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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:clear cell renal cell carcinoma
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Accession:DOID:4467 term browser 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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clear cell renal cell carcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G 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 9:98,246,605...98,260,214 		JBrowse link
G Ager advanced glycosylation end product-specific receptor ISO mRNA:increased expression:renal cortex (human) RGD PMID:21947243 RGD:7244181 NCBI chr20:4,152,758...4,155,956
Ensembl chr20:4,151,965...4,155,685 		JBrowse link
G 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 More... NCBI chr 8:62,724,939...62,829,040
Ensembl chr 8:62,727,291...62,828,629 		JBrowse link
G 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 7:135,669,848...135,678,231 		JBrowse link
G 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 2:196,112,108...196,124,387 		JBrowse link
G Atp5po ATP synthase peripheral stalk subunit OSCP ISO RGD PMID:28672194 RGD:14696810 NCBI chr11:44,651,171...44,657,483
Ensembl chr11:44,651,173...44,657,520 		JBrowse link
G Bap1 BRCA1 associated deubiquitinase 1 ISO ClinVar Annotator: match by term: Clear cell carcinoma of kidney ClinVar PMID:25741868 PMID:28492532 PMID:35483881 PMID:35992853 NCBI chr16:6,453,126...6,461,952
Ensembl chr16:6,452,974...6,461,952 		JBrowse link
G Bax BCL2 associated X, apoptosis regulator ISO mRNA, protein:increased expression:kidney RGD PMID:28551630 RGD:15036804 NCBI chr 1:105,076,472...105,081,906
Ensembl chr 1:105,076,473...105,086,429 		JBrowse link
G Birc3 baculoviral IAP repeat-containing 3 disease_progression ISO mRNA:increased expression:kidney (human) RGD PMID:31964418 RGD:153344516 NCBI chr 8:13,285,702...13,313,329
Ensembl chr 8:13,285,703...13,298,590 		JBrowse link
G Birc5 baculoviral IAP repeat-containing 5 exacerbates ISO mRNA:increased expression:kidney (human) RGD PMID:31964418 RGD:153344516 NCBI chr10:103,567,369...103,580,069
Ensembl chr10:103,572,080...103,582,155 		JBrowse link
G 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 6:26,474,843...26,668,507 		JBrowse link
G 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 More... NCBI chr 8:62,692,123...62,720,951
Ensembl chr 8:62,692,568...62,720,946 		JBrowse link
G 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 4:159,584,654...159,617,866 		JBrowse link
G Cxcl12 C-X-C motif chemokine ligand 12 ISO mRNA:decreased expression:kidney: RGD PMID:29218250 RGD:155804290 NCBI chr 4:152,060,781...152,073,628
Ensembl chr 4:152,060,780...152,073,627 		JBrowse link
G Cxcr4 C-X-C motif chemokine receptor 4 ISO mRNA:increased expression:kidney: RGD PMID:29218250 RGD:155804290 NCBI chr13:42,630,383...42,634,288
Ensembl chr13:42,630,104...42,634,459 		JBrowse link
G 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 chr20:3,047,269...3,069,277
Ensembl chr20:3,050,375...3,069,276 		JBrowse link
G Dnmt1 DNA methyltransferase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27292127 NCBI chr 8:27,716,797...27,763,405
Ensembl chr 8:27,716,797...27,763,119 		JBrowse link
G Dnmt3a DNA methyltransferase 3 alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:27292127 NCBI chr 6:32,507,316...32,621,678
Ensembl chr 6:32,512,070...32,614,970 		JBrowse link
G Egln3 egl-9 family hypoxia-inducible factor 3 disease_progression ISO RGD PMID:23788753 RGD:13506731 NCBI chr 6:77,385,549...77,411,015
Ensembl chr 6:77,385,549...77,411,015 		JBrowse link
G 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 3:36,332,190...36,370,324
Ensembl chr 3:36,326,202...36,370,933 		JBrowse link
G 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 7:114,987,857...115,058,652
Ensembl chr 7:114,946,982...115,058,574 		JBrowse link
G F2 coagulation factor II, thrombin ISO protein:increased expression:brain RGD PMID:22065054 RGD:6893520 NCBI chr 3:98,051,958...98,065,246
Ensembl chr 3:98,051,960...98,065,246 		JBrowse link
G 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 chr10:34,414,733...34,456,645 		JBrowse link
G 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 chr19:31,456,749...31,865,011
Ensembl chr19:31,522,293...31,864,957 		JBrowse link
G Gata1 GATA binding protein 1 disease_progression ISO RGD PMID:25230694 RGD:149735195 NCBI chr  X:17,193,291...17,209,462
Ensembl chr  X:17,201,633...17,209,459 		JBrowse link
G Gata2 GATA binding protein 2 disease_progression ISO RGD PMID:25230694 RGD:149735195 NCBI chr 4:122,211,501...122,225,058
Ensembl chr 4:122,211,829...122,225,055 		JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO RGD PMID:10383153 RGD:6906878 NCBI chr 1:210,767,237...210,770,242
Ensembl chr 1:210,767,237...210,769,705 		JBrowse link
G Hnf1a HNF1 homeobox A ISO ClinVar Annotator: match by term: Clear cell carcinoma of kidney | ClinVar Annotator: match by term: Clear cell renal carcinoma ClinVar PMID:8866553 PMID:8945470 PMID:9032114 PMID:9045858 PMID:9075818 More... NCBI chr12:47,299,171...47,333,457
Ensembl chr12:47,306,245...47,332,755 		JBrowse link
G 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 1:130,959,787...131,248,664
Ensembl chr 1:130,959,997...131,248,664 		JBrowse link
G 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 chr12:48,512,852...48,518,696 		JBrowse link
G 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 1:191,954,438...191,967,105 		JBrowse link
G 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 chr17:58,078,320...58,098,452 		JBrowse link
G 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 1:205,755,917...205,756,034 		JBrowse link
G Mmp12 matrix metallopeptidase 12 ISO RGD PMID:11576837 RGD:2290421 NCBI chr 8:4,581,785...4,591,687
Ensembl chr 8:12,866,641...12,884,478 		JBrowse link
G 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 5:163,748,346...163,768,141
Ensembl chr 5:163,748,321...163,768,105 		JBrowse link
G Myc MYC proto-oncogene, bHLH transcription factor severity ISO protein:increased expression:kidney (human) RGD PMID:21881486 RGD:7207420 NCBI chr 7:95,483,105...95,488,031
Ensembl chr 7:95,483,105...95,488,028 		JBrowse link
G 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 More... NCBI chr 4:146,474,701...146,481,959
Ensembl chr 4:148,030,349...148,037,604 		JBrowse link
G 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 1:92,977,437...93,016,721 		JBrowse link
G 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 3:126,093,013...126,128,318 		JBrowse link
G 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 chr16:6,219,917...6,319,336 		JBrowse link
G Pdgfb platelet derived growth factor subunit B disease_progression ISO RGD PMID:25766258 PMID:23879920 RGD:13504817, RGD:13506650 NCBI chr 7:113,419,882...113,438,343
Ensembl chr 7:113,420,710...113,438,343 		JBrowse link
G Pml PML nuclear body scaffold ISO protein:decreased expression:kidney (human) RGD PMID:25293974 RGD:41404694 NCBI chr 8:67,523,164...67,557,801
Ensembl chr 8:67,523,164...67,576,083 		JBrowse link
G 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 chr14:17,586,495...17,587,299 		JBrowse link
G 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 8:119,390,207...119,475,863
Ensembl chr 8:119,390,207...119,475,863 		JBrowse link
G Smarcb1 SWI/SNF related BAF chromatin remodeling complex subunit B1 ISO mRNA,protein:decreased expression:kidney: RGD PMID:29218250 RGD:155804290 NCBI chr20:12,741,164...12,763,616
Ensembl chr20:12,740,943...12,763,055 		JBrowse link
G 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 chr10:73,336,422...73,342,548 		JBrowse link
G 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 chr10:102,553,072...102,554,141 		JBrowse link
G 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 5:149,345,422...149,374,609 		JBrowse link
G 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 6:106,336,756...106,341,931 		JBrowse link
G 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 3:172,009,061...172,014,392 		JBrowse link
G 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 6:20,564,044...20,571,212 		JBrowse link
G Tp53 tumor protein p53 ISO mRNA, protein:increased expression:kidney RGD PMID:28551630 RGD:15036804 NCBI chr10:54,798,871...54,810,300
Ensembl chr10:54,798,851...54,810,299 		JBrowse link
G Vegfa vascular endothelial growth factor A ISO CTD Direct Evidence: marker/mechanism CTD PMID:25239121 NCBI chr 9:22,452,854...22,468,194
Ensembl chr 9:22,439,392...22,468,194 		JBrowse link
G Xiap X-linked inhibitor of apoptosis ameliorates ISO mRNA:increased expression:kidney (human) RGD PMID:31964418 RGD:153344516 NCBI chr  X:125,756,107...125,803,979
Ensembl chr  X:125,737,971...125,803,978 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19167
    disease of cellular proliferation 7905
      cancer 5732
        cell type cancer 3786
          carcinoma 3274
            adenocarcinoma 1700
              renal cell carcinoma 355
                clear cell renal cell carcinoma 54
                  multilocular clear cell renal cell carcinoma 0
Path 2
Term Annotations click to browse term
  disease 19167
    disease of cellular proliferation 7905
      Neoplasms by Site 7344
        Urogenital Neoplasms 2350
          Urologic Neoplasms 729
            urinary system cancer 678
              kidney cancer 478
                renal carcinoma 361
                  renal cell carcinoma 355
                    clear cell renal cell carcinoma 54
                      multilocular clear cell renal cell carcinoma 0
paths to the root