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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:Urinary Calculi
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Accession:DOID:9003311 term browser browse the term
Definition:Low-density crystals or stones in any part of the URINARY TRACT. Their chemical compositions often include CALCIUM OXALATE, magnesium ammonium phosphate (struvite), CYSTINE, or URIC ACID.
Synonyms:exact_synonym: Urinary Calculus;   Urinary Stone;   Urinary Stones;   Urinary Tract Stone;   Urinary Tract Stones
 primary_id: MESH:D014545



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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 chr28:21,402,068...21,527,006
Ensembl chr28:21,403,680...21,525,063
JBrowse link
G F2 coagulation factor II, thrombin ISO RGD PMID:22494008 RGD:6893519 NCBI chr18:42,782,744...42,799,531
Ensembl chr18:42,782,751...42,799,459
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 chr17:37,236,690...37,250,424
Ensembl chr17:37,212,751...37,249,329
JBrowse link
G SPP1 secreted phosphoprotein 1 no_association ISO DNA:polymorphism: :p.N9171S (human)
DNA:polymorphism: :p.R9402H (human)
RGD PMID:16145474 RGD:1581368 NCBI chr32:11,354,070...11,362,325
Ensembl chr32:11,353,953...11,362,069
JBrowse link
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 chr14:31,743,704...31,793,484
Ensembl chr14:31,686,170...31,791,444
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 7:41,630,092...41,630,976
Ensembl chr 7:41,630,098...41,665,791
JBrowse link
G CA2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chr29:31,959,225...31,975,309
Ensembl chr29:31,935,172...31,980,579
JBrowse link
G CAT catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr18:33,383,005...33,422,447
Ensembl chr18:33,383,005...33,422,447
JBrowse link
G CD44 CD44 molecule ISO RGD PMID:16850024 RGD:2289370 NCBI chr18:32,735,493...32,826,483
Ensembl chr18:32,737,907...32,827,107
JBrowse link
G CLDN14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr31:31,677,410...31,725,794
Ensembl chr31:31,677,733...31,678,446
JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr18:42,782,744...42,799,531
Ensembl chr18:42,782,751...42,799,459
JBrowse link
G GSTP1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr18:49,905,161...49,908,182
Ensembl chr18:49,905,161...49,908,182
JBrowse link
G IFNG interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr10:10,406,866...10,411,698
Ensembl chr10:10,406,867...10,411,698
JBrowse link
G MGP matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr27:31,735,301...31,738,673
Ensembl chr27:31,734,660...31,738,673
JBrowse link
G MPO myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr 9:32,927,483...32,938,007
Ensembl chr 9:32,927,483...32,937,820
JBrowse link
G POMC proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr17:19,431,396...19,438,247
Ensembl chr17:19,431,585...19,434,440
JBrowse link
G SOD1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr31:26,540,291...26,544,212
Ensembl chr31:26,486,274...26,662,815
JBrowse link
G SPP1 secreted phosphoprotein 1 ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:8325891 PMID:10890885 PMID:15954903 PMID:16105024 PMID:21378157 RGD:1581334 RGD:1581372 RGD:6903839 NCBI chr32:11,354,070...11,362,325
Ensembl chr32:11,353,953...11,362,069
JBrowse link
G TRPM7 transient receptor potential cation channel subfamily M member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr30:16,465,546...16,579,874
Ensembl chr30:16,466,234...16,579,594
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 chr20:42,231,994...42,263,202
Ensembl chr20:42,231,994...42,263,202
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: Dalmatian hypouricemia | ClinVar Annotator: match by term: Renal hypouricemia OMIM
ClinVar
PMID:12024214 PMID:14655203 PMID:14694169 PMID:15054642 PMID:15327384 More... NCBI chr18:52,541,820...52,550,037
Ensembl chr18:52,542,497...52,549,655
JBrowse link
G SLC2A9 solute carrier family 2 member 9 ISO ClinVar Annotator: match by term: Dalmatian hypouricemia ClinVar NCBI chr 3:69,394,304...69,588,462
Ensembl chr 3:69,394,152...69,595,802
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 chr18:33,383,005...33,422,447
Ensembl chr18:33,383,005...33,422,447
JBrowse link
G GSR glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:33,633,949...33,680,411
Ensembl chr16:33,633,968...33,679,752
JBrowse link
G GSTP1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr18:49,905,161...49,908,182
Ensembl chr18:49,905,161...49,908,182
JBrowse link
G SOD1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr31:26,540,291...26,544,212
Ensembl chr31:26,486,274...26,662,815
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 17773
    Pathological Conditions, Signs and Symptoms 11989
      Anatomical Pathological Conditions 2484
        Calculi 27
          Urinary Calculi 21
            Kidney Calculi + 14
            Renal Hypouricemia 2
            Ureteral Calculi 4
            lower urinary tract calculus + 2
Path 2
Term Annotations click to browse term
  disease 17773
    disease of anatomical entity 15139
      Urogenital Diseases 4728
        urinary system disease 2396
          urolithiasis 66
            Urinary Calculi 21
              Kidney Calculi + 14
              Renal Hypouricemia 2
              Ureteral Calculi 4
              lower urinary tract calculus + 2
paths to the root