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: clear cell renal cell carcinoma
Accession: DOID:4467
browse the term
Definition: A renal cell carcinoma that has_material_basis_in cells that appear very pale or clear when examined under microscope. (DO)
Synonyms: exact_synonym: ccRCC; clear cell RCC; clear cell carcinoma of kidney; clear cell kidney carcinoma; conventional (Clear cell) renal cell carcinoma; conventional renal cell carcinoma; cystic-multilocular variant; renal clear cell carcinoma
related_synonym: clear-cell metastatic renal cell carcinoma
primary_id: MESH:C538445
xref: EFO:0000349 ; EFO:0000376 ; EFO:0000682 ; GARD:9574 ; MONDO:0005005 ; NCI:C4033 ; ORDO:319276
For additional species annotation, visit the
Alliance of Genome Resources .
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Ackr3
atypical chemokine receptor 3
ISO
mRNA:increased expression:kidney:
RGD
PMID:29218250
RGD:155804290
NCBI chr 9:90,799,682...90,811,246
Ensembl chr 9:90,799,686...90,811,237
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Ager
advanced glycosylation end product-specific receptor
ISO
mRNA:increased expression:renal cortex (human)
RGD
PMID:21947243
RGD:7244181
NCBI chr20:4,148,150...4,151,361
Ensembl chr20:4,147,890...4,151,078
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Atm
ATM serine/threonine kinase
ISO
ClinVar Annotator: match by term: Clear cell carcinoma of kidney
ClinVar
PMID:8755918 PMID:9792409 PMID:10980530 PMID:18560558 PMID:19431188 PMID:19691550 PMID:19779456 PMID:25186627 PMID:25741868 PMID:26628246 PMID:28492532 PMID:29522266 PMID:33747920 More...
NCBI chr 8:53,828,741...53,932,773
Ensembl chr 8:53,831,093...53,932,437
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Atp5mc2
ATP synthase membrane subunit c locus 2
ISO
RGD
PMID:28672194
RGD:14696810
NCBI chr 7:133,791,341...133,799,713
Ensembl chr 7:133,791,342...133,799,733
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Atp5pb
ATP synthase peripheral stalk-membrane subunit b
ISO
RGD
PMID:28672194
RGD:14696810
NCBI chr 2:193,424,138...193,435,418
Ensembl chr 2:193,424,047...193,435,418
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Atp5po
ATP synthase peripheral stalk subunit OSCP
ISO
RGD
PMID:28672194
RGD:14696810
NCBI chr11:31,165,218...31,171,530
Ensembl chr11:31,165,217...31,171,592
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Bap1
Brca1 associated protein 1
ISO
ClinVar Annotator: match by term: Clear cell carcinoma of kidney
ClinVar
PMID:25741868 PMID:28492532 PMID:35483881 PMID:35992853
NCBI chr16:6,446,709...6,455,535
Ensembl chr16:6,446,709...6,455,535
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Bax
BCL2 associated X, apoptosis regulator
ISO
mRNA, protein:increased expression:kidney
RGD
PMID:28551630
RGD:15036804
NCBI chr 1:95,940,001...95,945,407
Ensembl chr 1:95,938,808...95,945,368
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Birc3
baculoviral IAP repeat-containing 3
disease_progression
ISO
mRNA:increased expression:kidney (human)
RGD
PMID:31964418
RGD:153344516
NCBI chr 8:5,000,844...5,028,470
Ensembl chr 8:5,000,845...5,015,802
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Birc5
baculoviral IAP repeat-containing 5
exacerbates
ISO
mRNA:increased expression:kidney (human)
RGD
PMID:31964418
RGD:153344516
NCBI chr10:103,072,530...103,081,382
Ensembl chr10:103,073,408...103,081,380
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Birc6
baculoviral IAP repeat-containing 6
ameliorates
ISO
mRNA:increased expression:kidney (human)
RGD
PMID:31964418
RGD:153344516
NCBI chr 6:20,722,922...20,916,396
Ensembl chr 6:20,722,922...20,916,434
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C8h11orf65
similar to human chromosome 11 open reading frame 65
ISO
ClinVar Annotator: match by term: Clear cell carcinoma of kidney
ClinVar
PMID:8755918 PMID:9792409 PMID:10980530 PMID:18560558 PMID:19431188 PMID:19691550 PMID:19779456 PMID:25186627 PMID:25741868 PMID:26628246 PMID:28492532 PMID:29522266 PMID:33747920 More...
NCBI chr 8:53,796,033...53,825,277
Ensembl chr 8:53,796,366...53,824,748
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Chd4
chromodomain helicase DNA binding protein 4
ISO
mRNA:decreased expression:kidney (human)
RGD
PMID:28486105
RGD:153323299
NCBI chr 4:157,898,503...157,931,632
Ensembl chr 4:157,899,391...157,931,541
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Cxcl12
C-X-C motif chemokine ligand 12
ISO
mRNA:decreased expression:kidney:
RGD
PMID:29218250
RGD:155804290
NCBI chr 4:150,388,326...150,401,173
Ensembl chr 4:150,388,325...150,401,168
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Cxcr4
C-X-C motif chemokine receptor 4
ISO
mRNA:increased expression:kidney:
RGD
PMID:29218250
RGD:155804290
NCBI chr13:40,077,976...40,081,883
Ensembl chr13:40,077,976...40,081,883
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Ddr1
discoidin domain receptor tyrosine kinase 1
severity
ISO
mRNA, protein:decreased expression:kidney (human) mRNA:increased expression:kidney, lymph nodes (human)
RGD
PMID:31018949 PMID:27020590
RGD:151347528 , RGD:151347863
NCBI chr20:3,042,494...3,064,442
Ensembl chr20:3,044,320...3,064,468
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Dnmt1
DNA methyltransferase 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:27292127
NCBI chr 8:19,440,611...19,486,659
Ensembl chr 8:19,440,611...19,486,659
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Dnmt3a
DNA methyltransferase 3 alpha
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:27292127
NCBI chr 6:26,791,517...26,902,161
Ensembl chr 6:26,822,609...26,896,687
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Egln3
egl-9 family hypoxia-inducible factor 3
disease_progression
ISO
RGD
PMID:23788753
RGD:13506731
NCBI chr 6:71,650,297...71,675,766
Ensembl chr 6:71,650,297...71,675,766
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Eng
endoglin
severity
ISO
protein:increased expression:tumor, vasculature (human) protein:decreased expression:kidney, tumor (human)
RGD
PMID:22204709 PMID:16536758
RGD:7248775 , RGD:7248780
NCBI chr 3:15,934,566...15,972,618
Ensembl chr 3:15,934,518...15,973,230
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Ep300
E1A binding protein p300
severity
ISO
mRNA:altered expression:kidney, tumor (human) mRNA, protein:increased expression:kidney
RGD
PMID:23029358 PMID:28551630
RGD:7296925 , RGD:15036804
NCBI chr 7:113,108,476...113,178,529
Ensembl chr 7:113,106,247...113,136,088 Ensembl chr 7:113,106,247...113,136,088
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F2
coagulation factor II, thrombin
ISO
protein:increased expression:brain
RGD
PMID:22065054
RGD:6893520
NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486
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Flt4
Fms related receptor tyrosine kinase 4
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:25239121
NCBI chr10:33,913,725...33,954,770
Ensembl chr10:33,913,608...33,954,770
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Fto
FTO, alpha-ketoglutarate dependent dioxygenase
disease_progression treatment
ISO
mRNA:decreased expression:kidney mRNA:increased expression:kidney
RGD
PMID:30648791 PMID:32817424 PMID:32817424
RGD:329812005 , RGD:329812006 , RGD:329812006
NCBI chr19:15,284,898...15,692,142
Ensembl chr19:15,349,696...15,692,083
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Gata1
GATA binding protein 1
disease_progression
ISO
RGD
PMID:25230694
RGD:149735195
NCBI chr X:14,529,706...14,537,530
Ensembl chr X:14,529,702...14,537,530
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Gata2
GATA binding protein 2
disease_progression
ISO
RGD
PMID:25230694
RGD:149735195
NCBI chr 4:120,654,205...120,667,763
Ensembl chr 4:120,658,986...120,667,761
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Gstp1
glutathione S-transferase pi 1
ISO
RGD
PMID:10383153
RGD:6906878
NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226
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Hnf1a
HNF1 homeobox A
ISO
ClinVar Annotator: match by term: Clear cell carcinoma of kidney
ClinVar
PMID:8866553 PMID:8945470 PMID:9032114 PMID:9045858 PMID:9075818 PMID:9166684 PMID:9313763 PMID:9392505 PMID:9439666 PMID:9754819 PMID:10333057 PMID:10447526 PMID:10754480 PMID:10966642 PMID:11058894 PMID:11315851 PMID:11393552 PMID:12050210 PMID:12355088 PMID:12530534 PMID:12574234 PMID:12618559 PMID:14747304 PMID:15649945 PMID:15928245 PMID:17054605 PMID:17407387 PMID:17440016 PMID:17573900 PMID:17937063 PMID:17989309 PMID:18003757 PMID:18672310 PMID:19169489 PMID:19929997 PMID:21051477 PMID:21628466 PMID:21696527 PMID:22348187 PMID:22432108 PMID:23348805 PMID:23551881 PMID:23607861 PMID:24097065 PMID:25174781 PMID:25555642 PMID:25741868 PMID:26059258 PMID:26431509 PMID:26467025 PMID:27148439 PMID:28395978 PMID:28492532 PMID:28862987 PMID:29417725 PMID:30814848 PMID:31365591 PMID:31576961 PMID:31638168 PMID:32741144 PMID:34373539 More...
NCBI chr12:41,638,536...41,672,806
Ensembl chr12:41,645,587...41,672,104
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Igf1r
insulin-like growth factor 1 receptor
ISO
xenograph of human clear cell renal cancer cells in mouse
RGD
PMID:19509240
RGD:7242921
NCBI chr 1:121,549,831...121,838,548
Ensembl chr 1:121,550,743...121,831,777
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Iscu
iron-sulfur cluster assembly enzyme
disease_progression
ISO
mRNA,protein:decreased expression:kidney (human)
RGD
PMID:23449350
RGD:155260320
NCBI chr12:42,852,305...42,858,150
Ensembl chr12:42,852,305...42,858,150
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Kat8
lysine acetyltransferase 8
ISO
mRNA, protein:decreased expression:kidney (human)
RGD
PMID:23394073
RGD:9586034
NCBI chr 1:182,524,355...182,536,638
Ensembl chr 1:182,515,327...182,536,633
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Map3k8
mitogen-activated protein kinase kinase kinase 8
disease_progression ameliorates
ISO
RGD
PMID:23982215 PMID:23982215
RGD:151356974 , RGD:151356974
NCBI chr17:53,382,908...53,403,216
Ensembl chr17:53,383,131...53,403,216
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Mir210
microRNA 210
ISO
miRNA:increased expression:kidney (human)
RGD
PMID:23449350
RGD:155260320
NCBI chr 1:196,326,343...196,326,452
Ensembl chr 1:196,326,337...196,326,454
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Mmp12
matrix metallopeptidase 12
ISO
RGD
PMID:11576837
RGD:2290421
NCBI chr 8:4,581,785...4,591,687
Ensembl chr 8:4,581,785...4,599,611
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Mthfr
methylenetetrahydrofolate reductase
susceptibility severity
ISO
DNA:transition, transversion:cds:g.677C>T, g.1298A>C (human)
RGD
PMID:21489764 PMID:20039875
RGD:6893474 , RGD:6893632
NCBI chr 5:158,465,248...158,484,999
Ensembl chr 5:158,465,296...158,483,797
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Myc
MYC proto-oncogene, bHLH transcription factor
severity
ISO
protein:increased expression:kidney (human)
RGD
PMID:21881486
RGD:7207420
NCBI chr 7:93,593,705...93,598,633
Ensembl chr 7:93,593,705...93,598,630
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Ogg1
8-oxoguanine DNA glycosylase
ISO
ClinVar Annotator: match by term: Clear cell carcinoma of kidney
ClinVar
PMID:9681819 PMID:10987279 PMID:12172214 PMID:19537786 PMID:21195604 PMID:25741868 More...
NCBI chr 4:146,474,701...146,481,959
Ensembl chr 4:146,474,750...146,484,766
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Pak4
p21 (RAC1) activated kinase 4
disease_progression
ISO
RGD
PMID:25744653
RGD:13504816
NCBI chr 1:83,849,904...83,889,188
Ensembl chr 1:83,849,904...83,859,413
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Pak6
p21 (RAC1) activated kinase 6
disease_progression
ISO
RGD
PMID:24715215
RGD:13506722
NCBI chr 3:105,638,248...105,674,399
Ensembl chr 3:105,638,653...105,672,975
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Pbrm1
polybromo 1
ISO
ClinVar Annotator: match by term: Clear cell carcinoma of kidney
ClinVar
PMID:25911086
NCBI chr16:6,213,507...6,312,895
Ensembl chr16:6,213,300...6,311,780
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Pdgfb
platelet derived growth factor subunit B
disease_progression
ISO
RGD
PMID:25766258 PMID:23879920
RGD:13504817 , RGD:13506650
NCBI chr 7:111,539,444...111,557,984
Ensembl chr 7:111,540,345...111,557,984
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Pml
PML nuclear body scaffold
ISO
protein:decreased expression:kidney (human)
RGD
PMID:25293974
RGD:41404694
NCBI chr 8:58,627,347...58,661,927
Ensembl chr 8:58,628,837...58,658,971
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Ppbp
pro-platelet basic protein
disease_progression ameliorates
ISO
RGD
PMID:24335961 PMID:24335961
RGD:401794956 , RGD:401794956
NCBI chr14:17,302,326...17,303,130
Ensembl chr14:17,302,326...17,303,130
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Setd2
SET domain containing 2, histone lysine methyltransferase
severity
ISO
DNA:SNPs,loss of heterozygosity:multiple (human) DNA:mutations:multiple (human)
RGD
PMID:26864202 PMID:26891804
RGD:150429635 , RGD:150429640
NCBI chr 8:110,511,808...110,597,475
Ensembl chr 8:110,511,772...110,597,489
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Smarcb1
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
ISO
mRNA,protein:decreased expression:kidney:
RGD
PMID:29218250
RGD:155804290
NCBI chr20:12,741,164...12,763,616
Ensembl chr20:12,741,477...12,763,620
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Srsf1
serine and arginine rich splicing factor 1
ISO
mRNA:altered expression:kidney (human)
RGD
PMID:21082031
RGD:11039407
NCBI chr10:72,838,926...72,859,066
Ensembl chr10:72,839,274...72,845,336
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Srsf2
serine and arginine rich splicing factor 2
ISO
mRNA:altered expression:kidney (human)
RGD
PMID:21082031
RGD:11039407
NCBI chr10:102,052,158...102,055,365
Ensembl chr10:102,052,314...102,055,338
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Srsf4
serine and arginine rich splicing factor 4
ISO
mRNA:altered expression:kidney (human)
RGD
PMID:21082031
RGD:11039407
NCBI chr 5:144,060,981...144,090,798
Ensembl chr 5:144,061,463...144,089,229
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Srsf5
serine and arginine rich splicing factor 5
ISO
mRNA:altered expression:kidney (human)
RGD
PMID:21082031
RGD:11039407
NCBI chr 6:100,605,165...100,610,192
Ensembl chr 6:100,605,456...100,610,177
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Srsf6
serine and arginine rich splicing factor 6
ISO
mRNA:altered expression:kidney (human)
RGD
PMID:21082031
RGD:11039407
NCBI chr 3:151,589,546...151,594,869
Ensembl chr 3:151,589,535...151,594,860
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Srsf7
serine and arginine rich splicing factor 7
ISO
mRNA:altered expression:kidney (human)
RGD
PMID:21082031
RGD:11039407
NCBI chr 6:14,811,775...14,818,968
Ensembl chr 6:14,811,808...14,818,965
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Tp53
tumor protein p53
ISO
mRNA, protein:increased expression:kidney
RGD
PMID:28551630
RGD:15036804
NCBI chr10:54,300,070...54,311,525
Ensembl chr10:54,300,048...54,311,524
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Vegfa
vascular endothelial growth factor A
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:25239121
NCBI chr 9:14,955,300...14,970,641
Ensembl chr 9:14,955,300...14,970,641
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Xiap
X-linked inhibitor of apoptosis
ameliorates
ISO
mRNA:increased expression:kidney (human)
RGD
PMID:31964418
RGD:153344516
NCBI chr X:120,890,537...120,938,413
Ensembl chr X:120,897,907...120,934,700
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