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
Accession: DOID:9005602
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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 .
G
Ahr
aryl hydrocarbon receptor
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:22232670
NCBI chr 6:52,234,089...52,271,568
Ensembl chr 6:52,234,089...52,271,568
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Abcb4
ATP binding cassette subfamily B member 4
ISO
ClinVar Annotator: match by term: Gallbladder disease 1 | ClinVar Annotator: match by term: Low phospholipid associated cholelithiasis DNA:missense mutation:cds:p.Thr175Ala(human)
OMIM ClinVar RGD
PMID:8666348 PMID:9419367 PMID:11313316 PMID:12891548 PMID:14999697 PMID:15077010 PMID:16763017 PMID:16890614 PMID:17726488 PMID:18482588 PMID:19018976 PMID:19490418 PMID:19584064 PMID:19840255 PMID:21119540 PMID:22331132 PMID:23022423 PMID:23533021 PMID:24033266 PMID:24381502 PMID:24594635 PMID:24806754 PMID:24914347 PMID:25741868 PMID:25807286 PMID:26153658 PMID:26324191 PMID:26474921 PMID:26699824 PMID:28492532 PMID:28733223 PMID:28776642 PMID:31538484 PMID:32581362 PMID:24914347 More...
RGD:14694981
NCBI chr 4:25,150,998...25,209,489
Ensembl chr 4:25,151,953...25,209,202
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Abcg8
ATP binding cassette subfamily G member 8
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:17632509
NCBI chr 6:9,945,629...9,964,912
Ensembl chr 6:9,945,629...9,964,912
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Cck
cholecystokinin
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:1631261
NCBI chr 8:121,153,499...121,160,194
Ensembl chr 8:121,153,500...121,160,084
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Gnas
GNAS complex locus
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:21823526
NCBI chr 3:163,071,003...163,136,350
Ensembl chr 3:163,071,417...163,127,262 Ensembl chr 3:163,071,417...163,127,262
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Hmgcr
3-hydroxy-3-methylglutaryl-CoA reductase
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:7461467
NCBI chr 2:27,997,523...28,018,983
Ensembl chr 2:27,997,525...28,019,703
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Smad4
SMAD family member 4
ISO
mRNA,protein:decreased expression:intrahepatic bile duct
RGD
PMID:16917866
RGD:18936999
NCBI chr18:67,243,742...67,274,438
Ensembl chr18:67,243,742...67,274,438
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 9:88,801,344...88,808,465
Ensembl chr 9:88,713,184...88,808,465
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Bglap
bone gamma-carboxyglutamate protein
ISO
RGD
PMID:12674322
RGD:7207412
NCBI chr 2:173,838,518...173,839,495
Ensembl chr 2:173,838,518...173,839,495
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Car2
carbonic anhydrase 2
IEP
RGD
PMID:10977795
RGD:1600710
NCBI chr 2:86,741,625...86,756,766
Ensembl chr 2:86,741,626...86,756,818
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Cat
catalase
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr 3:89,842,393...89,874,577
Ensembl chr 3:89,842,399...89,874,478
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Cd44
CD44 molecule (Indian blood group)
IEP
RGD
PMID:16850024
RGD:2289370
NCBI chr 3:89,155,850...89,244,615
Ensembl chr 3:89,157,058...89,244,620
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Cldn14
claudin 14
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:19561606
NCBI chr11:33,232,281...33,329,440
Ensembl chr11:33,232,220...33,329,171
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F2
coagulation factor II
susceptibility
ISO
DNA:haplotypes: :
RGD
PMID:21067798
RGD:6893526
NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486
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Gstp1
glutathione S-transferase pi 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226
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Ifng
interferon gamma
ISO
associated with type 2 diabetes mellitus; mRNA:increased expression:kidney
RGD
PMID:21514417
RGD:6893463
NCBI chr 7:53,903,339...53,907,375
Ensembl chr 7:53,903,337...53,907,375
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Mgp
matrix Gla protein
IDA
RGD
PMID:10460895
RGD:1582511
NCBI chr 4:169,766,290...169,769,612
Ensembl chr 4:169,766,279...169,769,667
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Mpo
myeloperoxidase
ISO
protein:increased activity:blood
RGD
PMID:18022927
RGD:7174700
NCBI chr10:72,594,458...72,608,862
Ensembl chr10:72,594,661...72,604,819
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Pomc
proopiomelanocortin
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:1324751
NCBI chr 6:26,939,844...26,945,666
Ensembl chr 6:26,939,837...26,945,664
G
Sod1
superoxide dismutase 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr11:29,456,673...29,462,249
Ensembl chr11:29,456,558...29,462,249
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Spp1
secreted phosphoprotein 1
ISO IEP
CTD Direct Evidence: marker/mechanism
CTD RGD
PMID:8325891 PMID:10890885 PMID:15954903 PMID:21378157 PMID:16105024
RGD:1581372 , RGD:6903839 , RGD:1581334
NCBI chr14:5,308,885...5,315,120
Ensembl chr14:5,308,885...5,315,162
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Trpm7
transient receptor potential cation channel, subfamily M, member 7
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24291744
NCBI chr 3:114,046,258...114,134,799
Ensembl chr 3:114,046,258...114,135,190
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Ltf
lactotransferrin
ISO
RGD
PMID:19202053
RGD:7243107
NCBI chr 8:110,999,948...111,022,795
Ensembl chr 8:110,999,948...111,022,795
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Slc22a12
solute carrier family 22 member 12
ISO
CTD Direct Evidence: marker/mechanism ClinVar Annotator: match by term: Dalmatian hypouricemia
OMIM CTD ClinVar
PMID:12024214 PMID:14655203 PMID:14694169 PMID:15054642 PMID:15327384 PMID:15634722 PMID:15741204 PMID:15912381 PMID:16385546 PMID:16703794 PMID:17103332 PMID:17362586 PMID:18492088 PMID:18760270 PMID:19019168 PMID:21148271 PMID:21211204 PMID:21366895 PMID:21614936 PMID:22045201 PMID:22132990 PMID:22194875 PMID:23043931 PMID:23386035 PMID:23525542 PMID:24033266 PMID:24827988 PMID:25264011 PMID:25658588 PMID:25741868 PMID:26603249 PMID:28492532 PMID:29486147 PMID:29659532 PMID:31591475 More...
NCBI chr 1:203,845,039...203,852,496
Ensembl chr 1:203,845,048...203,853,555
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Slc2a9
solute carrier family 2 member 9
ISO
CTD Direct Evidence: marker/mechanism ClinVar Annotator: match by term: Dalmatian hypouricemia
CTD ClinVar
PMID:18989453 PMID:22132990
NCBI chr14:72,328,334...72,461,981
Ensembl chr14:72,328,320...72,461,981
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Cat
catalase
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr 3:89,842,393...89,874,577
Ensembl chr 3:89,842,399...89,874,478
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Gsr
glutathione-disulfide reductase
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr16:58,482,209...58,525,256
Ensembl chr16:58,482,505...58,525,661
G
Gstp1
glutathione S-transferase pi 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226
G
Sod1
superoxide dismutase 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr11:29,456,673...29,462,249
Ensembl chr11:29,456,558...29,462,249
G
Add3
adducin 3
IEP
RGD
PMID:15329129
RGD:2317717
NCBI chr 1:252,147,341...252,255,126
Ensembl chr 1:252,147,386...252,255,124
G
F2
coagulation factor II
ISO
RGD
PMID:22494008
RGD:6893519
NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486
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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 3:7,111,567...7,127,451
Ensembl chr 3:7,111,550...7,127,445
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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 chr14:5,308,885...5,315,120
Ensembl chr14:5,308,885...5,315,162
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Vdr
vitamin D receptor
ISO
GAD
PMID:15118671
RGD:1331525
NCBI chr 7:128,987,981...129,037,677
Ensembl chr 7:128,987,981...129,037,677
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