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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:cholelithiasis
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Accession:DOID:10211 term browser browse the term
Definition:Presence or formation of GALLSTONES in the BILIARY TRACT, usually in the gallbladder (CHOLECYSTOLITHIASIS) or the common bile duct (CHOLEDOCHOLITHIASIS).
Synonyms:exact_synonym: Cholelithiases
 primary_id: MESH:D002769;   RDO:0005194
 xref: ICD9CM:574.5
For additional species annotation, visit the Alliance of Genome Resources.


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cholelithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apoe apolipoprotein E susceptibility ISO DNA:SNP:intron:rs440446 (human) RGD PMID:18296645 RGD:2317550 NCBI chr 1:80,612,894...80,616,820
Ensembl chr 1:80,612,895...80,617,057
JBrowse link
G Aspg asparaginase ISO CTD Direct Evidence: marker/mechanism CTD PMID:12902918 NCBI chr 6:136,682,279...136,701,673
Ensembl chr 6:136,682,126...136,701,628
JBrowse link
G Cckar cholecystokinin A receptor ISO associated with Diabetes Mellitus, Non-Insulin-Dependent; mRNA:decreased expression:gallbladder,smooth muscle RGD PMID:15908333 RGD:2314139 NCBI chr14:59,610,939...59,619,786
Ensembl chr14:59,611,434...59,619,783
JBrowse link
G Cftr CF transmembrane conductance regulator ISO mRNA, protein:altered expression:liver (human) RGD PMID:12184527 RGD:21408573 NCBI chr 4:42,693,263...42,860,679
Ensembl chr 4:42,692,836...42,860,676
JBrowse link
G Cyp17a1 cytochrome P450, family 17, subfamily a, polypeptide 1 ISO associated with Diabetes Mellitus; DNA:transition:5' utr:-34T>C rs743572 (human) RGD PMID:16381022 RGD:2317619 NCBI chr 1:266,422,127...266,429,947
Ensembl chr 1:266,422,132...266,428,239
JBrowse link
G Soat2 sterol O-acyltransferase 2 susceptibility ISO RGD PMID:11100118 RGD:1556516 NCBI chr 7:143,754,892...143,767,989
Ensembl chr 7:143,754,892...143,767,989
JBrowse link
G Sqle squalene epoxidase ISO RGD PMID:14684588 RGD:1581398 NCBI chr 7:99,609,929...99,624,803
Ensembl chr 7:99,609,191...99,624,732
JBrowse link
G Srebf2 sterol regulatory element binding transcription factor 2 ISO RGD PMID:15062879 RGD:1581417 NCBI chr 7:123,381,082...123,438,605
Ensembl chr 7:123,381,077...123,438,603
JBrowse link
G Ugt1a1 UDP glucuronosyltransferase family 1 member A1 susceptibility ISO associated with Spherocytosis, Hereditary;DNA:insertion:promoter
associated with Alpha-Thalassemia;DNA:repeat:promoter:(TA)
associated with Beta-Thalassemia; DNA:mutation,repeat:cds,promoter; p. G71R,(TA) (human)
RGD PMID:10498597, PMID:17593033, PMID:18081723 RGD:6482853, RGD:10769341, RGD:10768828 NCBI chr 9:95,295,701...95,302,822
Ensembl chr 9:95,161,157...95,302,822
JBrowse link
cholecystolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Pla2g2a phospholipase A2 group IIA ISO RGD PMID:9695991 RGD:6482724 NCBI chr 5:157,282,650...157,285,295
Ensembl chr 5:157,282,669...157,285,328
JBrowse link
G Ugt1a1 UDP glucuronosyltransferase family 1 member A1 susceptibility ISO associated with Anemia, Sickle Cell;DNA:polymorphism:promoter: RGD PMID:18392554 RGD:10768868 NCBI chr 9:95,295,701...95,302,822
Ensembl chr 9:95,161,157...95,302,822
JBrowse link
choledocholithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Aspg asparaginase ISO CTD Direct Evidence: marker/mechanism CTD PMID:12902918 NCBI chr 6:136,682,279...136,701,673
Ensembl chr 6:136,682,126...136,701,628
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

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16108
    disease of anatomical entity 15356
      gastrointestinal system disease 4673
        biliary tract disease 437
          cholelithiasis 16
            Gallstones + 7
            cholecystolithiasis + 8
            choledocholithiasis 1
Path 2
Term Annotations click to browse term
  disease 16108
    disease of anatomical entity 15356
      gastrointestinal system disease 4673
        hepatobiliary disease 2486
          biliary tract disease 437
            gallbladder disease 74
              cholelithiasis 16
                Gallstones + 7
                cholecystolithiasis + 8
                choledocholithiasis 1
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.