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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:Calculi
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Accession:DOID:9005602 term browser browse the term
Definition:An abnormal concretion occurring mostly in the urinary and biliary tracts, usually composed of mineral salts. Also called stones.
Synonyms:exact_synonym: Biliary or Urinary Stones;   Calculus
 primary_id: MESH:D002137


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bladder calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ahr aryl hydrocarbon receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:22232670 NCBI chr 6:52,234,089...52,271,568
Ensembl chr 6:52,234,089...52,271,568 		JBrowse link
Gallbladder Disease 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb4 ATP binding cassette subfamily B member 4 ISO ClinVar Annotator: match by term: Gallbladder disease 1 | ClinVar Annotator: match by term: Low phospholipid associated cholelithiasis
DNA:missense mutation:cds:p.Thr175Ala(human)		 OMIM
ClinVar
RGD		 PMID:8666348 PMID:9419367 PMID:11313316 PMID:12891548 PMID:14999697 More... RGD:14694981 NCBI chr 4:25,150,998...25,209,489
Ensembl chr 4:25,151,953...25,209,202 		JBrowse link
Gallstones term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcg8 ATP binding cassette subfamily G member 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17632509 NCBI chr 6:9,945,629...9,964,912
Ensembl chr 6:9,945,629...9,964,912 		JBrowse link
G Cck cholecystokinin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1631261 NCBI chr 8:121,153,499...121,160,194
Ensembl chr 8:121,153,500...121,160,084 		JBrowse link
G Gnas GNAS complex locus ISO CTD Direct Evidence: marker/mechanism CTD PMID:21823526 NCBI chr 3:163,071,003...163,136,350
Ensembl chr 3:163,071,417...163,127,262
Ensembl chr 3:163,071,417...163,127,262 		JBrowse link
G Hmgcr 3-hydroxy-3-methylglutaryl-CoA reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:7461467 NCBI chr 2:27,997,523...28,018,983
Ensembl chr 2:27,997,525...28,019,703 		JBrowse link
G Smad4 SMAD family member 4 ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 RGD:18936999 NCBI chr18:67,243,742...67,274,438
Ensembl chr18:67,243,742...67,274,438 		JBrowse link
G Ugt1a1 UDP glucuronosyltransferase family 1 member A1 susceptibility ISO associated with Anemia, Sickle Cell;DNA:repeat:promoter:(TA)
associated with Beta-Thalassemia;DNA:repeat:promoter:(TA)		 RGD PMID:15388579 PMID:14555305 RGD:10769331, RGD:10769338 NCBI chr 9:88,801,344...88,808,465
Ensembl chr 9:88,713,184...88,808,465 		JBrowse link
Kidney Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bglap bone gamma-carboxyglutamate protein ISO RGD PMID:12674322 RGD:7207412 NCBI chr 2:173,838,518...173,839,495
Ensembl chr 2:173,838,518...173,839,495 		JBrowse link
G Car2 carbonic anhydrase 2 IEP RGD PMID:10977795 RGD:1600710 NCBI chr 2:86,741,625...86,756,766
Ensembl chr 2:86,741,626...86,756,818 		JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 3:89,842,393...89,874,577
Ensembl chr 3:89,842,399...89,874,478 		JBrowse link
G Cd44 CD44 molecule IEP RGD PMID:16850024 RGD:2289370 NCBI chr 3:89,155,850...89,244,615
Ensembl chr 3:89,157,058...89,244,620 		JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr11:33,232,281...33,329,440
Ensembl chr11:33,232,220...33,329,171 		JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486 		JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226 		JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr 7:53,903,339...53,907,375
Ensembl chr 7:53,903,337...53,907,375 		JBrowse link
G Mgp matrix Gla protein IDA RGD PMID:10460895 RGD:1582511 NCBI chr 4:169,766,290...169,769,612
Ensembl chr 4:169,766,279...169,769,667 		JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr10:72,594,883...72,608,862
Ensembl chr10:72,594,661...72,604,819 		JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 6:26,939,844...26,945,666
Ensembl chr 6:26,939,837...26,945,664 		JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:29,456,673...29,462,249
Ensembl chr11:29,456,558...29,462,249 		JBrowse link
G Spp1 secreted phosphoprotein 1 ISO
IEP		 CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:8325891 PMID:10890885 PMID:15954903 PMID:21378157 PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr14:5,308,885...5,315,120
Ensembl chr14:5,308,885...5,315,162 		JBrowse link
G Trpm7 transient receptor potential cation channel, subfamily M, member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 3:114,046,258...114,134,799
Ensembl chr 3:114,046,258...114,135,190 		JBrowse link
prostate calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ltf lactotransferrin ISO RGD PMID:19202053 RGD:7243107 NCBI chr 8:110,999,948...111,022,795
Ensembl chr 8:110,999,948...111,022,795 		JBrowse link
Renal Hypouricemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Slc22a12 solute carrier family 22 member 12 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dalmatian hypouricemia | ClinVar Annotator: match by term: Renal hypouricemia		 OMIM
CTD
ClinVar		 PMID:12024214 PMID:14655203 PMID:14694169 PMID:15054642 PMID:15327384 More... NCBI chr 1:203,845,039...203,852,496
Ensembl chr 1:203,845,048...203,853,555 		JBrowse link
G Slc2a9 solute carrier family 2 member 9 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dalmatian hypouricemia		 CTD
ClinVar		 PMID:18989453 PMID:22132990 NCBI chr14:72,328,334...72,461,981
Ensembl chr14:72,328,320...72,461,981 		JBrowse link
Ureteral Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 3:89,842,393...89,874,577
Ensembl chr 3:89,842,399...89,874,478 		JBrowse link
G Gsr glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:58,482,209...58,525,256
Ensembl chr16:58,482,505...58,525,661 		JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226 		JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:29,456,673...29,462,249
Ensembl chr11:29,456,558...29,462,249 		JBrowse link
Urinary Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Add3 adducin 3 IEP RGD PMID:15329129 RGD:2317717 NCBI chr 1:252,147,341...252,255,126
Ensembl chr 1:252,147,386...252,255,124 		JBrowse link
G F2 coagulation factor II, thrombin ISO RGD PMID:22494008 RGD:6893519 NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486 		JBrowse link
G Il1rn interleukin 1 receptor antagonist susceptibility ISO DNA:repeats, haplotype:intron:IVS2+914_1000dup IL1RN*1, IL1RN*2 IL1RN*3 (human) RGD PMID:18186699 RGD:6907399 NCBI chr 3:7,111,567...7,127,451
Ensembl chr 3:7,111,550...7,127,445 		JBrowse link
G Spp1 secreted phosphoprotein 1 no_association ISO DNA:polymorphism: :p.R9402H (human)
DNA:polymorphism: :p.N9171S (human)		 RGD PMID:16145474 PMID:16145474 RGD:1581368, RGD:1581368 NCBI chr14:5,308,885...5,315,120
Ensembl chr14:5,308,885...5,315,162 		JBrowse link
G Vdr vitamin D receptor ISO GAD PMID:15118671 RGD:1331525 NCBI chr 7:128,987,981...129,037,677
Ensembl chr 7:128,987,981...129,037,677 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19047
    Pathological Conditions, Signs and Symptoms 13529
      Anatomical Pathological Conditions 2745
        Calculi 38
          Dental Calculus 0
          Gallstones + 7
          Salivary Calculi + 0
          Testicular Microlithiasis 0
          Urinary Calculi + 31
paths to the root