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: urolithiasis
Accession: DOID:0080653
browse the term
Definition: A urinary system disease that is characterized by the formation of stony concretions in the bladder or urinary tract. (DO)
Synonyms: exact_synonym: urinary lithiasis
primary_id: MESH:D052878
alt_id: DOID:9001149; OMIA:001033
For additional species annotation, visit the
Alliance of Genome Resources .
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Aprt
adenine phosphoribosyl transferase
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:7766 PMID:3876264
NCBI chr19:55,387,288...55,389,256
Ensembl chr19:55,387,288...55,389,256
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Ggcx
gamma-glutamyl carboxylase
IEP ISO
protein:increased activity:kidney: CTD Direct Evidence: marker/mechanism
CTD
PMID:9471053 , PMID:9471053
RGD:11040514
NCBI chr 4:100,277,345...100,293,097
Ensembl chr 4:100,277,391...100,293,250
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Plau
plasminogen activator, urokinase
ISO
DNA:snp:3' utr:g.4065C>T (human)
RGD
PMID:18240004
RGD:7241142
NCBI chr15:3,644,296...3,650,765
Ensembl chr15:3,644,769...3,650,819
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Slc26a1
solute carrier family 26 member 1
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:19002488 PMID:20160351
NCBI chr14:2,050,805...2,056,091
Ensembl chr14:2,050,483...2,056,089
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Aprt
adenine phosphoribosyl transferase
ISO
ClinVar Annotator: match by OMIM:614723 ClinVar Annotator: match by term: Adenine phosphoribosyltransferase deficiency
ClinVar OMIM
PMID:1353080 PMID:1673292 PMID:1985452 PMID:2135300 PMID:2227951 PMID:2502918 PMID:3343350 PMID:3554238 PMID:3680503 PMID:7685481 PMID:7758207 PMID:7915931 PMID:8882882 PMID:9298830 PMID:9521589 PMID:10393170 PMID:11243733 PMID:15571218 PMID:17126311 PMID:19435978 PMID:20150536 PMID:21635362 PMID:22212387 PMID:22988602 PMID:23430916 PMID:24459232 PMID:24940675 PMID:24986359 PMID:25741868 PMID:25983915 PMID:25984046 PMID:26724837 PMID:27994857 PMID:28492532 PMID:28566603 PMID:30106368 PMID:30355577 PMID:30389108 PMID:30890413 PMID:30993240 PMID:31201003 PMID:31440706
NCBI chr19:55,387,288...55,389,256
Ensembl chr19:55,387,288...55,389,256
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Galns
galactosamine (N-acetyl)-6-sulfatase
ISO
ClinVar Annotator: match by term: Adenine phosphoribosyltransferase deficiency
ClinVar
PMID:25741868 PMID:28492532
NCBI chr19:55,391,004...55,423,328
Ensembl chr19:55,389,462...55,423,150
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Ahr
aryl hydrocarbon receptor
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:22232670
NCBI chr 6:54,963,990...55,001,806
Ensembl chr 6:54,963,990...55,001,464
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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
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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
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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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Slc36a2
solute carrier family 36 member 2
ISO
ClinVar Annotator: match by term: IMINOGLYCINURIA TYPE II ClinVar Annotator: match by term: Hyperglycinuria ClinVar Annotator: match by OMIM:138500
OMIM ClinVar
PMID:19033659 PMID:28492532
NCBI chr10:40,497,184...40,525,033
Ensembl chr10:40,496,622...40,525,008
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Slc6a19
solute carrier family 6 member 19
ISO
ClinVar Annotator: match by term: Hyperglycinuria ClinVar Annotator: match by OMIM:138500
OMIM ClinVar
PMID:15286788 PMID:17555458 PMID:18484095 PMID:19033659 PMID:19185582 PMID:24033266 PMID:25741868
NCBI chr 1:32,199,869...32,218,628
Ensembl chr 1:32,199,810...32,220,045
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Slc6a20
solute carrier family 6 member 20
ISO
ClinVar Annotator: match by term: IMINOGLYCINURIA TYPE II ClinVar Annotator: match by term: Hyperglycinuria ClinVar Annotator: match by OMIM:138500
OMIM ClinVar
PMID:19033659 PMID:28492532
NCBI chr 8:132,713,013...132,753,145
Ensembl chr 8:132,665,927...132,753,292
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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
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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
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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
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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
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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
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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
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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
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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 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
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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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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
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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Slc25a25
solute carrier family 25 member 25
ISO
ClinVar Annotator: match by term: Nephrolithiasis
ClinVar
NCBI chr 3:11,442,396...11,476,186
Ensembl chr 3:11,442,397...11,452,529
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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
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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Ltf
lactotransferrin
ISO
RGD
PMID:19202053
RGD:7243107
NCBI chr 8:119,290,416...119,313,261
Ensembl chr 8:119,290,416...119,313,261
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Slc22a12
solute carrier family 22 member 12
ISO
ClinVar Annotator: match by term: Hereditary renal hypouricemia CTD Direct Evidence: marker/mechanism
OMIM ClinVar CTD
PMID:14655203 PMID:14694169 PMID:15327384 PMID:15741204 PMID:15912381 PMID:16703794 PMID:17362586 PMID:18492088 PMID:19019168 PMID:22045201 PMID:22132990 PMID:22194875 PMID:24033266 PMID:29659532
NCBI chr 1:221,910,787...221,919,277
Ensembl chr 1:221,910,767...221,919,301
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Slc2a9
solute carrier family 2 member 9
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:18989453 PMID:22132990
NCBI chr14:77,067,537...77,192,702
Ensembl chr14:77,067,503...77,192,702
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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
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Gsr
glutathione-disulfide reductase
ISO
CTD Direct Evidence: marker/mechanism
CTD
PMID:24360074
NCBI chr16:62,197,617...62,239,987
Ensembl chr16:62,197,617...62,241,361
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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
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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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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
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Add3
adducin 3
IEP
RGD
PMID:15329129
RGD:2317717
NCBI chr 1:273,854,195...273,961,982
Ensembl chr 1:273,854,248...273,961,982
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F2
coagulation factor II
ISO
RGD
PMID:22494008
RGD:6893519
NCBI chr 3:80,529,468...80,542,993
Ensembl chr 3:80,529,428...80,543,031
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Il1rn
interleukin 1 receptor antagonist
susceptibility
ISO
DNA:repeats, haplotype:intron:IVS2+914_1000dup IL1RN*1, IL1RN*2 IL1RN*3 (human)
RGD
PMID:18186699
RGD:6907399
NCBI chr 3:1,449,778...1,468,624
Ensembl chr 3:1,452,644...1,468,614
G
Spp1
secreted phosphoprotein 1
no_association
ISO
DNA:polymorphism: :p.R9402H (human) DNA:polymorphism: :p.N9171S (human)
RGD
PMID:16145474 , PMID:16145474
RGD:1581368 , RGD:1581368
NCBI chr14:6,673,686...6,679,965
Ensembl chr14:6,673,686...6,679,901
G
Vdr
vitamin D receptor
ISO
GAD
PMID:15118671
RGD:1331525
NCBI chr 7:139,344,452...139,394,138
Ensembl chr 7:139,342,063...139,394,166
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
Term paths to the root one shortest all shortest one longest all longest one shortest and longest all