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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 IAGP DNA:polymorphisms:promoter, intron:g.-429T>C rs1800625, g.-374T>A rs1800624, g.2184A>G rs3134940 (human) RGD PMID:22513366 RGD:6767309 NCBI chr 6:32,180,969...32,184,253
Ensembl chr 6:32,180,968...32,184,322 		JBrowse link
G APOC3 apolipoprotein C3 IEP protein:increased expression:serum RGD PMID:17957542 RGD:7207211 NCBI chr11:116,829,907...116,833,072
Ensembl chr11:116,829,706...116,833,072 		JBrowse link
G C3 complement C3 IEP
EXP		 protein:decreased expression:serum
CTD Direct Evidence: marker/mechanism		 CTD
RGD		 PMID:31182691 PMID:21888025 RGD:7175544 NCBI chr19:6,677,704...6,720,650
Ensembl chr19:6,677,704...6,730,562 		JBrowse link
G CCL2 C-C motif chemokine ligand 2 severity
susceptibility		 IEP
IAGP		 protein:increased expression:urine (human)
DNA:snp:promoter:g.-2518A>G (human)		 RGD PMID:8558841 PMID:15188361 RGD:8549732, RGD:11528534 NCBI chr17:34,255,285...34,257,203
Ensembl chr17:34,255,274...34,257,208 		JBrowse link
G CCL3 C-C motif chemokine ligand 3 ISO RGD PMID:18187931 RGD:7241814 NCBI chr17:36,088,256...36,090,143
Ensembl chr17:36,088,256...36,090,169 		JBrowse link
G CCR1 C-C motif chemokine receptor 1 disease_progression ISO RGD PMID:15153561 RGD:5688164 NCBI chr 3:46,201,711...46,208,313
Ensembl chr 3:46,201,711...46,208,313 		JBrowse link
G CD40 CD40 molecule treatment ISO RGD PMID:23799000 PMID:19265127 PMID:18566369 RGD:7248418, RGD:7248425, RGD:7248429 NCBI chr20:46,118,314...46,129,858
Ensembl chr20:46,118,271...46,129,863 		JBrowse link
G CD40LG CD40 ligand treatment IEP
ISO
IMP
IDA		 protein:increased expression:serum RGD PMID:20726330 PMID:11751940 PMID:12632425 PMID:13130474 PMID:15693003 RGD:7248426, RGD:7248714, RGD:7248710, RGD:7248600, RGD:7248439 NCBI chr  X:136,648,158...136,660,390
Ensembl chr  X:136,648,158...136,660,390 		JBrowse link
G CFB complement factor B ISO
IEP		 RGD PMID:10623824 PMID:3183062 PMID:21893562 RGD:7242736, RGD:7242763, RGD:7242755 NCBI chr 6:31,946,095...31,952,084
Ensembl chr 6:31,945,650...31,952,086 		JBrowse link
G CFH complement factor H IAGP RGD PMID:22171659 RGD:5684551 NCBI chr 1:196,652,043...196,747,504
Ensembl chr 1:196,651,754...196,752,476 		JBrowse link
G CLU clusterin ISO mRNA:increased expression: epithelial cell of renal tubule RGD PMID:9546356 RGD:8890679 NCBI chr 8:27,596,917...27,614,700
Ensembl chr 8:27,596,917...27,614,700 		JBrowse link
G COL1A1 collagen type I alpha 1 chain IEP
ISO		 associated with Graft vs Host Disease
mRNA, protein:increased expression:kidney cortex		 RGD PMID:21354048 PMID:7700025 PMID:7723234 RGD:5688301, RGD:5688333, RGD:5688332 NCBI chr17:50,184,101...50,201,631
Ensembl chr17:50,184,101...50,201,632 		JBrowse link
G CRP C-reactive protein no_association IDA
IAGP		 DNA:SNP RGD PMID:18852001 PMID:17596285 PMID:20039408 PMID:15692982 RGD:6907400, RGD:5508454, RGD:6909146, RGD:6909145 NCBI chr 1:159,712,289...159,714,589
Ensembl chr 1:159,712,289...159,714,589 		JBrowse link
G CSF1 colony stimulating factor 1 ISO
IEP		 RGD PMID:21885670 PMID:17659436 RGD:7257567, RGD:7257589 NCBI chr 1:109,910,506...109,930,992
Ensembl chr 1:109,910,242...109,930,992 		JBrowse link
G CTLA4 cytotoxic T-lymphocyte associated protein 4 IDA RGD PMID:15146424 RGD:7204726 NCBI chr 2:203,867,771...203,873,965
Ensembl chr 2:203,853,888...203,873,965 		JBrowse link
G EGF epidermal growth factor IEP RGD PMID:21354048 RGD:5688301 NCBI chr 4:109,912,883...110,013,766
Ensembl chr 4:109,912,883...110,013,766 		JBrowse link
G FAS Fas cell surface death receptor EXP CTD Direct Evidence: marker/mechanism CTD PMID:33632240 PMID:38555047 NCBI chr10:88,964,050...89,017,059
Ensembl chr10:88,953,813...89,029,605 		JBrowse link
G FCGR2A Fc gamma receptor IIa IAGP 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 chr 1:161,505,457...161,524,048
Ensembl chr 1:161,505,430...161,524,013 		JBrowse link
G FCGR2B Fc gamma receptor IIb ISO RGD PMID:15681388 RGD:7240529 NCBI chr 1:161,647,243...161,678,654
Ensembl chr 1:161,663,143...161,678,654 		JBrowse link
G FCGR3A Fc gamma receptor IIIa susceptibility IAGP DNA:SNP:cds:p.V158F (human) RGD PMID:17596285 RGD:5508454 NCBI chr 1:161,541,759...161,550,737
Ensembl chr 1:161,541,759...161,550,968 		JBrowse link
G FCGR3B Fc gamma receptor IIIb EXP CTD Direct Evidence: marker/mechanism CTD PMID:16482158 NCBI chr 1:161,623,196...161,631,963
Ensembl chr 1:161,623,196...161,631,963 		JBrowse link
G HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 susceptibility IAGP DNA:polymorphisms:cds:HLA-DQA1*0101 (human)
DNA:polymorphisms:cds:HLA-DQA1*0102 (human)		 RGD PMID:12651073 PMID:12651073 RGD:40902999, RGD:40902999 NCBI chr 6:32,637,406...32,655,272
Ensembl chr 6:32,628,179...32,647,062 		JBrowse link
G HLA-DRB1 major histocompatibility complex, class II, DR beta 1 susceptibility IAGP DNA:polymorphisms:cds:HLA-DRB1*1501 (human) RGD PMID:12651073 RGD:40902999 NCBI chr 6:32,578,775...32,589,848
Ensembl chr 6:32,577,902...32,589,848 		JBrowse link
G IFNG interferon gamma IEP
EXP
IDA		 protein:increased expression:serum,urine
CTD Direct Evidence: marker/mechanism
protein:increased processing:kidney		 CTD
RGD		 PMID:31182691 PMID:22764573 PMID:29925830 RGD:6893369, RGD:14974252 NCBI chr12:68,154,768...68,159,740
Ensembl chr12:68,154,768...68,159,740 		JBrowse link
G IL17A interleukin 17A treatment ISO RGD PMID:25129462 RGD:9244623 NCBI chr 6:52,186,375...52,190,638
Ensembl chr 6:52,186,375...52,190,638 		JBrowse link
G IL18 interleukin 18 ISO RGD PMID:20980973 RGD:6893449 NCBI chr11:112,143,260...112,164,094
Ensembl chr11:112,143,251...112,164,096 		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 2:112,829,751...112,836,779
Ensembl chr 2:112,829,751...112,836,816 		JBrowse link
G IL1RN interleukin 1 receptor antagonist resistance IEP associated with Lupus Erythematosus, Systemic; protein:increased expression:serum (human) RGD PMID:20538031 RGD:6907068 NCBI chr 2:113,099,360...113,134,014
Ensembl chr 2:113,099,315...113,134,016 		JBrowse link
G ITGAM integrin subunit alpha M IAGP RGD PMID:21719445 RGD:5147916 NCBI chr16:31,259,975...31,332,877
Ensembl chr16:31,259,967...31,332,892 		JBrowse link
G JAK1 Janus kinase 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:31182691 NCBI chr 1:64,833,229...65,067,746
Ensembl chr 1:64,833,223...65,067,754 		JBrowse link
G KLKB1 kallikrein B1 susceptibility IAGP DNA:SNPs:promoter: RGD PMID:19307730 RGD:7327150 NCBI chr 4:186,210,853...186,258,471
Ensembl chr 4:186,226,438...186,258,471 		JBrowse link
G MBL2 mannose binding lectin 2 disease_progression IAGP DNA:polymorphism:exon: RGD PMID:24850777 RGD:12910847 NCBI chr10:52,765,380...52,772,784
Ensembl chr10:52,765,380...52,772,784 		JBrowse link
G MIR125A microRNA 125a ISO RNA:decreased expression:kidney RGD PMID:30972208 RGD:26884458 NCBI chr19:51,693,254...51,693,339
Ensembl chr19:51,693,254...51,693,339 		JBrowse link
G MMP2 matrix metallopeptidase 2 EXP CTD Direct Evidence: marker/mechanism CTD PMID:22479529 NCBI chr16:55,478,830...55,506,691
Ensembl chr16:55,389,700...55,506,691 		JBrowse link
G MMP9 matrix metallopeptidase 9 EXP CTD Direct Evidence: marker/mechanism CTD PMID:22479529 NCBI chr20:46,008,908...46,016,561
Ensembl chr20:46,008,908...46,016,561 		JBrowse link
G MPO myeloperoxidase susceptibility IAGP DNA:polymorphism: :−463G > A (human) RGD PMID:17896805 RGD:7174701 NCBI chr17:58,269,855...58,280,935
Ensembl chr17:58,269,855...58,280,935 		JBrowse link
G MTOR mechanistic target of rapamycin kinase ISO RGD PMID:17283580 RGD:7245502 NCBI chr 1:11,106,535...11,262,551
Ensembl chr 1:11,106,535...11,262,556 		JBrowse link
G MUC20 mucin 20, cell surface associated ISO RGD PMID:14565953 RGD:7364790 NCBI chr 3:195,720,978...195,733,551
Ensembl chr 3:195,720,884...195,741,123 		JBrowse link
G NR3C1 nuclear receptor subfamily 3 group C member 1 ISO
IEP		 RGD PMID:21509671 PMID:17880936 RGD:7174713, RGD:7174734 NCBI chr 5:143,277,931...143,435,512
Ensembl chr 5:143,277,931...143,435,512 		JBrowse link
G OTUB1 OTU deubiquitinase, ubiquitin aldehyde binding 1 IEP protein:increased expression:kidney RGD PMID:22279542 RGD:7175260 NCBI chr11:63,986,438...63,998,412
Ensembl chr11:63,985,853...64,001,811 		JBrowse link
G PDCD1 programmed cell death 1 onset IAGP
ISO		 DNA:polymorphism: :
DNA:polymorphism:intron:6867 C>T (human)		 RGD PMID:15934088 PMID:21041733 PMID:15352422 RGD:7248675, RGD:7248678, RGD:7248676 NCBI chr 2:241,849,884...241,858,894
Ensembl chr 2:241,849,884...241,858,894 		JBrowse link
G SELL selectin L ISO RGD PMID:20512127 RGD:7175284 NCBI chr 1:169,690,667...169,711,620
Ensembl chr 1:169,690,665...169,711,702 		JBrowse link
G SERPING1 serpin family G member 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:4014294 NCBI chr11:57,597,685...57,614,848
Ensembl chr11:57,597,387...57,619,171 		JBrowse link
G SNRPE small nuclear ribonucleoprotein polypeptide E treatment IDA mouse model RGD PMID:15494537 RGD:10760401 NCBI chr 1:203,861,599...203,871,152
Ensembl chr 1:203,861,599...203,871,152 		JBrowse link
G STAT1 signal transducer and activator of transcription 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:31182691 NCBI chr 2:190,969,149...191,014,171
Ensembl chr 2:190,908,460...191,020,960 		JBrowse link
G STAT4 signal transducer and activator of transcription 4 ISO RGD PMID:20980973 RGD:6893449 NCBI chr 2:191,029,576...191,151,596
Ensembl chr 2:191,029,576...191,178,435 		JBrowse link
G STAT6 signal transducer and activator of transcription 6 disease_progression ISO RGD PMID:12874250 RGD:7244140 NCBI chr12:57,095,408...57,111,362
Ensembl chr12:57,095,408...57,132,139 		JBrowse link
G TLR7 toll like receptor 7 ISO RGD PMID:19944565 RGD:7246905 NCBI chr  X:12,867,072...12,890,361
Ensembl chr  X:12,867,072...12,890,361 		JBrowse link
G TLR9 toll like receptor 9 severity
treatment
no_association		 ISO
IEP
IAGP		 mRNA, protein:increased expression:kidney (mouse)
associated with Graft vs Host Disease
protein:increased expression:renal glomerulus (human)
associated with Lupus Erythematosus, Systemic; DNA:snps:promoter, intron:g.-1486T>C, g.+1174A>G (rs187084, rs352139) (human, North Indian)
DNA:snps:intron, exon:g.+1174G>A, g.+1635C>T (rs352139, rs352140) (human, Chinese)		 RGD PMID:23467932 PMID:17469139 PMID:21127878 PMID:19578108 PMID:22787315 More... RGD:7245987, RGD:7246911, RGD:7246897, RGD:7246896, RGD:7245989, RGD:7246884 NCBI chr 3:52,221,080...52,225,645
Ensembl chr 3:52,221,080...52,225,645 		JBrowse link
G TNF tumor necrosis factor IEP protein:increased expression:glomerular mesangial cell RGD PMID:7750940 RGD:7394786 NCBI chr 6:31,575,565...31,578,336
Ensembl chr 6:31,575,565...31,578,336 		JBrowse link
G TNFRSF11B TNF receptor superfamily member 11b IEP associated with Lupus Erythematosus, Systemic;protein:increased expression:urine RGD PMID:21691937 RGD:7205483 NCBI chr 8:118,923,557...118,951,885
Ensembl chr 8:118,923,557...118,951,885 		JBrowse link
G TNFRSF1A TNF receptor superfamily member 1A severity ISO
IEP		 RGD PMID:19201910 PMID:10906156 RGD:7245569, RGD:7245572 NCBI chr12:6,328,771...6,342,076
Ensembl chr12:6,328,757...6,342,114 		JBrowse link
G TNFRSF1B TNF receptor superfamily member 1B treatment IDA
ISO		 RGD PMID:22846145 PMID:22674120 RGD:7245541, RGD:7245544 NCBI chr 1:12,166,991...12,209,220
Ensembl chr 1:12,166,991...12,209,228 		JBrowse link
G VCAM1 vascular cell adhesion molecule 1 severity IEP protein:increased expression:urine RGD PMID:22788914 RGD:7241032 NCBI chr 1:100,719,742...100,739,045
Ensembl chr 1:100,719,742...100,739,045 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 145369
    disease of anatomical entity 132557
      Immune & Inflammatory Diseases 27359
        Inflammation 15345
          nephritis 840
            lupus nephritis 73
Path 2
Term Annotations click to browse term
  disease 145369
    disease of anatomical entity 132557
      Immune & Inflammatory Diseases 27359
        immune system disease 23205
          primary immunodeficiency disease 17469
            autoimmune disease 13419
              autoimmune disease of musculoskeletal system 8450
                lupus erythematosus 1724
                  systemic lupus erythematosus 1701
                    lupus nephritis 73
paths to the root