Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   

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
go back to main search page
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
 alt_id: OMIM:167030
For additional species annotation, visit the Alliance of Genome Resources.


show annotations for term's descendants           Sort by:
 
calcium oxalate nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ambp alpha-1-microglobulin/bikunin precursor ISO
IEP
protein:increased expression:urine RGD PMID:16622176, PMID:15533056 RGD:6904147, RGD:6904219 NCBI chr 5:78,975,690...78,986,021
Ensembl chr 5:78,975,678...78,985,990
JBrowse link
G Bglap bone gamma-carboxyglutamate protein ISO protein:increased expression:serum: RGD PMID:21908029 RGD:7207408 NCBI chr 2:187,741,770...187,748,445
Ensembl chr 2:187,741,770...187,742,747
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:21183554, PMID:21966463, PMID:20602573 RGD:13464331, RGD:7205447, RGD:7205446, RGD:7205445 NCBI chr11:67,188,204...67,262,261
Ensembl chr11:67,188,630...67,258,771
JBrowse link
G Cat catalase ISO RGD PMID:21557843 RGD:7205663 NCBI chr 3:93,379,872...93,412,058
Ensembl chr 3:93,379,874...93,412,058
JBrowse link
G F2 coagulation factor II IEP mRNA:decreased expression:kidney RGD PMID:16981243 RGD:6893592 NCBI chr 3:80,529,468...80,542,993
Ensembl chr 3:80,529,428...80,543,031
JBrowse link
G Fn1 fibronectin 1 ISO
IEP
DNA:polymorphism: :
protein:increased expression:kidney
RGD PMID:19616291, PMID:11025758 RGD:7206842, RGD:7206846 NCBI chr 9:78,900,111...78,969,018
Ensembl chr 9:78,900,103...78,969,078
JBrowse link
G Il1rn interleukin 1 receptor antagonist ISO DNA:repeats:intron:IVS2+914_1000dup IL1RN*1 (human) RGD PMID:17258699 RGD:6907128 NCBI chr 3:1,449,778...1,468,624
Ensembl chr 3:1,452,644...1,468,614
JBrowse link
G Pth parathyroid hormone ISO protein:decreased expression:serum (human) RGD PMID:23470222 RGD:7242417 NCBI chr 1:178,215,829...178,218,761
Ensembl chr 1:178,215,829...178,218,761
JBrowse link
G Slc26a1 solute carrier family 26 member 1 ISO OMIM NCBI chr14:2,050,805...2,056,091
Ensembl chr14:2,050,483...2,056,089
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: Hypophosphatemic Nephrolithiasis/Osteoporosis
ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic
ClinVar PMID:8528215 PMID:9354665 PMID:21920016 PMID:23348723 PMID:24029428 PMID:24033266 PMID:25524745 PMID:25741868 PMID:28492532 NCBI chr17:9,736,577...9,744,420
Ensembl chr17:9,736,577...9,744,420
JBrowse link
G Slc34a1 solute carrier family 34 member 1 ISO ClinVar Annotator: match by term: Hypophosphatemic Nephrolithiasis/Osteoporosis
ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic
ClinVar PMID:8528215 PMID:9354665 PMID:21920016 PMID:23348723 PMID:24029428 PMID:24033266 PMID:25524745 PMID:25741868 PMID:28492532 NCBI chr17:9,747,766...9,762,739
Ensembl chr17:9,747,752...9,762,813
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: Nephrolithiasis/osteoporosis, hypophosphatemic, 1 ClinVar PMID:28492532 NCBI chr17:9,736,577...9,744,420
Ensembl chr17:9,736,577...9,744,420
JBrowse link
G Slc34a1 solute carrier family 34 member 1 ISO ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic, 1
ClinVar Annotator: match by OMIM:612286
OMIM
ClinVar
PMID:12324554 PMID:16688119 PMID:24033266 PMID:25082825 PMID:25741868 PMID:26047794 PMID:26272126 PMID:27378183 PMID:28492532 PMID:28893421 NCBI chr17:9,747,766...9,762,739
Ensembl chr17:9,747,752...9,762,813
JBrowse link
hypophosphatemic nephrolithiasis/osteoporosis 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Slc9a3r1 SLC9A3 regulator 1 ISO ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic, 2
ClinVar Annotator: match by OMIM:612287
OMIM
ClinVar
PMID:18784102 PMID:24033266 PMID:25326635 PMID:25741868 PMID:28492532 PMID:28893421 NCBI chr10:103,713,045...103,730,145
Ensembl chr10:103,713,045...103,730,145
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 2:187,741,770...187,748,445
Ensembl chr 2:187,741,770...187,742,747
JBrowse link
G Car2 carbonic anhydrase 2 IEP RGD PMID:10977795 RGD:1600710 NCBI chr 2:88,097,740...88,112,868
Ensembl chr 2:88,097,720...88,113,029
JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 3:93,379,872...93,412,058
Ensembl chr 3:93,379,874...93,412,058
JBrowse link
G Cd44 CD44 molecule (Indian blood group) IEP RGD PMID:16850024 RGD:2289370 NCBI chr 3:92,695,083...92,783,820
Ensembl chr 3:92,696,313...92,783,658
JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr11:34,132,581...34,142,813
Ensembl chr11:34,132,581...34,142,753
JBrowse link
G F2 coagulation factor II susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 3:80,529,468...80,542,993
Ensembl chr 3:80,529,428...80,543,031
JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 1:219,291,679...219,294,147
Ensembl chr 1:219,291,679...219,294,147
JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr 7:61,337,383...61,341,419
Ensembl chr 7:61,337,381...61,341,419
JBrowse link
G Mgp matrix Gla protein IDA RGD PMID:10460895 RGD:1582511 NCBI chr 4:170,856,783...170,860,105
Ensembl chr 4:170,856,751...170,860,225
JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr10:75,087,892...75,098,260
Ensembl chr10:75,087,892...75,098,260
JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 6:28,382,937...28,388,771
Ensembl chr 6:28,382,962...28,388,967
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:30,363,282...30,368,858
Ensembl chr11:30,363,280...30,368,862
JBrowse link
G Spp1 secreted phosphoprotein 1 ISO
IEP
CTD Direct Evidence: marker/mechanism CTD PMID:8325891 PMID:10890885, PMID:15954903, PMID:21378157, PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr14:6,673,686...6,679,965
Ensembl chr14:6,673,686...6,679,901
JBrowse link
G Trpm7 transient receptor potential cation channel, subfamily M, member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 3:119,258,189...119,347,084
Ensembl chr 3:119,259,467...119,330,345
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: X-linked recessive nephrolithiasis with renal failure
ClinVar Annotator: match by term: Nephrolithiasis, X-linked recessive
OMIM
ClinVar
PMID:8559248 PMID:9602200 PMID:25741868 NCBI chr  X:16,170,585...16,196,691
Ensembl chr  X:16,050,780...16,196,789
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16918
    disease of anatomical entity 16286
      Urogenital Diseases 4203
        urinary system disease 2107
          kidney disease 1886
            nephrolithiasis 47
              calcium oxalate nephrolithiasis 30
                Kidney Calculi + 20
                X-linked nephrolithiasis type I 1
                hypophosphatemic nephrolithiasis/osteoporosis + 3
paths to the root