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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 chr2B:123,795,664...123,810,067
Ensembl chr2B:242,666,173...242,667,261 		JBrowse link
G AGER advanced glycosylation end-product specific receptor ISO mRNA:increased expression:renal cortex (human) RGD PMID:21947243 RGD:7244181 NCBI chr 6:31,828,363...31,831,981
Ensembl chr 6:32,708,251...32,711,641 		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 chr11:103,109,979...103,256,405
Ensembl chr11:106,584,228...106,727,041 		JBrowse link
G ATP5MC2 ATP synthase membrane subunit c locus 2 ISO RGD PMID:28672194 RGD:14696810 NCBI chr12:35,078,290...35,089,480 JBrowse link
G ATP5PB ATP synthase peripheral stalk-membrane subunit b ISO RGD PMID:28672194 RGD:14696810 NCBI chr 1:114,110,749...114,122,715
Ensembl chr 1:126,224,725...126,235,897 		JBrowse link
G ATP5PO ATP synthase peripheral stalk subunit OSCP ISO RGD PMID:28672194 RGD:14696810 NCBI chr21:20,270,442...20,282,865 JBrowse link
G 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 chr 3:52,344,067...52,352,187
Ensembl chr 3:53,573,785...53,581,943 		JBrowse link
G BAX BCL2 associated X, apoptosis regulator ISO mRNA, protein:increased expression:kidney RGD PMID:28551630 RGD:15036804 NCBI chr19:45,955,926...45,962,870
Ensembl chr19:54,793,594...54,800,468 		JBrowse link
G BIRC3 baculoviral IAP repeat containing 3 disease_progression ISO mRNA:increased expression:kidney (human) RGD PMID:31964418 RGD:153344516 NCBI chr11:97,269,778...97,290,112
Ensembl chr11:100,763,274...100,785,194 		JBrowse link
G BIRC5 baculoviral IAP repeat containing 5 exacerbates ISO mRNA:increased expression:kidney (human) RGD PMID:31964418 RGD:153344516 NCBI chr17:72,292,332...72,303,493
Ensembl chr17:77,842,724...77,854,159 		JBrowse link
G BIRC6 baculoviral IAP repeat containing 6 ameliorates ISO mRNA:increased expression:kidney (human) RGD PMID:31964418 RGD:153344516 NCBI chr2A:32,373,479...32,633,088
Ensembl chr2A:33,084,929...33,343,245 		JBrowse link
G C9H11orf65 chromosome 9 C11orf65 homolog ISO ClinVar Annotator: match by term: Clear cell carcinoma of kidney ClinVar PMID:8755918 PMID:9792409 PMID:10980530 PMID:18560558 PMID:19431188 More... NCBI chr11:103,195,244...103,352,211
Ensembl chr11:106,670,277...106,817,886 		JBrowse link
G CHD4 chromodomain helicase DNA binding protein 4 ISO mRNA:decreased expression:kidney (human) RGD PMID:28486105 RGD:153323299 NCBI chr12:6,701,004...6,738,621
Ensembl chr12:6,619,089...6,656,076 		JBrowse link
G CXCL12 C-X-C motif chemokine ligand 12 ISO mRNA:decreased expression:kidney: RGD PMID:29218250 RGD:155804290 NCBI chr10:41,296,975...41,384,864
Ensembl chr10:44,552,480...44,564,231 		JBrowse link
G CXCR4 C-X-C motif chemokine receptor 4 ISO mRNA:increased expression:kidney: RGD PMID:29218250 RGD:155804290 NCBI chr2B:23,744,271...23,748,106
Ensembl chr2B:140,181,829...140,189,647 		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:27020590 PMID:31018949 RGD:151347528 RGD:151347863 NCBI chr 6:30,625,871...30,645,066
Ensembl chr 6:31,496,047...31,513,455 		JBrowse link
G DNMT1 DNA methyltransferase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27292127 NCBI chr19:9,681,847...9,745,334
Ensembl chr19:10,342,478...10,406,972 		JBrowse link
G DNMT3A DNA methyltransferase 3 alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:27292127 NCBI chr2A:25,229,593...25,344,733
Ensembl chr2A:25,331,095...25,412,605 		JBrowse link
G EGLN3 egl-9 family hypoxia inducible factor 3 disease_progression ISO RGD PMID:23788753 RGD:13506731 NCBI chr14:14,689,398...14,716,301
Ensembl chr14:32,880,324...32,907,241 		JBrowse link
G ENG endoglin severity ISO protein:increased expression:tumor, vasculature (human)
protein:decreased expression:kidney, tumor (human)		 RGD PMID:16536758 PMID:22204709 RGD:7248775 RGD:7248780 NCBI chr 9:98,934,080...98,973,862
Ensembl chr 9:127,605,608...127,644,641 		JBrowse link
G EP300 E1A binding protein p300 severity ISO mRNA, protein:increased expression:kidney
mRNA:altered expression:kidney, tumor (human)		 RGD PMID:23029358 PMID:28551630 RGD:15036804 RGD:7296925 NCBI chr22:21,986,467...22,076,921
Ensembl chr22:40,079,503...40,168,604 		JBrowse link
G F2 coagulation factor II, thrombin ISO protein:increased expression:brain RGD PMID:22065054 RGD:6893520 NCBI chr11:46,669,925...46,690,391
Ensembl chr11:47,227,891...47,249,157 		JBrowse link
G FLT4 fms related receptor tyrosine kinase 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25239121 NCBI chr 5:175,804,728...175,852,703
Ensembl chr 5:183,115,856...183,149,006 		JBrowse link
G FTO FTO alpha-ketoglutarate dependent dioxygenase treatment
disease_progression		 ISO mRNA:decreased expression:kidney
mRNA:increased expression:kidney		 RGD PMID:30648791 PMID:32817424 RGD:329812005 RGD:329812006 NCBI chr16:33,939,300...34,343,419
Ensembl chr16:53,023,425...53,490,231 		JBrowse link
G GATA1 GATA binding protein 1 disease_progression ISO RGD PMID:25230694 RGD:149735195 NCBI chr  X:41,088,724...41,092,190
Ensembl chr  X:48,945,394...48,953,126 		JBrowse link
G GATA2 GATA binding protein 2 disease_progression ISO RGD PMID:25230694 RGD:149735195 NCBI chr 3:125,526,537...125,535,649
Ensembl chr 3:132,890,508...132,899,035 		JBrowse link
G GSTP1 glutathione S-transferase pi 1 ISO RGD PMID:10383153 RGD:6906878 NCBI chr11:62,942,756...62,945,701
Ensembl chr11:66,253,421...66,256,472 		JBrowse link
G 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 More... NCBI chr12:118,562,308...118,584,596
Ensembl chr12:121,932,671...121,955,911 		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 chr15:77,332,926...77,648,474
Ensembl chr15:96,535,164...96,832,974 		JBrowse link
G ISCU iron-sulfur cluster assembly enzyme disease_progression ISO mRNA,protein:decreased expression:kidney (human) RGD PMID:23449350 RGD:155260320 NCBI chr12:106,132,987...106,140,879
Ensembl chr12:109,529,162...109,537,053 		JBrowse link
G KAT8 lysine acetyltransferase 8 ISO mRNA, protein:decreased expression:kidney (human) RGD PMID:23394073 RGD:9586034 NCBI chr16:23,837,540...23,851,376
Ensembl chr16:31,486,098...31,500,185 		JBrowse link
G MAP3K8 mitogen-activated protein kinase kinase kinase 8 ameliorates
disease_progression		 ISO RGD PMID:23982215 RGD:151356974 NCBI chr10:30,579,220...30,607,249
Ensembl chr10:30,933,483...30,960,824 		JBrowse link
G MMP12 matrix metallopeptidase 12 ISO RGD PMID:11576837 RGD:2290421 NCBI chr11:97,809,644...97,822,063
Ensembl chr11:101,294,475...101,306,762 		JBrowse link
G MTHFR methylenetetrahydrofolate reductase susceptibility
severity		 ISO DNA:transition, transversion:cds:g.677C>T, g.1298A>C (human) RGD PMID:20039875 PMID:21489764 RGD:6893474 RGD:6893632 NCBI chr 1:10,548,196...10,568,174
Ensembl chr 1:11,766,334...11,785,419 		JBrowse link
G MYC MYC proto-oncogene, bHLH transcription factor severity ISO protein:increased expression:kidney (human) RGD PMID:21881486 RGD:7207420 NCBI chr 8:124,387,561...124,393,551
Ensembl chr 8:127,131,512...127,136,863 		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 3:9,702,311...9,742,283
Ensembl chr 3:9,940,955...9,947,335 		JBrowse link
G PAK4 p21 (RAC1) activated kinase 4 disease_progression ISO RGD PMID:25744653 RGD:13504816 NCBI chr19:36,224,442...36,278,371
Ensembl chr19:44,816,601...44,825,827 		JBrowse link
G PAK6 p21 (RAC1) activated kinase 6 disease_progression ISO RGD PMID:24715215 RGD:13506722 NCBI chr15:19,173,171...19,211,572
Ensembl chr15:37,453,802...37,465,119 		JBrowse link
G PBRM1 polybromo 1 ISO ClinVar Annotator: match by term: Clear cell carcinoma of kidney ClinVar PMID:25911086 NCBI chr 3:52,487,083...52,626,418
Ensembl chr 3:53,718,051...53,850,146 		JBrowse link
G PDGFB platelet derived growth factor subunit B disease_progression ISO RGD PMID:23879920 PMID:25766258 RGD:13504817 RGD:13506650 NCBI chr22:20,127,223...20,148,407
Ensembl chr22:37,944,018...37,964,883 		JBrowse link
G PML PML nuclear body scaffold ISO protein:decreased expression:kidney (human) RGD PMID:25293974 RGD:41404694 NCBI chr15:52,903,874...52,955,151
Ensembl chr15:71,658,884...71,710,883 		JBrowse link
G PPBP pro-platelet basic protein ameliorates
disease_progression		 ISO RGD PMID:24335961 RGD:401794956 NCBI chr 4:50,203,168...50,204,303
Ensembl chr 4:56,035,060...56,037,702 		JBrowse link
G SETD2 SET domain containing 2, histone lysine methyltransferase severity ISO DNA:mutations:multiple (human)
DNA:SNPs,loss of heterozygosity:multiple (human)		 RGD PMID:26864202 PMID:26891804 RGD:150429635 RGD:150429640 NCBI chr 3:46,916,615...47,064,046
Ensembl chr 3:48,018,517...48,163,999 		JBrowse link
G 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 chr22:4,542,764...4,589,461
Ensembl chr22:22,627,982...22,673,921 		JBrowse link
G SRSF1 serine and arginine rich splicing factor 1 ISO mRNA:altered expression:kidney (human) RGD PMID:21082031 RGD:11039407 NCBI chr17:52,083,676...52,087,454
Ensembl chr17:56,937,295...56,944,425 		JBrowse link
G SRSF2 serine and arginine rich splicing factor 2 ISO mRNA:altered expression:kidney (human) RGD PMID:21082031 RGD:11039407 NCBI chr17:70,809,931...70,813,191
Ensembl chr17:76,375,957...76,379,759 		JBrowse link
G SRSF4 serine and arginine rich splicing factor 4 ISO mRNA:altered expression:kidney (human) RGD PMID:21082031 RGD:11039407 NCBI chr 1:28,418,297...28,452,595
Ensembl chr 1:29,444,269...29,478,035 		JBrowse link
G SRSF5 serine and arginine rich splicing factor 5 ISO mRNA:altered expression:kidney (human) RGD PMID:21082031 RGD:11039407 NCBI chr14:50,320,820...50,365,650
Ensembl chr14:69,230,730...69,236,596 		JBrowse link
G SRSF6 serine and arginine rich splicing factor 6 ISO mRNA:altered expression:kidney (human) RGD PMID:21082031 RGD:11039407 NCBI chr20:39,795,659...39,801,864
Ensembl chr20:40,888,560...40,891,853 		JBrowse link
G SRSF7 serine and arginine rich splicing factor 7 ISO mRNA:altered expression:kidney (human) RGD PMID:21082031 RGD:11039407 NCBI chr2A:38,780,879...38,787,470
Ensembl chr2A:39,536,731...39,545,562 		JBrowse link
G TP53 tumor protein p53 ISO mRNA, protein:increased expression:kidney RGD PMID:28551630 RGD:15036804 NCBI chr17:7,699,449...7,717,812
Ensembl chr17:7,684,922...7,706,120 		JBrowse link
G VEGFA vascular endothelial growth factor A ISO CTD Direct Evidence: marker/mechanism CTD PMID:25239121 NCBI chr 6:43,361,053...43,377,366
Ensembl chr 6:44,650,365...44,666,353 		JBrowse link
G XIAP X-linked inhibitor of apoptosis ameliorates ISO mRNA:increased expression:kidney (human) RGD PMID:31964418 RGD:153344516 NCBI chr  X:113,052,164...113,105,160
Ensembl chr  X:123,232,643...123,278,606 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 17996
    disease of cellular proliferation 7241
      cancer 5237
        cell type cancer 3593
          carcinoma 3059
            adenocarcinoma 1587
              renal cell carcinoma 347
                clear cell renal cell carcinoma 53
Path 2
Term Annotations click to browse term
  disease 17996
    disease of cellular proliferation 7241
      Neoplasms by Site 6710
        Urogenital Neoplasms 2130
          Urologic Neoplasms 691
            urinary system cancer 639
              kidney cancer 458
                renal carcinoma 353
                  renal cell carcinoma 347
                    clear cell renal cell carcinoma 53
paths to the root