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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 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 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 16085
    disease of anatomical entity 15340
      Urogenital Diseases 4175
        urinary system disease 2087
          kidney disease 1874
            nephrolithiasis 45
              Dent disease + 6
              calcium oxalate nephrolithiasis + 30
              uric acid nephrolithiasis 1
paths to the root