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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 9:101,122,793...101,132,746
Ensembl chr 9:93,675,384...93,685,336 		JBrowse link
G Ahsg alpha-2-HS-glycoprotein ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr11:91,625,975...91,632,583
Ensembl chr11:78,117,918...78,145,999 		JBrowse link
G Bglap bone gamma-carboxyglutamate protein ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 2:176,136,341...176,137,318
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 chr11:77,738,398...77,813,639
Ensembl chr11:64,235,251...64,304,811 		JBrowse link
G Cd44 CD44 molecule ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 3:109,610,824...109,699,776
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 3:179,694,647...179,709,083
Ensembl chr 3:159,275,947...159,290,383 		JBrowse link
G Gsr glutathione-disulfide reductase IEP RGD PMID:16670437 RGD:7257558 NCBI chr16:65,185,574...65,228,742
Ensembl chr16:58,482,505...58,525,661 		JBrowse link
G Hao1 hydroxyacid oxidase 1 ISO ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 3:142,102,873...142,281,527
Ensembl chr 3:121,771,836...121,828,721 		JBrowse link
G Idua alpha-L-iduronidase ISO ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis | ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr14:1,175,994...1,203,913
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
NCBI chr MT:8,599...9,382
NCBI chr MT:8,599...9,382
NCBI chr MT:8,599...9,382
NCBI chr MT:8,599...9,382
NCBI chr MT:8,599...9,382
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:28492532 PMID:28893421 NCBI chr10:100,902,165...100,919,265
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: Calcium oxalate urolithiasis 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 chr17:9,254,112...9,268,233
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 nephrolithiasis | ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr14:1,180,465...1,190,257
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 chr17:9,224,010...9,238,983
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 1:90,324,312...90,340,627
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:108,248,383...108,258,847
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 Ambp alpha-1-microglobulin/bikunin precursor ISO
IEP		 protein:increased expression:urine RGD PMID:16622176 PMID:15533056 RGD:6904147, RGD:6904219 NCBI chr 5:81,583,621...81,593,938
Ensembl chr 5:76,568,094...76,578,331 		JBrowse link
G Bglap bone gamma-carboxyglutamate protein ISO protein:increased expression:serum: RGD PMID:21908029 RGD:7207408 NCBI chr 2:176,136,341...176,137,318
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 chr11:77,738,398...77,813,639
Ensembl chr11:64,235,251...64,304,811 		JBrowse link
G Cat catalase ISO RGD PMID:21557843 RGD:7205663 NCBI chr 3:110,297,340...110,329,526
Ensembl chr 3:89,842,399...89,874,478 		JBrowse link
G F2 coagulation factor II, thrombin IEP mRNA:decreased expression:kidney RGD PMID:16981243 RGD:6893592 NCBI chr 3:98,051,958...98,065,246
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 9:80,645,507...80,714,200
Ensembl chr 9:73,196,044...73,264,678 		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 chr14:1,175,994...1,203,913
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 3:27,509,836...27,525,738
Ensembl chr 3:7,111,550...7,127,445 		JBrowse link
G Pth parathyroid hormone ISO protein:decreased expression:serum (human) RGD PMID:23470222 RGD:7242417 NCBI chr 1:176,942,901...176,946,034
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: Calcium oxalate nephrolithiasis		 CTD
ClinVar		 PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378 NCBI chr14:1,180,465...1,190,257
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 Idua alpha-L-iduronidase ISO ClinVar Annotator: match by term: NEPHROLITHIASIS, CALCIUM OXALATE, 1 | ClinVar Annotator: match by term: SLC26A1-related condition ClinVar PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378 NCBI chr14:1,175,994...1,203,913
Ensembl chr14:1,032,171...1,046,522 		JBrowse link
G Slc26a1 solute carrier family 26 member 1 ISO ClinVar Annotator: match by term: NEPHROLITHIASIS, CALCIUM OXALATE, 1 | ClinVar Annotator: match by term: SLC26A1-related condition OMIM
ClinVar		 PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378 NCBI chr14:1,180,465...1,190,257
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:25741868 PMID:36571463 NCBI chr15:103,551,338...103,573,611
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:17,857,260...18,011,844
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:131,955,775...132,018,298
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 ClinVar Annotator: match by term: NEPHROLITHIASIS, HYPERCALCIURIC, X-LINKED | ClinVar Annotator: match by term: Nephrolithiasis 2
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:7874126 PMID:7915957 PMID:8559248 PMID:8950885 PMID:9062355 More... NCBI chr  X:17,857,260...18,011,844
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:17,930,647...17,930,726
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:17,919,185...17,919,263
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:131,955,775...132,018,298
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 chr17:9,212,819...9,220,664
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 chr17:9,224,010...9,238,983
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 chr17:9,212,819...9,220,664
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 OMIM
ClinVar		 PMID:9536098 PMID:12324554 PMID:14672348 PMID:16199547 PMID:16688119 More... NCBI chr17:9,224,010...9,238,983
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 ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 2 | ClinVar Annotator: match by term: NHERF1-related condition OMIM
ClinVar		 PMID:18784102 PMID:24033266 PMID:25326635 PMID:25741868 PMID:28492532 More... NCBI chr10:100,902,165...100,919,265
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 2:176,136,341...176,137,318
Ensembl chr 2:173,838,518...173,839,495 		JBrowse link
G Car2 carbonic anhydrase 2 IEP RGD PMID:10977795 RGD:1600710 NCBI chr 2:88,462,883...88,478,012
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 3:110,297,340...110,329,526
Ensembl chr 3:89,842,399...89,874,478 		JBrowse link
G Cd44 CD44 molecule IEP RGD PMID:16850024 RGD:2289370 NCBI chr 3:109,610,824...109,699,776
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 chr11:46,701,940...46,799,049
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 3:98,051,958...98,065,246
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 1:210,767,237...210,770,242
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 7:55,789,180...55,793,216
Ensembl chr 7:53,903,337...53,907,375 		JBrowse link
G Mgp matrix Gla protein IDA RGD PMID:10460895 RGD:1582511 NCBI chr 4:171,497,472...171,500,888
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 chr10:73,092,124...73,102,057
Ensembl chr10:72,594,661...72,604,819 		JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 6:32,659,137...32,665,175
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 chr11:42,942,742...42,948,399
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:16105024 PMID:21378157 RGD:1581372, RGD:1581334, RGD:6903839 NCBI chr14:5,613,569...5,620,695
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 3:134,499,617...134,588,113
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:17,857,260...18,011,844
Ensembl chr  X:15,185,451...15,334,264 		JBrowse link
uric acid nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tlr2 toll-like receptor 2 IEP protein:increased expression:kidney RGD PMID:25046957 RGD:597538538 NCBI chr 2:171,499,189...171,504,831
Ensembl chr 2:169,197,419...169,206,630 		JBrowse link
G Tlr4 toll-like receptor 4 IEP mRNA, protein:increased expression:kidney RGD PMID:25046957 RGD:597538538 NCBI chr 5:85,161,247...85,174,882
Ensembl chr 5:80,145,826...80,159,628 		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:17,857,260...18,011,844
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 19141
    disease of anatomical entity 18453
      Urogenital Diseases 5391
        urinary system disease 2832
          kidney disease 2580
            nephrolithiasis 51
              AZOOSPERMIA, OBSTRUCTIVE, WITH NEPHROLITHIASIS 1
              Dent disease + 6
              calcium oxalate nephrolithiasis + 33
              uric acid nephrolithiasis 2
paths to the root