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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 EXP CTD Direct Evidence: marker/mechanism CTD PMID:22232670 NCBI chr 7:17,298,652...17,346,147
Ensembl chr 7:16,916,359...17,346,152
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 IAGP 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 7:87,398,988...87,476,722
Ensembl chr 7:87,401,696...87,480,435
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 EXP CTD Direct Evidence: marker/mechanism CTD PMID:17632509 NCBI chr 2:43,831,942...43,882,988
Ensembl chr 2:43,831,942...43,882,988
JBrowse link
G CCK cholecystokinin EXP CTD Direct Evidence: marker/mechanism CTD PMID:1631261 NCBI chr 3:42,257,826...42,266,185
Ensembl chr 3:42,257,825...42,266,185
JBrowse link
G GNAS GNAS complex locus EXP CTD Direct Evidence: marker/mechanism CTD PMID:21823526 NCBI chr20:58,839,681...58,911,192
Ensembl chr20:58,839,718...58,911,192
JBrowse link
G HMGCR 3-hydroxy-3-methylglutaryl-CoA reductase EXP CTD Direct Evidence: marker/mechanism CTD PMID:7461467 NCBI chr 5:75,336,334...75,362,116
Ensembl chr 5:75,336,329...75,364,001
JBrowse link
G SMAD4 SMAD family member 4 IEP mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 RGD:18936999 NCBI chr18:51,030,213...51,085,042
Ensembl chr18:51,028,394...51,085,045
JBrowse link
G UGT1A1 UDP glucuronosyltransferase family 1 member A1 susceptibility IAGP 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 2:233,760,270...233,773,300
Ensembl chr 2:233,760,270...233,773,300
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 1:156,242,184...156,243,317
Ensembl chr 1:156,242,184...156,243,317
JBrowse link
G CA2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chr 8:85,464,007...85,481,493
Ensembl chr 8:85,463,968...85,481,493
JBrowse link
G CAT catalase EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:34,438,934...34,472,060
Ensembl chr11:34,438,934...34,472,060
JBrowse link
G CD44 CD44 molecule (Indian blood group) ISO RGD PMID:16850024 RGD:2289370 NCBI chr11:35,139,168...35,232,402
Ensembl chr11:35,138,882...35,232,402
JBrowse link
G CLDN14 claudin 14 EXP CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr21:36,460,621...36,576,569
Ensembl chr21:36,460,621...36,576,569
JBrowse link
G F2 coagulation factor II, thrombin susceptibility IAGP DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr11:46,719,213...46,739,506
Ensembl chr11:46,719,196...46,739,506
JBrowse link
G GSTP1 glutathione S-transferase pi 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:67,583,812...67,586,653
Ensembl chr11:67,583,742...67,586,656
JBrowse link
G IFNG interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr12:68,154,768...68,159,740
Ensembl chr12:68,154,768...68,159,740
JBrowse link
G MGP matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr12:14,880,864...14,885,854
Ensembl chr12:14,880,864...14,885,857
JBrowse link
G MPO myeloperoxidase IEP protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr17:58,269,855...58,280,935
Ensembl chr17:58,269,855...58,280,935
JBrowse link
G POMC proopiomelanocortin EXP CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 2:25,160,860...25,168,580
Ensembl chr 2:25,160,853...25,168,903
JBrowse link
G SOD1 superoxide dismutase 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr21:31,659,693...31,668,931
Ensembl chr21:31,659,666...31,668,931
JBrowse link
G SPP1 secreted phosphoprotein 1 IDA
EXP
ISO
CTD Direct Evidence: marker/mechanism CTD PMID:8325891 PMID:10890885, PMID:15954903, PMID:21378157, PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr 4:87,975,714...87,983,411
Ensembl chr 4:87,975,667...87,983,532
JBrowse link
G TRPM7 transient receptor potential cation channel subfamily M member 7 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr15:50,557,158...50,686,797
Ensembl chr15:50,552,473...50,686,797
JBrowse link
prostate calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LTF lactotransferrin IEP RGD PMID:19202053 RGD:7243107 NCBI chr 3:46,435,645...46,485,234
Ensembl chr 3:46,435,645...46,485,234
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 IAGP
EXP
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 chr11:64,591,219...64,603,250
Ensembl chr11:64,590,641...64,602,353
JBrowse link
G SLC2A9 solute carrier family 2 member 9 EXP CTD Direct Evidence: marker/mechanism CTD PMID:18989453 PMID:22132990 NCBI chr 4:9,771,125...10,040,270
Ensembl chr 4:9,771,153...10,054,936
JBrowse link
Ureteral Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CAT catalase EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:34,438,934...34,472,060
Ensembl chr11:34,438,934...34,472,060
JBrowse link
G GSR glutathione-disulfide reductase EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 8:30,678,066...30,727,846
Ensembl chr 8:30,678,066...30,727,846
JBrowse link
G GSTP1 glutathione S-transferase pi 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:67,583,812...67,586,653
Ensembl chr11:67,583,742...67,586,656
JBrowse link
G SOD1 superoxide dismutase 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr21:31,659,693...31,668,931
Ensembl chr21:31,659,666...31,668,931
JBrowse link
Urinary Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADD3 adducin 3 ISO RGD PMID:15329129 RGD:2317717 NCBI chr10:109,996,365...110,135,565
Ensembl chr10:109,996,368...110,135,565
JBrowse link
G F2 coagulation factor II, thrombin IDA RGD PMID:22494008 RGD:6893519 NCBI chr11:46,719,213...46,739,506
Ensembl chr11:46,719,196...46,739,506
JBrowse link
G IL1RN interleukin 1 receptor antagonist susceptibility IAGP DNA:repeats, haplotype:intron:IVS2+914_1000dup IL1RN*1, IL1RN*2 IL1RN*3 (human) RGD PMID:18186699 RGD:6907399 NCBI chr 2:113,099,365...113,134,016
Ensembl chr 2:113,107,214...113,134,016
JBrowse link
G SPP1 secreted phosphoprotein 1 no_association IAGP DNA:polymorphism: :p.R9402H (human)
DNA:polymorphism: :p.N9171S (human)
RGD PMID:16145474, PMID:16145474 RGD:1581368, RGD:1581368 NCBI chr 4:87,975,714...87,983,411
Ensembl chr 4:87,975,667...87,983,532
JBrowse link
G VDR vitamin D receptor IEA GAD PMID:15118671 RGD:1331525 NCBI chr12:47,841,537...47,905,022
Ensembl chr12:47,841,537...47,943,048
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 20158
    Pathological Conditions, Signs and Symptoms 11385
      Anatomical Pathological Conditions 1994
        Calculi 29
          Dental Calculus 0
          Gallstones + 7
          Salivary Calculi + 0
          Testicular Microlithiasis 0
          Urinary Calculi + 22
paths to the root