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: EFO:0004253 ; ICD10CM:N20 ; ICD9CM:592
For additional species annotation, visit the
Alliance of Genome Resources .
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AGXT
alanine--glyoxylate aminotransferase
ISO
ClinVar Annotator: match by term: Nephrolithiasis
ClinVar
PMID:9192270 PMID:10541294 PMID:10960483 PMID:12777626 PMID:15327387 PMID:16912707 PMID:17460142 PMID:23229545 PMID:24012869 PMID:24988064 PMID:25741868 PMID:28492532 PMID:28893421 More...
NCBI chr15:139,720,648...139,730,737
Ensembl chr15:139,720,612...139,730,736
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AHSG
alpha 2-HS glycoprotein
ISO
ClinVar Annotator: match by term: Calcium oxalate urolithiasis
ClinVar
PMID:24886237
NCBI chr13:124,426,313...124,438,848
Ensembl chr13:124,426,308...124,438,840
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CASR
calcium sensing receptor
ISO
DNA:snps, haplotypes:multiple (human)
RGD
PMID:20067903
RGD:7205448
NCBI chr13:138,279,785...138,364,934
Ensembl chr13:138,280,364...138,364,252
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CD44
CD44 molecule
ISO
ClinVar Annotator: match by term: Calcium oxalate urolithiasis
ClinVar
PMID:24886237
NCBI chr 2:25,788,699...25,884,209
Ensembl chr 2:25,788,703...25,884,153
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CYP24A1
cytochrome P450 family 24 subfamily A member 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:22337913
NCBI chr17:55,110,546...55,130,328
Ensembl chr17:55,110,590...55,130,363
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GSR
glutathione-disulfide reductase
ISO
RGD
PMID:16670437
RGD:7257558
NCBI chr15:54,382,564...54,433,989
Ensembl chr15:54,382,567...54,433,984
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HAO1
hydroxyacid oxidase 1
ISO
ClinVar Annotator: match by term: Calcium oxalate urolithiasis
ClinVar
PMID:24886237
NCBI chr17:16,746,153...16,802,460
Ensembl chr17:16,744,442...16,802,442
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IDUA
alpha-L-iduronidase
ISO
ClinVar Annotator: match by term: Calcium oxalate urolithiasis
ClinVar
PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 PMID:28492532 PMID:30586318 PMID:32432561 PMID:36719378 More...
NCBI chr 8:334,604...351,970
Ensembl chr 8:334,617...351,969
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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:9,800...10,583
Ensembl chr MT:9,800...10,583
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NHERF1
NHERF family PDZ scaffold protein 1
ISO
ClinVar Annotator: match by term: Nephrolithiasis
ClinVar
PMID:18784102 PMID:24033266 PMID:28492532 PMID:28893421
NCBI chr12:6,466,138...6,483,539
Ensembl chr12:6,466,121...6,483,548
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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 4:93,802,721...93,807,624
Ensembl chr 4:93,801,863...93,807,597
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RGS14
regulator of G protein signaling 14
ISO
DNA:SNP: :rs11746443 (human)
RGD
PMID:22396660
RGD:7242927
NCBI chr 2:80,574,411...80,589,998
Ensembl chr 2:80,574,415...80,590,003
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SLC25A25
solute carrier family 25 member 25
ISO
ClinVar Annotator: match by term: Nephrolithiasis
ClinVar
NCBI chr 1:268,531,752...268,575,195
Ensembl chr 1:268,531,752...268,576,994
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SLC26A1
solute carrier family 26 member 1
ISO
ClinVar Annotator: match by term: Calcium oxalate urolithiasis
ClinVar
PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 PMID:28492532 PMID:30586318 PMID:32432561 PMID:36719378 More...
NCBI chr 8:335,420...345,955
Ensembl chr 8:335,427...342,444
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SLC34A1
solute carrier family 34 member 1
onset
ISO
associated with Hyperoxaluria ClinVar Annotator: match by term: Nephrolithiasis
RGD ClinVar
PMID:18337544 PMID:25741868 PMID:28492532 PMID:28893421
RGD:7243005
NCBI chr 2:80,548,208...80,563,380
Ensembl chr 2:80,548,232...80,563,321
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TGFB1
transforming growth factor beta 1
treatment
ISO
RGD
PMID:24712822
RGD:11073675
NCBI chr 6:49,332,169...49,348,642
Ensembl chr 6:49,332,173...49,349,046
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CLDN2
claudin 2
ISO
ClinVar Annotator: match by term: Azoospermia, obstructive, with nephrolithiasis
OMIM ClinVar
PMID:31320686
NCBI chr X:87,352,695...87,355,724
Ensembl chr X:87,321,152...87,355,721
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AMBP
alpha-1-microglobulin/bikunin precursor
ISO
protein:increased expression:urine
RGD
PMID:15533056 PMID:16622176
RGD:6904147 RGD:6904219
NCBI chr 1:254,683,885...254,703,220
Ensembl chr 1:254,683,891...254,703,225
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CASR
calcium sensing receptor
susceptibility
ISO
DNA:missense mutations:cds:p.A986S, p.E1011Q (human) associated with Hyperparathyroidism, Primary; DNA:snp:intron:IVS1 G>A rs1501899 (human) DNA:snp:intron:IVS4+11988A>G rs17251221 (human) DNA:missense mutation:cds:p.R990G (rs1042636)(human)
RGD
PMID:17018660 PMID:20602573 PMID:21183554 PMID:21966463
RGD:13464331 RGD:7205445 RGD:7205446 RGD:7205447
NCBI chr13:138,279,785...138,364,934
Ensembl chr13:138,280,364...138,364,252
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CAT
catalase
ISO
RGD
PMID:21557843
RGD:7205663
NCBI chr 2:26,493,664...26,533,881
Ensembl chr 2:26,487,653...26,581,452
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F2
coagulation factor II, thrombin
ISO
mRNA:decreased expression:kidney
RGD
PMID:16981243
RGD:6893592
NCBI chr 2:15,793,257...15,819,151
Ensembl chr 2:15,791,455...15,819,137
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FN1
fibronectin 1
ISO
protein:increased expression:kidney DNA:polymorphism: :
RGD
PMID:11025758 PMID:19616291
RGD:7206842 RGD:7206846
NCBI chr15:117,658,158...117,737,145
Ensembl chr15:117,658,099...117,731,014
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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 chr 8:334,604...351,970
Ensembl chr 8:334,617...351,969
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IL1RN
interleukin 1 receptor antagonist
ISO
DNA:repeats:intron:IVS2+914_1000dup IL1RN*1 (human)
RGD
PMID:17258699
RGD:6907128
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PTH
parathyroid hormone
ISO
protein:decreased expression:serum (human)
RGD
PMID:23470222
RGD:7242417
NCBI chr 2:45,757,398...45,760,433
Ensembl chr 2:45,757,398...45,760,415
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SLC26A1
solute carrier family 26 member 1
ISO
ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis
ClinVar
PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378
NCBI chr 8:335,420...345,955
Ensembl chr 8:335,427...342,444
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SLC26A1
solute carrier family 26 member 1
ISO
OMIM
NCBI chr 8:335,420...345,955
Ensembl chr 8:335,427...342,444
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OXGR1
oxoglutarate receptor 1
ISO
ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate, 2, with or without nephrocalcinosis
OMIM ClinVar
PMID:36571463
NCBI chr11:66,289,131...66,295,826
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CLCN5
chloride voltage-gated channel 5
ISO
ClinVar Annotator: match by term: Dent disease | ClinVar Annotator: match by term: Dent's disease
ClinVar
PMID:11136179 PMID:15719255 PMID:15814539 PMID:15895257 PMID:16822791 PMID:18038239 PMID:19076289 PMID:19546586 PMID:22876375 PMID:24081861 PMID:25741868 PMID:25907713 PMID:27889724 PMID:28492532 PMID:31672324 PMID:32683654 More...
NCBI chr X:43,779,016...43,809,472
Ensembl chr X:43,613,628...43,811,526
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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:106,124,991...106,188,066
Ensembl chr X:106,135,431...106,190,110
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CLCN5
chloride voltage-gated channel 5
ISO
ClinVar Annotator: match by term: NEPHROLITHIASIS, HYPERCALCIURIC, X-LINKED | ClinVar Annotator: match by term: Nephrolithiasis 2
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:21305656 PMID:22876375 PMID:24081861 PMID:25001568 PMID:25326635 PMID:25741868 PMID:25907713 PMID:26822237 PMID:27117801 PMID:27889724 PMID:28492532 PMID:28580211 PMID:30773290 PMID:31328266 PMID:31672324 PMID:31674016 PMID:31852738 PMID:32201916 PMID:32289351 PMID:32683654 PMID:33532864 PMID:35738466 More...
NCBI chr X:43,779,016...43,809,472
Ensembl chr X:43,613,628...43,811,526
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MIR500
microRNA mir-500
ISO
ClinVar Annotator: match by term: Nephrolithiasis 2
ClinVar
PMID:7874126 PMID:9328929 PMID:15052463
NCBI chr X:43,711,254...43,711,333
Ensembl chr X:43,711,254...43,711,333
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MIR532
microRNA mir-532
ISO
ClinVar Annotator: match by term: Nephrolithiasis 2
ClinVar
PMID:7874126 PMID:9328929 PMID:15052463
NCBI chr X:43,705,258...43,705,337
Ensembl chr X:43,705,258...43,705,337
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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 6:93,885,471...93,944,398
Ensembl chr 6:93,885,465...93,944,342
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OCRL
OCRL inositol polyphosphate-5-phosphatase
ISO
ClinVar Annotator: match by term: Dent disease type 2
OMIM ClinVar
PMID:1321346 PMID:8504307 PMID:15627218 PMID:16381338 PMID:17162149 PMID:17384968 PMID:19390221 PMID:21031565 PMID:22381590 PMID:23047739 PMID:24081861 PMID:25480730 PMID:25741868 PMID:26694549 PMID:27625797 PMID:27708066 PMID:28018608 PMID:28492532 PMID:28803024 PMID:31674016 PMID:34125233 PMID:34139759 More...
NCBI chr X:106,124,991...106,188,066
Ensembl chr X:106,135,431...106,190,110
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F12
coagulation factor XII
ISO
ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic
ClinVar
PMID:8528215 PMID:9354665 PMID:9536098 PMID:17576681 PMID:21920016 PMID:23348723 PMID:24029428 PMID:24033266 PMID:25050900 PMID:25524745 PMID:25741868 PMID:28492532 PMID:30943683 PMID:33727708 More...
NCBI chr 2:80,527,451...80,544,835
Ensembl chr 2:80,527,446...80,544,828
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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 chr 2:80,548,208...80,563,380
Ensembl chr 2:80,548,232...80,563,321
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F12
coagulation factor XII
ISO
ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1
ClinVar
PMID:25050900 PMID:25741868 PMID:28492532 PMID:30943683
NCBI chr 2:80,527,451...80,544,835
Ensembl chr 2:80,527,446...80,544,828
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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 PMID:17576681 PMID:21597970 PMID:24033266 PMID:25050900 PMID:25082825 PMID:25296721 PMID:25741868 PMID:26047794 PMID:26272126 PMID:26787776 PMID:27378183 PMID:28492532 PMID:28893421 PMID:29924459 PMID:29959532 PMID:30778725 PMID:30943683 PMID:31672324 PMID:33099630 PMID:33226606 PMID:33536578 PMID:34805638 More...
NCBI chr 2:80,548,208...80,563,380
Ensembl chr 2:80,548,232...80,563,321
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SLC34A3
solute carrier family 34 member 3
ISO
ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1
ClinVar
PMID:25741868 PMID:28492532 PMID:31672324
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NHERF1
NHERF family PDZ scaffold protein 1
ISO
ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 2
OMIM ClinVar
PMID:18784102 PMID:24033266 PMID:25326635 PMID:25741868 PMID:28492532 PMID:28893421 More...
NCBI chr12:6,466,138...6,483,539
Ensembl chr12:6,466,121...6,483,548
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CA2
carbonic anhydrase 2
ISO
RGD
PMID:10977795
RGD:1600710
NCBI chr 4:51,194,686...51,211,436
Ensembl chr 4:51,193,756...51,211,259
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CAT
catalase
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr 2:26,493,664...26,533,881
Ensembl chr 2:26,487,653...26,581,452
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CD44
CD44 molecule
ISO
RGD
PMID:16850024
RGD:2289370
NCBI chr 2:25,788,699...25,884,209
Ensembl chr 2:25,788,703...25,884,153
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CLDN14
claudin 14
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:19561606
NCBI chr13:200,121,796...200,201,712
Ensembl chr13:200,128,477...200,145,525
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F2
coagulation factor II, thrombin
susceptibility
ISO
DNA:haplotypes: :
RGD
PMID:21067798
RGD:6893526
NCBI chr 2:15,793,257...15,819,151
Ensembl chr 2:15,791,455...15,819,137
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IFNG
interferon gamma
ISO
associated with type 2 diabetes mellitus; mRNA:increased expression:kidney
RGD
PMID:21514417
RGD:6893463
NCBI chr 5:32,477,906...32,482,670
Ensembl chr 5:32,477,906...32,482,670
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LOC100739508
glutathione S-transferase P-like
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr 2:5,005,498...5,009,247
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MGP
matrix Gla protein
ISO
RGD
PMID:10460895
RGD:1582511
NCBI chr 5:57,665,272...57,669,360
Ensembl chr 5:57,665,248...57,669,764
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MPO
myeloperoxidase
ISO
protein:increased activity:blood
RGD
PMID:18022927
RGD:7174700
NCBI chr12:34,557,031...34,570,091
Ensembl chr12:34,556,408...34,567,904
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POMC
proopiomelanocortin
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:1324751
NCBI chr 3:113,661,712...113,668,558
Ensembl chr 3:113,661,004...113,670,418
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SOD1
superoxide dismutase 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr13:195,326,573...195,335,273
Ensembl chr13:195,326,649...195,337,729
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SPP1
secreted phosphoprotein 1
ISO
CTD Direct Evidence: marker/mechanism
CTD RGD
PMID:8325891 PMID:10890885 PMID:15954903 PMID:16105024 PMID:21378157
RGD:1581334 RGD:1581372 RGD:6903839
NCBI chr 8:131,077,786...131,085,334
Ensembl chr 8:131,077,786...131,085,340
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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 1:121,146,093...121,250,227
Ensembl chr 1:121,146,117...121,250,224
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CLCN5
chloride voltage-gated channel 5
ISO
ClinVar Annotator: match by term: Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
OMIM ClinVar
PMID:7915957 PMID:8559248 PMID:9062355 PMID:9187673 PMID:9734595 PMID:11136179 PMID:15719255 PMID:15895257 PMID:16822791 PMID:18038239 PMID:19076289 PMID:19546586 PMID:19546591 PMID:22876375 PMID:24081861 PMID:25741868 PMID:25907713 PMID:26822237 PMID:27117801 PMID:27889724 PMID:28492532 PMID:28580211 PMID:31672324 PMID:32683654 More...
NCBI chr X:43,779,016...43,809,472
Ensembl chr X:43,613,628...43,811,526
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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
OMIM ClinVar
PMID:7915957 PMID:8559248 PMID:9187673 PMID:9602200 PMID:9734595 PMID:11136179 PMID:12637640 PMID:15719255 PMID:15895257 PMID:16822791 PMID:18038239 PMID:19076289 PMID:19546586 PMID:19546591 PMID:22876375 PMID:24081861 PMID:25741868 PMID:25907713 PMID:26822237 PMID:27117801 PMID:27889724 PMID:28492532 PMID:28580211 PMID:31672324 PMID:32683654 More...
NCBI chr X:43,779,016...43,809,472
Ensembl chr X:43,613,628...43,811,526
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