA:SNPs:promoter: RGD PMID:19307730 RGD:7327150 NCBI chr 8:45,719,725...45,747,872
Ensembl chr 8:45,719,726...45,747,896 		JBrowse link
G Mbl2 mannose-binding lectin (protein C) 2 disease_progression ISO DNA:polymorphism:exon: RGD PMID:24850777 RGD:12910847 NCBI chr19:30,210,306...30,217,087
Ensembl chr19:30,210,342...30,217,087 		JBrowse link
G Mir125a microRNA 125a ISO RNA:decreased expression:kidney RGD PMID:30972208 RGD:26884458 NCBI chr17:18,051,074...18,051,141
Ensembl chr17:18,051,074...18,051,141 		JBrowse link
G Mmp2 matrix metallopeptidase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22479529 NCBI chr 8:93,553,920...93,580,049
Ensembl chr 8:93,553,919...93,580,048 		JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22479529 NCBI chr 2:164,782,246...164,797,770
Ensembl chr 2:164,782,700...164,797,770 		JBrowse link
G Mpo myeloperoxidase susceptibility ISO DNA:polymorphism: :−463G > A (human) RGD PMID:17896805 RGD:7174701 NCBI chr11:87,684,610...87,695,238
Ensembl chr11:87,684,407...87,695,239 		JBrowse link
G Mtor mechanistic target of rapamycin kinase IMP RGD PMID:17283580 RGD:7245502 NCBI chr 4:148,533,039...148,642,142
Ensembl chr 4:148,533,068...148,642,140 		JBrowse link
G Muc20 mucin 20 IEP RGD PMID:14565953 RGD:7364790 NCBI chr16:32,597,793...32,617,805
Ensembl chr16:32,597,793...32,617,805 		JBrowse link
G Nr3c1 nuclear receptor subfamily 3, group C, member 1 IEP
ISO		 RGD PMID:21509671 PMID:17880936 RGD:7174713, RGD:7174734 NCBI chr18:39,543,598...39,652,485
Ensembl chr18:39,543,598...39,652,474 		JBrowse link
G Otub1 OTU domain, ubiquitin aldehyde binding 1 ISO protein:increased expression:kidney RGD PMID:22279542 RGD:7175260 NCBI chr19:7,175,571...7,183,649
Ensembl chr19:7,175,567...7,183,681 		JBrowse link
G Pdcd1 programmed cell death 1 onset ISO
IMP		 DNA:polymorphism: :
DNA:polymorphism:intron:6867 C>T (human)		 RGD PMID:15934088 PMID:15352422 PMID:21041733 RGD:7248675, RGD:7248676, RGD:7248678 NCBI chr 1:93,966,027...93,980,278
Ensembl chr 1:93,966,027...93,980,278 		JBrowse link
G Sell selectin, lymphocyte IEP RGD PMID:20512127 RGD:7175284 NCBI chr 1:163,889,556...163,908,354
Ensembl chr 1:163,889,551...163,911,750 		JBrowse link
G Serping1 serine (or cysteine) peptidase inhibitor, clade G, member 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:4014294 NCBI chr 2:84,595,704...84,605,748
Ensembl chr 2:84,595,731...84,605,788 		JBrowse link
G Snrpe small nuclear ribonucleoprotein E treatment IDA mouse model RGD PMID:15494537 RGD:10760401 NCBI chr 1:133,531,609...133,538,018
Ensembl chr 1:133,531,609...133,538,029 		JBrowse link
G Stat1 signal transducer and activator of transcription 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31182691 NCBI chr 1:52,158,588...52,201,024
Ensembl chr 1:52,158,599...52,201,024 		JBrowse link
G Stat4 signal transducer and activator of transcription 4 IMP RGD PMID:20980973 RGD:6893449 NCBI chr 1:52,026,265...52,146,348
Ensembl chr 1:52,026,307...52,146,348 		JBrowse link
G Stat6 signal transducer and activator of transcription 6 disease_progression IMP RGD PMID:12874250 RGD:7244140 NCBI chr10:127,478,855...127,496,856
Ensembl chr10:127,478,855...127,496,826 		JBrowse link
G Tlr7 toll-like receptor 7 IMP RGD PMID:19944565 RGD:7246905 NCBI chr  X:166,086,376...166,113,570
Ensembl chr  X:166,087,925...166,113,554 		JBrowse link
G Tlr9 toll-like receptor 9 no_association
treatment
severity		 IMP
ISO
IDA
IEP		 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 9:106,099,797...106,104,075
Ensembl chr 9:106,099,797...106,104,082 		JBrowse link
G Tnf tumor necrosis factor ISO protein:increased expression:glomerular mesangial cell RGD PMID:7750940 RGD:7394786 NCBI chr17:35,418,343...35,420,983
Ensembl chr17:35,418,357...35,420,983 		JBrowse link
G Tnfrsf11b tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) ISO associated with Lupus Erythematosus, Systemic;protein:increased expression:urine RGD PMID:21691937 RGD:7205483 NCBI chr15:54,114,014...54,141,700
Ensembl chr15:54,114,015...54,141,880 		JBrowse link
G Tnfrsf1a tumor necrosis factor receptor superfamily, member 1a severity IGI
ISO		 RGD PMID:19201910 PMID:10906156 RGD:7245569, RGD:7245572 NCBI chr 6:125,326,686...125,339,446
Ensembl chr 6:125,326,325...125,339,447 		JBrowse link
G Tnfrsf1b tumor necrosis factor receptor superfamily, member 1b treatment ISO
IDA		 RGD PMID:22846145 PMID:22674120 RGD:7245541, RGD:7245544 NCBI chr 4:144,938,938...144,973,453
Ensembl chr 4:144,940,033...144,973,440 		JBrowse link
G Vcam1 vascular cell adhesion molecule 1 severity ISO protein:increased expression:urine RGD PMID:22788914 RGD:7241032 NCBI chr 3:115,903,669...115,923,337
Ensembl chr 3:115,903,598...115,923,337 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16268
    disease of anatomical entity 15860
      Immune & Inflammatory Diseases 5361
        Inflammation 2605
          nephritis 423
            lupus nephritis 53
Path 2
Term Annotations click to browse term
  disease 16268
    disease of anatomical entity 15860
      Immune & Inflammatory Diseases 5361
        immune system disease 4766
          primary immunodeficiency disease 4192
            autoimmune disease 2126
              autoimmune disease of musculoskeletal system 939
                lupus erythematosus 220
                  systemic lupus erythematosus 212
                    lupus nephritis 53
paths to the root