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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:calcium oxalate nephrolithiasis
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Accession:DOID:0080652 term browser browse the term
Definition:A nephrolithiasis that is characterized by characterized by stones composed of calcium oxalate and that has_material_basis_in compound heterozygous mutation in the SLC26A1 gene on chromosome 4p16. (DO)
Synonyms:exact_synonym: CAON;   calcium oxalate urolithiasis
 primary_id: MESH:C563477
 xref: EFO:0009065;   MIM:PS167030


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calcium oxalate nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AHSG alpha 2-HS glycoprotein ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 3:183,644,223...183,652,620
Ensembl chr 3:192,110,770...192,119,915 		JBrowse link
G AMBP alpha-1-microglobulin/bikunin precursor ISO protein:increased expression:urine RGD PMID:15533056 PMID:16622176 RGD:6904147 RGD:6904219 NCBI chr 9:85,157,680...85,176,253
Ensembl chr 9:113,525,835...113,543,422 		JBrowse link
G BGLAP bone gamma-carboxyglutamate protein ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 1:131,583,789...131,586,459
Ensembl chr 1:135,413,871...135,416,432 		JBrowse link
G CASR calcium sensing receptor susceptibility ISO DNA:missense mutation:cds:p.R990G (rs1042636)(human)
associated with Hyperparathyroidism, Primary; DNA:snp:intron:IVS1 G>A rs1501899 (human)
DNA:snp:intron:IVS4+11988A>G rs17251221 (human)
DNA:missense mutations:cds:p.A986S, p.E1011Q (human)		 RGD PMID:17018660 PMID:20602573 PMID:21183554 PMID:21966463 RGD:13464331 RGD:7205445 RGD:7205446 RGD:7205447 NCBI chr 3:119,278,071...119,383,901
Ensembl chr 3:126,252,765...126,285,268 		JBrowse link
G CAT catalase ISO RGD PMID:21557843 RGD:7205663 NCBI chr11:34,413,253...34,446,831
Ensembl chr11:34,289,603...34,323,160 		JBrowse link
G CD44 CD44 molecule (IN blood group) ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr11:35,110,732...35,258,238
Ensembl chr11:34,985,634...35,079,009 		JBrowse link
G F2 coagulation factor II, thrombin ISO mRNA:decreased expression:kidney RGD PMID:16981243 RGD:6893592 NCBI chr11:46,669,925...46,690,391
Ensembl chr11:47,227,891...47,249,157 		JBrowse link
G FN1 fibronectin 1 ISO protein:increased expression:kidney
DNA:polymorphism: :		 RGD PMID:11025758 PMID:19616291 RGD:7206842 RGD:7206846 NCBI chr2B:102,623,568...102,698,747
Ensembl chr2B:221,208,431...221,284,003 		JBrowse link
G HAO1 hydroxyacid oxidase 1 ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr20:7,856,967...7,914,818
Ensembl chr20:7,633,861...7,695,120 		JBrowse link
G IL1RN interleukin 1 receptor antagonist ISO DNA:repeats:intron:IVS2+914_1000dup IL1RN*1 (human) RGD PMID:17258699 RGD:6907128 NCBI chr2A:88,991,646...89,008,013
Ensembl chr2A:114,061,182...114,078,839 		JBrowse link
G PAQR6 progestin and adipoQ receptor family member 6 ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 1:131,586,557...131,591,263
Ensembl chr 1:135,416,530...135,421,662 		JBrowse link
G PTH parathyroid hormone ISO protein:decreased expression:serum (human) RGD PMID:23470222 RGD:7242417 NCBI chr11:13,653,777...13,657,901
Ensembl chr11:13,347,838...13,351,802 		JBrowse link
Calcium Oxalate Nephrolithiasis 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G IDUA alpha-L-iduronidase ISO ClinVar Annotator: match by term: NEPHROLITHIASIS, CALCIUM OXALATE, 1 | ClinVar Annotator: match by term: SLC26A1-related condition ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:28492532 PMID:30586318 More... NCBI chr 4:1,102,288...1,120,973
Ensembl chr 4:1,020,582...1,037,877 		JBrowse link
G SLC26A1 solute carrier family 26 member 1 ISO ClinVar Annotator: match by term: NEPHROLITHIASIS, CALCIUM OXALATE, 1 | ClinVar Annotator: match by term: SLC26A1-related condition OMIM
ClinVar		 PMID:25741868 PMID:27125215 PMID:27210743 PMID:28492532 PMID:30586318 More... NCBI chr 4:1,102,938...1,112,987
Ensembl chr 4:1,012,920...1,026,402 		JBrowse link
Calcium Oxalate Nephrolithiasis 2 with Nephrocalcinosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G OXGR1 oxoglutarate receptor 1 ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate, 2, with or without nephrocalcinosis OMIM
ClinVar		 PMID:25741868 PMID:36571463 NCBI chr13:78,145,794...78,154,555 JBrowse link
hypophosphatemic nephrolithiasis/osteoporosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G F12 coagulation factor XII ISO ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic ClinVar PMID:24033266 PMID:25050900 PMID:25741868 PMID:28492532 PMID:30943683 NCBI chr 5:172,703,724...172,711,618
Ensembl chr 5:179,766,243...179,773,485 		JBrowse link
G SLC34A1 solute carrier family 34 member 1 ISO ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic ClinVar PMID:24033266 PMID:25050900 PMID:25741868 PMID:28492532 PMID:30943683 NCBI chr 5:172,685,862...172,700,440
Ensembl chr 5:179,748,492...179,762,975 		JBrowse link
hypophosphatemic nephrolithiasis/osteoporosis 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G F12 coagulation factor XII ISO ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1 ClinVar PMID:25050900 PMID:25741868 PMID:28492532 PMID:30943683 NCBI chr 5:172,703,724...172,711,618
Ensembl chr 5:179,766,243...179,773,485 		JBrowse link
G SLC34A1 solute carrier family 34 member 1 ISO ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1 OMIM
ClinVar		 PMID:9536098 PMID:12324554 PMID:14672348 PMID:16199547 PMID:16688119 More... NCBI chr 5:172,685,862...172,700,440
Ensembl chr 5:179,748,492...179,762,975 		JBrowse link
G SLC34A3 solute carrier family 34 member 3 ISO ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1 ClinVar PMID:25741868 PMID:28492532 PMID:31672324 NCBI chr 9:108,290,905...108,296,186
Ensembl chr 9:137,259,243...137,264,947 		JBrowse link
hypophosphatemic nephrolithiasis/osteoporosis 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G NHERF1 NHERF family PDZ scaffold protein 1 ISO ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 2 | ClinVar Annotator: match by term: NHERF1-related condition OMIM
ClinVar		 PMID:18784102 PMID:24033266 PMID:25326635 PMID:25741868 PMID:28492532 More... NCBI chr17:68,694,468...68,715,157
Ensembl chr17:74,250,406...74,271,234 		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 1:131,583,789...131,586,459
Ensembl chr 1:135,413,871...135,416,432 		JBrowse link
G CA2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chr 8:81,991,037...82,009,010
Ensembl chr 8:83,597,440...83,632,580 		JBrowse link
G CAT catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:34,413,253...34,446,831
Ensembl chr11:34,289,603...34,323,160 		JBrowse link
G CD44 CD44 molecule (IN blood group) ISO RGD PMID:16850024 RGD:2289370 NCBI chr11:35,110,732...35,258,238
Ensembl chr11:34,985,634...35,079,009 		JBrowse link
G CLDN14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr21:22,830,770...22,946,594
Ensembl chr21:36,187,306...36,188,025 		JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr11:46,669,925...46,690,391
Ensembl chr11:47,227,891...47,249,157 		JBrowse link
G GSTP1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:62,942,756...62,945,701
Ensembl chr11:66,253,421...66,256,472 		JBrowse link
G IFNG interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr12:65,663,764...65,668,732
Ensembl chr12:68,448,861...68,453,829 		JBrowse link
G MGP matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr12:14,887,806...14,891,796
Ensembl chr12:15,284,883...15,288,523 		JBrowse link
G MPO myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr17:52,333,882...52,357,838
Ensembl chr17:57,201,073...57,212,111 		JBrowse link
G POMC proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr2A:25,161,668...25,165,600
Ensembl chr2A:25,258,768...25,262,706 		JBrowse link
G SOD1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr21:18,029,831...18,037,526 JBrowse link
G SPP1 secreted phosphoprotein 1 ISO CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:8325891 PMID:10890885 PMID:15954903 PMID:16105024 PMID:21378157 RGD:1581334 RGD:1581372 RGD:6903839 NCBI chr 4:80,263,711...80,271,466
Ensembl chr 4:90,988,200...90,995,935 		JBrowse link
G TRPM7 transient receptor potential cation channel subfamily M member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr15:29,513,220...29,639,506
Ensembl chr15:47,853,187...47,977,451 		JBrowse link
X-linked nephrolithiasis type I term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLCN5 chloride voltage-gated channel 5 ISO ClinVar Annotator: match by term: UROLITHIASIS, X-LINKED RECESSIVE, TYPE 1 | ClinVar Annotator: match by term: X-linked recessive nephrolithiasis with renal failure OMIM
ClinVar		 PMID:7915957 PMID:8559248 PMID:9187673 PMID:9328929 PMID:9602200 More... NCBI chr  X:42,137,523...42,299,716
Ensembl chr  X:49,854,165...50,006,363 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 15832
    disease of anatomical entity 15489
      Urogenital Diseases 4911
        urinary system disease 2411
          kidney disease 2174
            nephrolithiasis 41
              calcium oxalate nephrolithiasis 30
                Calcium Oxalate Nephrolithiasis 1 2
                Calcium Oxalate Nephrolithiasis 2 with Nephrocalcinosis 1
                Kidney Calculi + 14
                X-linked nephrolithiasis type I 1
                hypophosphatemic nephrolithiasis/osteoporosis + 4
paths to the root