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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 chr12:35,497,979...35,534,989
Ensembl chr12:35,497,974...35,535,038
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, sub-family B (MDR/TAP), 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 5:8,893,614...8,959,226
Ensembl chr 5:8,893,717...8,959,231
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 chr17:84,676,302...84,700,333
Ensembl chr17:84,676,302...84,700,333
JBrowse link
G Cck cholecystokinin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1631261 NCBI chr 9:121,489,824...121,495,694
Ensembl chr 9:121,489,824...121,495,694
JBrowse link
G Gnas GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus ISO CTD Direct Evidence: marker/mechanism CTD PMID:21823526 NCBI chr 2:174,284,320...174,346,744
Ensembl chr 2:174,284,320...174,346,744
JBrowse link
G Hmgcr 3-hydroxy-3-methylglutaryl-Coenzyme A reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:7461467 NCBI chr13:96,648,962...96,670,936
Ensembl chr13:96,648,967...96,670,936
JBrowse link
G Smad4 SMAD family member 4 ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 RGD:18936999 NCBI chr18:73,634,790...73,703,791
Ensembl chr18:73,639,009...73,703,780
JBrowse link
G Ugt1a1 UDP glucuronosyltransferase 1 family, polypeptide 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 1:88,211,959...88,220,002
Ensembl chr 1:88,211,959...88,218,997
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 IDA RGD PMID:12674322 RGD:7207412 NCBI chr 3:88,383,495...88,384,466
Ensembl chr 3:88,383,501...88,384,464
JBrowse link
G Car2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chr 3:14,886,269...14,900,770
Ensembl chr 3:14,886,273...14,900,770
JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:103,453,904...103,485,153
Ensembl chr 2:103,453,849...103,485,160
JBrowse link
G Cd44 CD44 antigen ISO RGD PMID:16850024 RGD:2289370 NCBI chr 2:102,811,141...102,901,669
Ensembl chr 2:102,811,141...102,901,665
JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr16:93,919,031...94,008,837
Ensembl chr16:93,919,031...94,008,837
JBrowse link
G F2 coagulation factor II susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 2:91,612,397...91,636,457
Ensembl chr 2:91,625,320...91,636,414
JBrowse link
G Gstp1 glutathione S-transferase, pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr19:4,035,411...4,037,912
Ensembl chr19:4,035,407...4,037,985
JBrowse link
G Ifng interferon gamma IEP associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr10:118,441,046...118,445,894
Ensembl chr10:118,441,046...118,445,892
JBrowse link
G Mgp matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr 6:136,872,435...136,875,823
Ensembl chr 6:136,872,435...136,875,823
JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr11:87,793,784...87,804,412
Ensembl chr11:87,793,581...87,804,413
JBrowse link
G Pomc pro-opiomelanocortin-alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr12:3,954,945...3,960,643
Ensembl chr12:3,954,951...3,960,642
JBrowse link
G Sod1 superoxide dismutase 1, soluble ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:90,220,762...90,226,333
Ensembl chr16:90,220,754...90,226,329
JBrowse link
G Spp1 secreted phosphoprotein 1 ISO
IDA
CTD Direct Evidence: marker/mechanism CTD PMID:8325891 PMID:10890885, PMID:15954903, PMID:21378157, PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr 5:104,435,111...104,441,053
Ensembl chr 5:104,435,118...104,441,050
JBrowse link
G Trpm7 transient receptor potential cation channel, subfamily M, member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 2:126,791,558...126,876,261
Ensembl chr 2:126,791,565...126,876,230
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 9:111,019,292...111,042,766
Ensembl chr 9:111,019,271...111,042,767
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 (organic anion/cation transporter), member 12 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Hereditary renal hypouricemia
OMIM
CTD
ClinVar
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 chr19:6,535,854...6,543,070
Ensembl chr19:6,535,845...6,543,032
JBrowse link
G Slc2a9 solute carrier family 2 (facilitated glucose transporter), member 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18989453 PMID:22132990 NCBI chr 5:38,349,272...38,503,147
Ensembl chr 5:38,349,273...38,503,143
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 2:103,453,904...103,485,153
Ensembl chr 2:103,453,849...103,485,160
JBrowse link
G Gsr glutathione reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 8:33,653,238...33,698,162
Ensembl chr 8:33,652,523...33,698,163
JBrowse link
G Gstp1 glutathione S-transferase, pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr19:4,035,411...4,037,912
Ensembl chr19:4,035,407...4,037,985
JBrowse link
G Sod1 superoxide dismutase 1, soluble ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:90,220,762...90,226,333
Ensembl chr16:90,220,754...90,226,329
JBrowse link
Urinary Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Add3 adducin 3 (gamma) ISO RGD PMID:15329129 RGD:2317717 NCBI chr19:53,140,443...53,247,326
Ensembl chr19:53,140,443...53,247,399
JBrowse link
G F2 coagulation factor II ISO RGD PMID:22494008 RGD:6893519 NCBI chr 2:91,612,397...91,636,457
Ensembl chr 2:91,625,320...91,636,414
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 2:24,336,860...24,351,491
Ensembl chr 2:24,336,853...24,351,494
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 chr 5:104,435,111...104,441,053
Ensembl chr 5:104,435,118...104,441,050
JBrowse link
G Vdr vitamin D (1,25-dihydroxyvitamin D3) receptor ISO GAD PMID:15118671 RGD:1331525 NCBI chr15:97,854,427...97,908,296
Ensembl chr15:97,854,425...97,910,630
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 14439
    Pathological Conditions, Signs and Symptoms 9435
      Anatomical Pathological Conditions 1907
        Calculi 29
          Dental Calculus 0
          Gallstones + 7
          Salivary Calculi + 0
          Testicular Microlithiasis 0
          Urinary Calculi + 22
paths to the root