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:nephrolithiasis
go back to main search page
Accession:DOID:585 term browser browse the term
Definition:A kidney disease characterized by the formation of stoney concentrations in the kidneys. (DO)
Synonyms:exact_synonym: NEPHROLITHIASIS, CALCIUM OXALATE;   UAN;   calcium oxalate urolithiasis;   calculus of kidney and ureter;   stone - kidney/ureter
 primary_id: MESH:D053040
 xref: EFO:0004253;   ICD10CM:N20;   ICD9CM:592
For additional species annotation, visit the Alliance of Genome Resources.



show annotations for term's descendants           Sort by:
nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AGXT alanine--glyoxylate aminotransferase ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:9192270 PMID:10541294 PMID:10960483 PMID:12777626 PMID:15327387 More... NCBI chr15:139,720,648...139,730,737
Ensembl chr15:139,720,612...139,730,736
JBrowse link
G AHSG alpha 2-HS glycoprotein ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr13:124,426,313...124,438,848
Ensembl chr13:124,426,308...124,438,840
JBrowse link
G CASR calcium sensing receptor ISO DNA:snps, haplotypes:multiple (human) RGD PMID:20067903 RGD:7205448 NCBI chr13:138,279,785...138,364,934
Ensembl chr13:138,280,364...138,364,252
JBrowse link
G CD44 CD44 molecule ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 2:25,788,699...25,884,209
Ensembl chr 2:25,788,703...25,884,153
JBrowse link
G CYP24A1 cytochrome P450 family 24 subfamily A member 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22337913 NCBI chr17:55,110,546...55,130,328
Ensembl chr17:55,110,590...55,130,363
JBrowse link
G GSR glutathione-disulfide reductase ISO RGD PMID:16670437 RGD:7257558 NCBI chr15:54,382,564...54,433,989
Ensembl chr15:54,382,567...54,433,984
JBrowse link
G HAO1 hydroxyacid oxidase 1 ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr17:16,746,153...16,802,460
Ensembl chr17:16,744,442...16,802,442
JBrowse link
G IDUA alpha-L-iduronidase ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr 8:334,604...351,970
Ensembl chr 8:334,617...351,969
JBrowse link
G MT-CO3 mitochondrially encoded cytochrome c oxidase III ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:25741868 NCBI chr MT:9,800...10,583
Ensembl chr MT:9,800...10,583
JBrowse link
G NHERF1 NHERF family PDZ scaffold protein 1 ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:18784102 PMID:24033266 PMID:28492532 PMID:28893421 NCBI chr12:6,466,138...6,483,539
Ensembl chr12:6,466,121...6,483,548
JBrowse link
G PAQR6 progestin and adipoQ receptor family member 6 ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 4:93,802,721...93,807,624
Ensembl chr 4:93,801,863...93,807,597
JBrowse link
G RGS14 regulator of G protein signaling 14 ISO DNA:SNP: :rs11746443 (human) RGD PMID:22396660 RGD:7242927 NCBI chr 2:80,574,411...80,589,998
Ensembl chr 2:80,574,415...80,590,003
JBrowse link
G SLC25A25 solute carrier family 25 member 25 ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar NCBI chr 1:268,531,752...268,575,195
Ensembl chr 1:268,531,752...268,576,994
JBrowse link
G SLC26A1 solute carrier family 26 member 1 ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr 8:335,420...345,955
Ensembl chr 8:335,427...342,444
JBrowse link
G SLC34A1 solute carrier family 34 member 1 onset ISO associated with Hyperoxaluria
ClinVar Annotator: match by term: Nephrolithiasis
RGD
ClinVar
PMID:18337544 PMID:25741868 PMID:28492532 PMID:28893421 RGD:7243005 NCBI chr 2:80,548,208...80,563,380
Ensembl chr 2:80,548,232...80,563,321
JBrowse link
G TGFB1 transforming growth factor beta 1 treatment ISO RGD PMID:24712822 RGD:11073675 NCBI chr 6:49,332,169...49,348,642
Ensembl chr 6:49,332,173...49,349,046
JBrowse link
AZOOSPERMIA, OBSTRUCTIVE, WITH NEPHROLITHIASIS term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLDN2 claudin 2 ISO ClinVar Annotator: match by term: Azoospermia, obstructive, with nephrolithiasis OMIM
ClinVar
PMID:31320686 NCBI chr  X:87,352,695...87,355,724
Ensembl chr  X:87,321,152...87,355,721
JBrowse link
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 protein:increased expression:urine RGD PMID:15533056 PMID:16622176 RGD:6904147 RGD:6904219 NCBI chr 1:254,683,885...254,703,220
Ensembl chr 1:254,683,891...254,703,225
JBrowse link
G CASR calcium sensing receptor susceptibility ISO DNA:missense mutations:cds:p.A986S, p.E1011Q (human)
associated with Hyperparathyroidism, Primary; DNA:snp:intron:IVS1 G>A rs1501899 (human)
DNA:snp:intron:IVS4+11988A>G rs17251221 (human)
DNA:missense mutation:cds:p.R990G (rs1042636)(human)
RGD PMID:17018660 PMID:20602573 PMID:21183554 PMID:21966463 RGD:13464331 RGD:7205445 RGD:7205446 RGD:7205447 NCBI chr13:138,279,785...138,364,934
Ensembl chr13:138,280,364...138,364,252
JBrowse link
G CAT catalase ISO RGD PMID:21557843 RGD:7205663 NCBI chr 2:26,493,664...26,533,881
Ensembl chr 2:26,487,653...26,581,452
JBrowse link
G F2 coagulation factor II, thrombin ISO mRNA:decreased expression:kidney RGD PMID:16981243 RGD:6893592 NCBI chr 2:15,793,257...15,819,151
Ensembl chr 2:15,791,455...15,819,137
JBrowse link
G FN1 fibronectin 1 ISO protein:increased expression:kidney
DNA:polymorphism: :
RGD PMID:11025758 PMID:19616291 RGD:7206842 RGD:7206846 NCBI chr15:117,658,158...117,737,145
Ensembl chr15:117,658,099...117,731,014
JBrowse link
G IDUA alpha-L-iduronidase ISO ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis ClinVar PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378 NCBI chr 8:334,604...351,970
Ensembl chr 8:334,617...351,969
JBrowse link
G IL1RN interleukin 1 receptor antagonist ISO DNA:repeats:intron:IVS2+914_1000dup IL1RN*1 (human) RGD PMID:17258699 RGD:6907128
G PTH parathyroid hormone ISO protein:decreased expression:serum (human) RGD PMID:23470222 RGD:7242417 NCBI chr 2:45,757,398...45,760,433
Ensembl chr 2:45,757,398...45,760,415
JBrowse link
G SLC26A1 solute carrier family 26 member 1 ISO ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis ClinVar PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378 NCBI chr 8:335,420...345,955
Ensembl chr 8:335,427...342,444
JBrowse link
Calcium Oxalate Nephrolithiasis 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SLC26A1 solute carrier family 26 member 1 ISO OMIM NCBI chr 8:335,420...345,955
Ensembl chr 8:335,427...342,444
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:36571463 NCBI chr11:66,289,131...66,295,826 JBrowse link
Dent disease 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: Dent disease | ClinVar Annotator: match by term: Dent's disease ClinVar PMID:11136179 PMID:15719255 PMID:15814539 PMID:15895257 PMID:16822791 More... NCBI chr  X:43,779,016...43,809,472
Ensembl chr  X:43,613,628...43,811,526
JBrowse link
G OCRL OCRL inositol polyphosphate-5-phosphatase ISO ClinVar Annotator: match by term: Dent disease ClinVar PMID:15108291 PMID:21031565 PMID:21971085 PMID:27398910 PMID:29300302 NCBI chr  X:106,124,991...106,188,066
Ensembl chr  X:106,135,431...106,190,110
JBrowse link
Dent Disease 1 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: NEPHROLITHIASIS, HYPERCALCIURIC, X-LINKED | ClinVar Annotator: match by term: Nephrolithiasis 2 OMIM
ClinVar
PMID:7874126 PMID:7915957 PMID:8559248 PMID:8950885 PMID:9062355 More... NCBI chr  X:43,779,016...43,809,472
Ensembl chr  X:43,613,628...43,811,526
JBrowse link
G MIR500 microRNA mir-500 ISO ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:43,711,254...43,711,333
Ensembl chr  X:43,711,254...43,711,333
JBrowse link
G MIR532 microRNA mir-532 ISO ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:43,705,258...43,705,337
Ensembl chr  X:43,705,258...43,705,337
JBrowse link
Dent Disease 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G INPP5B inositol polyphosphate-5-phosphatase B ISO ClinVar Annotator: match by term: Dent disease type 2 ClinVar PMID:28018608 NCBI chr 6:93,885,471...93,944,398
Ensembl chr 6:93,885,465...93,944,342
JBrowse link
G OCRL OCRL inositol polyphosphate-5-phosphatase ISO ClinVar Annotator: match by term: Dent disease type 2 OMIM
ClinVar
PMID:1321346 PMID:8504307 PMID:15627218 PMID:16381338 PMID:17162149 More... NCBI chr  X:106,124,991...106,188,066
Ensembl chr  X:106,135,431...106,190,110
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:8528215 PMID:9354665 PMID:9536098 PMID:17576681 PMID:21920016 More... NCBI chr 2:80,527,451...80,544,835
Ensembl chr 2:80,527,446...80,544,828
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 2:80,548,208...80,563,380
Ensembl chr 2:80,548,232...80,563,321
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 2:80,527,451...80,544,835
Ensembl chr 2:80,527,446...80,544,828
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 2:80,548,208...80,563,380
Ensembl chr 2:80,548,232...80,563,321
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
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 OMIM
ClinVar
PMID:18784102 PMID:24033266 PMID:25326635 PMID:25741868 PMID:28492532 More... NCBI chr12:6,466,138...6,483,539
Ensembl chr12:6,466,121...6,483,548
JBrowse link
Kidney Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CA2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chr 4:51,194,686...51,211,436
Ensembl chr 4:51,193,756...51,211,259
JBrowse link
G CAT catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:26,493,664...26,533,881
Ensembl chr 2:26,487,653...26,581,452
JBrowse link
G CD44 CD44 molecule ISO RGD PMID:16850024 RGD:2289370 NCBI chr 2:25,788,699...25,884,209
Ensembl chr 2:25,788,703...25,884,153
JBrowse link
G CLDN14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr13:200,121,796...200,201,712
Ensembl chr13:200,128,477...200,145,525
JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 2:15,793,257...15,819,151
Ensembl chr 2:15,791,455...15,819,137
JBrowse link
G IFNG interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr 5:32,477,906...32,482,670
Ensembl chr 5:32,477,906...32,482,670
JBrowse link
G LOC100739508 glutathione S-transferase P-like ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:5,005,498...5,009,247 JBrowse link
G MGP matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr 5:57,665,272...57,669,360
Ensembl chr 5:57,665,248...57,669,764
JBrowse link
G MPO myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr12:34,557,031...34,570,091
Ensembl chr12:34,556,408...34,567,904
JBrowse link
G POMC proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 3:113,661,712...113,668,558
Ensembl chr 3:113,661,004...113,670,418
JBrowse link
G SOD1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr13:195,326,573...195,335,273
Ensembl chr13:195,326,649...195,337,729
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 8:131,077,786...131,085,334
Ensembl chr 8:131,077,786...131,085,340
JBrowse link
G TRPM7 transient receptor potential cation channel subfamily M member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 1:121,146,093...121,250,227
Ensembl chr 1:121,146,117...121,250,224
JBrowse link
low molecular weight proteinuria with hypercalciuric nephrocalcinosis 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: Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis OMIM
ClinVar
PMID:7915957 PMID:8559248 PMID:9062355 PMID:9187673 PMID:9734595 More... NCBI chr  X:43,779,016...43,809,472
Ensembl chr  X:43,613,628...43,811,526
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:9602200 PMID:9734595 More... NCBI chr  X:43,779,016...43,809,472
Ensembl chr  X:43,613,628...43,811,526
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 17416
    disease of anatomical entity 14866
      Urogenital Diseases 4656
        urinary system disease 2356
          kidney disease 2124
            nephrolithiasis 41
              AZOOSPERMIA, OBSTRUCTIVE, WITH NEPHROLITHIASIS 1
              Dent disease + 5
              calcium oxalate nephrolithiasis + 26
              uric acid nephrolithiasis 0
paths to the root