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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;   RDO:0005094
For additional species annotation, visit the Alliance of Genome Resources.

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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 6:54,963,990...55,001,806
Ensembl chr 6:54,963,990...55,001,464 		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
DNA:missense mutation:cds:p.Thr175Ala(human)		 OMIM
ClinVar		 PMID:8666348 PMID:9419367 PMID:11313316 PMID:12891548 PMID:15077010 PMID:16763017 PMID:16890614 PMID:17726488 PMID:18482588 PMID:19018976 PMID:19490418 PMID:19584064 PMID:19840255 PMID:21119540 PMID:22331132 PMID:23533021 PMID:24033266 PMID:24381502 PMID:24594635 PMID:24806754 PMID:24914347 PMID:25741868 PMID:25807286 PMID:26153658 PMID:26474921 PMID:26699824 PMID:28776642 PMID:32581362, PMID:24914347 RGD:14694981 NCBI chr 4:22,133,984...22,192,687
Ensembl chr 4:22,133,521...22,425,515 		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 6:7,961,413...7,980,708
Ensembl chr 6:7,961,413...7,980,708 		JBrowse link
G Cck cholecystokinin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1631261 NCBI chr 8:130,120,525...130,127,515
Ensembl chr 8:130,120,523...130,127,392 		JBrowse link
G Gnas GNAS complex locus ISO CTD Direct Evidence: marker/mechanism CTD PMID:21823526 NCBI chr 3:172,374,957...172,434,988
Ensembl chr 3:172,374,957...172,428,483
Ensembl chr 3:172,374,957...172,428,483 		JBrowse link
G Hmgcr 3-hydroxy-3-methylglutaryl-CoA reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:7461467 NCBI chr 2:27,480,224...27,500,654
Ensembl chr 2:27,480,226...27,500,654 		JBrowse link
G Smad4 SMAD family member 4 ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 RGD:18936999 NCBI chr18:69,626,682...69,657,373
Ensembl chr18:69,627,757...69,671,199 		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 9:95,295,701...95,302,822
Ensembl chr 9:95,161,157...95,302,822 		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 2:187,741,770...187,748,445
Ensembl chr 2:187,741,770...187,742,747 		JBrowse link
G Car2 carbonic anhydrase 2 IEP RGD PMID:10977795 RGD:1600710 NCBI chr 2:88,097,740...88,112,868
Ensembl chr 2:88,097,720...88,113,029 		JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 3:93,379,872...93,412,058
Ensembl chr 3:93,379,874...93,412,058 		JBrowse link
G Cd44 CD44 molecule (Indian blood group) IEP RGD PMID:16850024 RGD:2289370 NCBI chr 3:92,695,083...92,783,820
Ensembl chr 3:92,696,313...92,783,658 		JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr11:34,132,581...34,142,813
Ensembl chr11:34,132,581...34,142,753 		JBrowse link
G F2 coagulation factor II susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 3:80,529,468...80,542,993
Ensembl chr 3:80,529,428...80,543,031 		JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 1:219,291,679...219,294,147
Ensembl chr 1:219,291,679...219,294,147 		JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr 7:61,337,383...61,341,419
Ensembl chr 7:61,337,381...61,341,419 		JBrowse link
G Mgp matrix Gla protein IDA RGD PMID:10460895 RGD:1582511 NCBI chr 4:170,856,783...170,860,105
Ensembl chr 4:170,856,751...170,860,225 		JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr10:75,087,892...75,098,260
Ensembl chr10:75,087,892...75,098,260 		JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 6:28,382,937...28,388,771
Ensembl chr 6:28,382,962...28,388,967 		JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:30,363,282...30,368,858
Ensembl chr11:30,363,280...30,368,862 		JBrowse link
G Spp1 secreted phosphoprotein 1 ISO
IEP		 CTD Direct Evidence: marker/mechanism CTD PMID:8325891 PMID:10890885, PMID:15954903, PMID:21378157, PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr14:6,673,686...6,679,965
Ensembl chr14:6,673,686...6,679,901 		JBrowse link
G Trpm7 transient receptor potential cation channel, subfamily M, member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 3:119,258,189...119,347,084
Ensembl chr 3:119,259,467...119,330,345 		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 8:119,290,416...119,313,261
Ensembl chr 8:119,290,416...119,313,261 		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 ClinVar Annotator: match by term: Hereditary renal hypouricemia
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:14655203 PMID:14694169 PMID:15327384 PMID:15741204 PMID:15912381 PMID:16703794 PMID:17362586 PMID:18492088 PMID:19019168 PMID:22045201 PMID:22132990 PMID:22194875 PMID:24033266 PMID:29659532 NCBI chr 1:221,910,787...221,919,277
Ensembl chr 1:221,910,767...221,919,301 		JBrowse link
G Slc2a9 solute carrier family 2 member 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18989453 PMID:22132990 NCBI chr14:77,067,537...77,192,702
Ensembl chr14:77,067,503...77,192,702 		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 3:93,379,872...93,412,058
Ensembl chr 3:93,379,874...93,412,058 		JBrowse link
G Gsr glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:62,197,617...62,239,987
Ensembl chr16:62,197,617...62,241,361 		JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 1:219,291,679...219,294,147
Ensembl chr 1:219,291,679...219,294,147 		JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:30,363,282...30,368,858
Ensembl chr11:30,363,280...30,368,862 		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 1:273,854,195...273,961,982
Ensembl chr 1:273,854,248...273,961,982 		JBrowse link
G F2 coagulation factor II ISO RGD PMID:22494008 RGD:6893519 NCBI chr 3:80,529,468...80,542,993
Ensembl chr 3:80,529,428...80,543,031 		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 3:1,449,778...1,468,624
Ensembl chr 3:1,452,644...1,468,614 		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 chr14:6,673,686...6,679,965
Ensembl chr14:6,673,686...6,679,901 		JBrowse link
G Vdr vitamin D receptor ISO GAD PMID:15118671 RGD:1331525 NCBI chr 7:139,344,452...139,394,138
Ensembl chr 7:139,342,063...139,394,166 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16937
    Pathological Conditions, Signs and Symptoms 9893
      Anatomical Pathological Conditions 1591
        Calculi 38
          Dental Calculus 0
          Gallstones + 7
          Salivary Calculi + 0
          Testicular Microlithiasis 0
          Urinary Calculi + 31
paths to the root