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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:nephrolithiasis
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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 chr 9:93,675,384...93,685,337
Ensembl chr 9:93,675,384...93,685,336
JBrowse link
G Ahsg alpha-2-HS-glycoprotein ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr11:78,121,388...78,127,998
Ensembl chr11:78,117,918...78,145,999
JBrowse link
G Bglap bone gamma-carboxyglutamate protein ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 2:173,838,518...173,839,495
Ensembl chr 2:173,838,518...173,839,495
JBrowse link
G Casr calcium-sensing receptor ISO DNA:snps, haplotypes:multiple (human) RGD PMID:20067903 RGD:7205448 NCBI chr11:64,235,251...64,304,811
Ensembl chr11:64,235,251...64,304,811
JBrowse link
G Cd44 CD44 molecule ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 3:89,155,850...89,244,615
Ensembl chr 3:89,157,058...89,244,620
JBrowse link
G Cyp24a1 cytochrome P450, family 24, subfamily a, polypeptide 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22337913 NCBI chr 3:159,275,947...159,290,383
Ensembl chr 3:159,275,947...159,290,383
JBrowse link
G Gsr glutathione-disulfide reductase IEP RGD PMID:16670437 RGD:7257558 NCBI chr16:58,482,209...58,525,256
Ensembl chr16:58,482,505...58,525,661
JBrowse link
G Hao1 hydroxyacid oxidase 1 ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 3:121,757,400...121,828,721
Ensembl chr 3:121,771,836...121,828,721
JBrowse link
G Idua alpha-L-iduronidase ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis | ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr14:1,031,588...1,059,494
Ensembl chr14:1,032,171...1,046,522
JBrowse link
G Mt-co3 mitochondrially encoded cytochrome c oxidase III ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:25741868 NCBI chr MT:8,599...9,382
NCBI chr MT:8,599...9,382
NCBI chr MT:8,599...9,382
Ensembl chr MT:8,599...9,382
JBrowse link
G Nherf1 NHERF family PDZ scaffold protein 1 ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:18784102 PMID:24033266 PMID:25741868 PMID:28492532 PMID:28893421 NCBI chr10:100,403,189...100,420,290
Ensembl chr10:100,403,069...100,420,598
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 2:173,832,241...173,838,443
Ensembl chr 2:173,833,880...173,838,456
JBrowse link
G Rgs14 regulator of G-protein signaling 14 ISO DNA:SNP: :rs11746443 (human) RGD PMID:22396660 RGD:7242927 NCBI chr17:9,248,982...9,263,104
Ensembl chr17:9,249,019...9,263,104
JBrowse link
G Slc25a25 solute carrier family 25 member 25 ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar NCBI chr 3:15,708,702...15,742,195
Ensembl chr 3:15,708,703...15,742,216
JBrowse link
G Slc26a1 solute carrier family 26 member 1 ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis | ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr14:1,040,565...1,045,851
Ensembl chr14:1,040,243...1,045,849
JBrowse link
G Slc34a1 solute carrier family 34 member 1 onset ISO DNA:snp:intron:IVS4+54C>T rs3812036 (human)
ClinVar Annotator: match by term: Nephrolithiasis
associated with Hyperoxaluria
ClinVar
RGD
PMID:16199547 PMID:25741868 PMID:26047794 PMID:28492532 PMID:28893421 More... RGD:7242927, RGD:7243005 NCBI chr17:9,218,876...9,233,852
Ensembl chr17:9,218,876...9,233,852
JBrowse link
G Tgfb1 transforming growth factor, beta 1 treatment IEP RGD PMID:24712822 RGD:11073675 NCBI chr 1:81,196,532...81,212,848
Ensembl chr 1:81,196,532...81,212,847
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 ClinVar
OMIM
PMID:31320686 NCBI chr  X:103,459,870...103,473,794
Ensembl chr  X:103,459,780...103,474,838
JBrowse link
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 chr11:78,121,388...78,127,998
Ensembl chr11:78,117,918...78,145,999
JBrowse link
G Ambp alpha-1-microglobulin/bikunin precursor ISO
IEP
protein:increased expression:urine RGD PMID:16622176 PMID:15533056 RGD:6904147, RGD:6904219 NCBI chr 5:76,568,094...76,578,416
Ensembl chr 5:76,568,094...76,578,331
JBrowse link
G Bglap bone gamma-carboxyglutamate protein ISO protein:increased expression:serum:
ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate
ClinVar
RGD
PMID:24886237 PMID:21908029 RGD:7207408 NCBI chr 2:173,838,518...173,839,495
Ensembl chr 2:173,838,518...173,839,495
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 chr11:64,235,251...64,304,811
Ensembl chr11:64,235,251...64,304,811
JBrowse link
G Cat catalase ISO RGD PMID:21557843 RGD:7205663 NCBI chr 3:89,842,393...89,874,577
Ensembl chr 3:89,842,399...89,874,478
JBrowse link
G Cd44 CD44 molecule ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 3:89,155,850...89,244,615
Ensembl chr 3:89,157,058...89,244,620
JBrowse link
G F2 coagulation factor II, thrombin IEP mRNA:decreased expression:kidney RGD PMID:16981243 RGD:6893592 NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486
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 9:73,196,044...73,264,695
Ensembl chr 9:73,196,044...73,264,678
JBrowse link
G Hao1 hydroxyacid oxidase 1 ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:24886237 NCBI chr 3:121,757,400...121,828,721
Ensembl chr 3:121,771,836...121,828,721
JBrowse link
G Idua alpha-L-iduronidase ISO ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr14:1,031,588...1,059,494
Ensembl chr14:1,032,171...1,046,522
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 3:7,111,567...7,127,451
Ensembl chr 3:7,111,550...7,127,445
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 2:173,832,241...173,838,443
Ensembl chr 2:173,833,880...173,838,456
JBrowse link
G Pth parathyroid hormone ISO protein:decreased expression:serum (human) RGD PMID:23470222 RGD:7242417 NCBI chr 1:167,508,121...167,511,530
Ensembl chr 1:167,508,598...167,511,530
JBrowse link
G Slc26a1 solute carrier family 26 member 1 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate
CTD
ClinVar
PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr14:1,040,565...1,045,851
Ensembl chr14:1,040,243...1,045,849
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 chr14:1,040,565...1,045,851
Ensembl chr14:1,040,243...1,045,849
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 chr15:97,145,947...97,146,960
Ensembl chr15:97,144,293...97,166,612
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
ISS
CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dent disease | ClinVar Annotator: match by term: Dent's disease
OMIM:300009 | OMIM:300555
CTD
ClinVar
MouseDO
PMID:10561751 PMID:11136179 PMID:15719255 PMID:15814539 PMID:15895257 More... NCBI chr  X:15,185,380...15,339,977
Ensembl chr  X:15,185,451...15,334,264
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:127,089,508...127,140,362
Ensembl chr  X:127,089,590...127,140,362
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 CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: NEPHROLITHIASIS, HYPERCALCIURIC, X-LINKED | ClinVar Annotator: match by term: Nephrolithiasis 2
OMIM
CTD
ClinVar
PMID:7874126 PMID:7915957 PMID:8559248 PMID:8950885 PMID:9062355 More... NCBI chr  X:15,185,380...15,339,977
Ensembl chr  X:15,185,451...15,334,264
JBrowse link
G Mir188 microRNA 188 ISO ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:15,247,715...15,247,794
Ensembl chr  X:15,247,715...15,247,794
JBrowse link
G Mir500 microRNA 500 ISO ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:15,258,778...15,258,857
Ensembl chr  X:15,258,768...15,258,859
JBrowse link
G Mir532 microRNA 532 ISO ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:15,247,315...15,247,393
Ensembl chr  X:15,247,315...15,247,393
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 5:136,996,766...137,061,315
Ensembl chr 5:136,996,686...137,061,315
JBrowse link
G Ocrl OCRL, inositol polyphosphate-5-phosphatase ISO ClinVar Annotator: match by term: Dent disease type 2
CTD Direct Evidence: marker/mechanism
OMIM
ClinVar
CTD
PMID:1321346 PMID:8504307 PMID:15627218 PMID:16381338 PMID:17162149 More... NCBI chr  X:127,089,508...127,140,362
Ensembl chr  X:127,089,590...127,140,362
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 chr17:9,207,683...9,215,530
Ensembl chr17:9,207,683...9,215,530
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 chr17:9,218,876...9,233,852
Ensembl chr17:9,218,876...9,233,852
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 chr17:9,207,683...9,215,530
Ensembl chr17:9,207,683...9,215,530
JBrowse link
G Slc34a1 solute carrier family 34 member 1 ISO ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1
CTD Direct Evidence: marker/mechanism
OMIM
ClinVar
CTD
PMID:9536098 PMID:12324554 PMID:14672348 PMID:16199547 PMID:16688119 More... NCBI chr17:9,218,876...9,233,852
Ensembl chr17:9,218,876...9,233,852
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 3:8,044,294...8,050,034
Ensembl chr 3:8,044,296...8,049,970
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 CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 2
OMIM
CTD
ClinVar
PMID:18784102 PMID:24033266 PMID:25326635 PMID:25741868 PMID:28492532 More... NCBI chr10:100,403,189...100,420,290
Ensembl chr10:100,403,069...100,420,598
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 2:173,838,518...173,839,495
Ensembl chr 2:173,838,518...173,839,495
JBrowse link
G 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
JBrowse link
G 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
JBrowse link
G Cd44 CD44 molecule IEP RGD PMID:16850024 RGD:2289370 NCBI chr 3:89,155,850...89,244,615
Ensembl chr 3:89,157,058...89,244,620
JBrowse link
G 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
JBrowse link
G F2 coagulation factor II, thrombin 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
JBrowse link
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
JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr 7:53,903,339...53,907,375
Ensembl chr 7:53,903,337...53,907,375
JBrowse link
G 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
JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr10:72,594,883...72,608,862
Ensembl chr10:72,594,661...72,604,819
JBrowse link
G 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
JBrowse link
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
JBrowse link
G 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
JBrowse link
G Trpm7 transient receptor potential cation channel, subfamily M, member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 3:114,046,258...114,134,799
Ensembl chr 3:114,046,258...114,135,190
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
CTD Direct Evidence: marker/mechanism
OMIM
ClinVar
CTD
PMID:7915957 PMID:8559248 PMID:9062355 PMID:9187673 PMID:9734595 More... NCBI chr  X:15,185,380...15,339,977
Ensembl chr  X:15,185,451...15,334,264
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
CTD Direct Evidence: marker/mechanism
OMIM
ClinVar
CTD
PMID:7915957 PMID:8559248 PMID:9187673 PMID:9602200 PMID:9734595 More... NCBI chr  X:15,185,380...15,339,977
Ensembl chr  X:15,185,451...15,334,264
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 21128
    disease of anatomical entity 18212
      Urogenital Diseases 5216
        urinary system disease 2823
          kidney disease 2579
            nephrolithiasis 49
              AZOOSPERMIA, OBSTRUCTIVE, WITH NEPHROLITHIASIS 1
              Dent disease + 6
              calcium oxalate nephrolithiasis + 36
              uric acid nephrolithiasis 0
paths to the root