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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: ICD10CM:N20;   ICD9CM:592
For additional species annotation, visit the Alliance of Genome Resources.


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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: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr11:81,711,269...81,717,594 JBrowse link
G Bglap bone gamma-carboxyglutamate protein ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 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 ISO DNA:snps, haplotypes:multiple (human) RGD PMID:20067903 RGD:7205448 NCBI chr11:67,188,204...67,262,261
Ensembl chr11:67,188,630...67,258,771
JBrowse link
G Cd44 CD44 molecule (Indian blood group) ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 3:92,695,083...92,783,820
Ensembl chr 3:92,696,313...92,783,658
JBrowse link
G Cyp24a1 cytochrome P450, family 24, subfamily a, polypeptide 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22337913 NCBI chr 3:168,097,484...168,111,920
Ensembl chr 3:168,097,485...168,111,920
JBrowse link
G Gsr glutathione-disulfide reductase IEP RGD PMID:16670437 RGD:7257558 NCBI chr16:62,197,617...62,239,987
Ensembl chr16:62,197,617...62,241,361
JBrowse link
G Hao1 hydroxyacid oxidase 1 ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 3:127,444,900...127,500,709
Ensembl chr 3:127,444,902...127,500,709
JBrowse link
G Idua alpha-L-iduronidase ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:25741868, PMID:27210743, PMID:28492532, PMID:30311386 NCBI chr14:2,041,828...2,056,762
Ensembl chr14:2,042,411...2,056,762
JBrowse link
G Men1 menin 1 ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:30311386 NCBI chr 1:221,704,394...221,710,343
Ensembl chr 1:221,704,493...221,710,331
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
Ensembl chr MT:8,599...9,382
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 2:187,736,774...187,741,696
Ensembl chr 2:187,737,770...187,741,696
JBrowse link
G Rgs14 regulator of G-protein signaling 14 ISO DNA:SNP: :rs11746443 (human) RGD PMID:22396660 RGD:7242927 NCBI chr17:9,777,925...9,792,007
Ensembl chr17:9,777,842...9,792,007
JBrowse link
G Slc26a1 solute carrier family 26 member 1 ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:25741868, PMID:27210743, PMID:28492532, PMID:30311386 NCBI chr14:2,050,805...2,056,091
Ensembl chr14:2,050,483...2,056,089
JBrowse link
G Slc34a1 solute carrier family 34 member 1 onset ISO DNA:snp:intron:IVS4+54C>T rs3812036 (human)
associated with Hyperoxaluria
RGD PMID:22396660, PMID:18337544 RGD:7242927, RGD:7243005 NCBI chr17:9,747,766...9,762,739
Ensembl chr17:9,747,752...9,762,813
JBrowse link
G Slc9a3r1 SLC9A3 regulator 1 ISO ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:18784102, PMID:24033266, PMID:28893421 NCBI chr10:103,713,045...103,730,145
Ensembl chr10:103,713,045...103,730,145
JBrowse link
G Tgfb1 transforming growth factor, beta 1 treatment IEP RGD PMID:24712822 RGD:11073675 NCBI chr 1:82,480,875...82,497,196
Ensembl chr 1:82,480,195...82,497,199
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
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
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 CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dent's disease
ClinVar Annotator: match by term: Dent Disease
CTD
ClinVar
PMID:10561751, PMID:15719255, PMID:15814539, PMID:20804101, PMID:28492532 NCBI chr  X:16,170,585...16,196,691
Ensembl chr  X:16,050,780...16,196,789
JBrowse link
G Ocrl OCRL, inositol polyphosphate-5-phosphatase ISS OMIM:300009 | OMIM:300555 MouseDO NCBI chr  X:134,742,226...134,793,411
Ensembl chr  X:134,742,356...134,792,618
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 2
ClinVar Annotator: match by term: Dent disease 1
ClinVar Annotator: match by OMIM:300009
OMIM
ClinVar
PMID:7874126, PMID:7915957, PMID:8559248, PMID:8950885, PMID:9062355, PMID:9187673, PMID:9259268, PMID:9328929, PMID:9734595, PMID:9853249, PMID:10469281, PMID:10906159, PMID:11136179, PMID:12637640, PMID:14569459, PMID:15052463, PMID:15086899, PMID:15719255, PMID:15895257, PMID:16041495, PMID:16247550, PMID:16822791, PMID:16861240, PMID:18038239, PMID:18184518, PMID:19076289, PMID:19546586, PMID:19546591, PMID:19657328, PMID:19673950, PMID:19806368, PMID:24081861, PMID:25326635, PMID:25741868, PMID:25907713, PMID:26822237, PMID:28492532 NCBI chr  X:16,170,585...16,196,691
Ensembl chr  X:16,050,780...16,196,789
JBrowse link
G Mir188 microRNA 188 ISO ClinVar Annotator: match by term: Dent disease 1 ClinVar PMID:7874126, PMID:9328929, PMID:15052463 NCBI chr  X:16,110,270...16,110,349
Ensembl chr  X:16,110,270...16,110,349
JBrowse link
G Mir500 microRNA 500 ISO ClinVar Annotator: match by term: Dent disease 1 ClinVar PMID:7874126, PMID:9328929, PMID:15052463 NCBI chr  X:16,121,332...16,121,411
Ensembl chr  X:16,121,322...16,121,413
JBrowse link
G Mir532 microRNA 532 ISO ClinVar Annotator: match by term: Dent disease 1 ClinVar PMID:7874126, PMID:9328929, PMID:15052463 NCBI chr  X:16,109,870...16,109,948
Ensembl chr  X:16,109,870...16,109,948
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 5:142,731,767...142,796,305
Ensembl chr 5:142,731,767...142,796,305
JBrowse link
G Ocrl OCRL, inositol polyphosphate-5-phosphatase ISO ClinVar Annotator: match by term: Dent disease type 2 OMIM
ClinVar
PMID:15627218, PMID:17162149, PMID:17384968, PMID:21031565, PMID:24081861, PMID:25480730, PMID:25741868, PMID:27625797, PMID:28018608, PMID:28492532 NCBI chr  X:134,742,226...134,793,411
Ensembl chr  X:134,742,356...134,792,618
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 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 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 Men1 menin 1 ISO ClinVar Annotator: match by term: Renal calculi ClinVar PMID:30311386 NCBI chr 1:221,704,394...221,710,343
Ensembl chr 1:221,704,493...221,710,331
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
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
ClinVar Annotator: match by OMIM:308990
OMIM
ClinVar
PMID:8559248, PMID:9062355, PMID:25741868 NCBI chr  X:16,170,585...16,196,691
Ensembl chr  X:16,050,780...16,196,789
JBrowse link
uric acid nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Zfp365 zinc finger protein 365 susceptibility ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Uric acid nephrolithiasis, susceptibility to
CTD
ClinVar
OMIM
PMID:12740763, PMID:28492532 NCBI chr20:22,060,160...22,083,766
Ensembl chr20:22,060,224...22,086,108
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 16096
    disease of anatomical entity 15346
      Urogenital Diseases 4143
        urinary system disease 2066
          kidney disease 1854
            nephrolithiasis 48
              Dent disease + 6
              calcium oxalate nephrolithiasis + 33
              uric acid nephrolithiasis 1
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.