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
Accession: DOID:585
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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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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
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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
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
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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
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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
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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
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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
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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
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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
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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
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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
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
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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
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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
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
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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
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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
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
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
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
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
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
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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
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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
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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
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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
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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
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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
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
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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
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
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