Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	7498
Gene name Gene Name - the full gene name approved by the HGNC.	Xanthine dehydrogenase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	XDH
Synonyms (NCBI Gene) Gene synonyms aliases	XAN1, XO, XOR
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2p23.1
Summary Summary of gene provided in NCBI Entrez Gene.	Xanthine dehydrogenase belongs to the group of molybdenum-containing hydroxylases involved in the oxidative metabolism of purines. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct f

Show/Hide all(10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs72549369	G>A	Pathogenic	Coding sequence variant, missense variant
rs119460972	G>A,C,T	Pathogenic	Synonymous variant, stop gained, coding sequence variant, missense variant
rs148412639	C>G,T	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Splice donor variant
rs376882470	C>G,T	Likely-pathogenic	Splice donor variant
rs760186813	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs773456900	->C	Pathogenic	Coding sequence variant, frameshift variant
rs1172253757	C>A,G	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1553411468	G>C	Likely-pathogenic	Stop gained, coding sequence variant, genic downstream transcript variant
rs1558674294	T>-	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs1572530443	G>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all(120)

miRTarBase ID	miRNA	Experiments	Reference
MIRT028928	hsa-miR-26b-5p	Microarray	19088304
MIRT756459	hsa-miR-199a-5p	Luciferase reporter assay, qRT-PCR	36920714
MIRT1495289	hsa-miR-103b	CLIP-seq
MIRT1495290	hsa-miR-1178	CLIP-seq
MIRT1495291	hsa-miR-1184	CLIP-seq
MIRT1495292	hsa-miR-129-5p	CLIP-seq
MIRT1495293	hsa-miR-154	CLIP-seq
MIRT1495294	hsa-miR-204	CLIP-seq
MIRT1495295	hsa-miR-211	CLIP-seq
MIRT1495296	hsa-miR-2116	CLIP-seq
MIRT1495297	hsa-miR-2117	CLIP-seq
MIRT1495298	hsa-miR-3074-3p	CLIP-seq
MIRT1495299	hsa-miR-3156-5p	CLIP-seq
MIRT1495300	hsa-miR-3606	CLIP-seq
MIRT1495301	hsa-miR-3660	CLIP-seq
MIRT1495302	hsa-miR-3692	CLIP-seq
MIRT1495303	hsa-miR-375	CLIP-seq
MIRT1495304	hsa-miR-4264	CLIP-seq
MIRT1495305	hsa-miR-4273	CLIP-seq
MIRT1495306	hsa-miR-4418	CLIP-seq
MIRT1495307	hsa-miR-4436b-5p	CLIP-seq
MIRT1495308	hsa-miR-4526	CLIP-seq
MIRT1495309	hsa-miR-455-3p	CLIP-seq
MIRT1495310	hsa-miR-4645-3p	CLIP-seq
MIRT1495311	hsa-miR-4677-5p	CLIP-seq
MIRT1495312	hsa-miR-4714-3p	CLIP-seq
MIRT1495313	hsa-miR-4729	CLIP-seq
MIRT1495314	hsa-miR-4753-3p	CLIP-seq
MIRT1495315	hsa-miR-4755-5p	CLIP-seq
MIRT1495316	hsa-miR-4761-5p	CLIP-seq
MIRT1495317	hsa-miR-4780	CLIP-seq
MIRT1495318	hsa-miR-4803	CLIP-seq
MIRT1495319	hsa-miR-496	CLIP-seq
MIRT1495320	hsa-miR-509-3-5p	CLIP-seq
MIRT1495321	hsa-miR-509-5p	CLIP-seq
MIRT1495322	hsa-miR-579	CLIP-seq
MIRT1495323	hsa-miR-623	CLIP-seq
MIRT1495324	hsa-miR-921	CLIP-seq
MIRT1495291	hsa-miR-1184	CLIP-seq
MIRT2149203	hsa-miR-124	CLIP-seq
MIRT2149204	hsa-miR-1244	CLIP-seq
MIRT2149205	hsa-miR-1297	CLIP-seq
MIRT2149206	hsa-miR-1302	CLIP-seq
MIRT2149207	hsa-miR-26a	CLIP-seq
MIRT2149208	hsa-miR-26b	CLIP-seq
MIRT2149209	hsa-miR-27a	CLIP-seq
MIRT2149210	hsa-miR-27b	CLIP-seq
MIRT2149211	hsa-miR-3122	CLIP-seq
MIRT2149212	hsa-miR-3199	CLIP-seq
MIRT2149213	hsa-miR-3913-5p	CLIP-seq
MIRT2149214	hsa-miR-4259	CLIP-seq
MIRT2149215	hsa-miR-4298	CLIP-seq
MIRT1495306	hsa-miR-4418	CLIP-seq
MIRT2149216	hsa-miR-4425	CLIP-seq
MIRT2149217	hsa-miR-4465	CLIP-seq
MIRT2149218	hsa-miR-4476	CLIP-seq
MIRT2149219	hsa-miR-4703-3p	CLIP-seq
MIRT1495312	hsa-miR-4714-3p	CLIP-seq
MIRT2149220	hsa-miR-4715-5p	CLIP-seq
MIRT2149221	hsa-miR-498	CLIP-seq
MIRT2149222	hsa-miR-506	CLIP-seq
MIRT1495320	hsa-miR-509-3-5p	CLIP-seq
MIRT1495321	hsa-miR-509-5p	CLIP-seq
MIRT2149223	hsa-miR-513a-5p	CLIP-seq
MIRT1495289	hsa-miR-103b	CLIP-seq
MIRT2369640	hsa-miR-106a	CLIP-seq
MIRT2369641	hsa-miR-106b	CLIP-seq
MIRT1495291	hsa-miR-1184	CLIP-seq
MIRT2369642	hsa-miR-1200	CLIP-seq
MIRT2149203	hsa-miR-124	CLIP-seq
MIRT2369643	hsa-miR-150	CLIP-seq
MIRT2369644	hsa-miR-17	CLIP-seq
MIRT2369645	hsa-miR-1976	CLIP-seq
MIRT2369646	hsa-miR-20a	CLIP-seq
MIRT2369647	hsa-miR-20b	CLIP-seq
MIRT2149209	hsa-miR-27a	CLIP-seq
MIRT2149210	hsa-miR-27b	CLIP-seq
MIRT2369648	hsa-miR-302a	CLIP-seq
MIRT2369649	hsa-miR-302b	CLIP-seq
MIRT2369650	hsa-miR-302c	CLIP-seq
MIRT2369651	hsa-miR-302d	CLIP-seq
MIRT2369652	hsa-miR-302e	CLIP-seq
MIRT2369653	hsa-miR-3119	CLIP-seq
MIRT2369654	hsa-miR-372	CLIP-seq
MIRT2369655	hsa-miR-373	CLIP-seq
MIRT2369656	hsa-miR-4269	CLIP-seq
MIRT2369657	hsa-miR-4279	CLIP-seq
MIRT2369658	hsa-miR-4324	CLIP-seq
MIRT1495306	hsa-miR-4418	CLIP-seq
MIRT2369659	hsa-miR-4422	CLIP-seq
MIRT2369660	hsa-miR-4433	CLIP-seq
MIRT2149218	hsa-miR-4476	CLIP-seq
MIRT2369661	hsa-miR-4514	CLIP-seq
MIRT2369662	hsa-miR-4692	CLIP-seq
MIRT1495312	hsa-miR-4714-3p	CLIP-seq
MIRT2369663	hsa-miR-4722-3p	CLIP-seq
MIRT2369664	hsa-miR-4722-5p	CLIP-seq
MIRT2369665	hsa-miR-4731-5p	CLIP-seq
MIRT2369666	hsa-miR-4742-5p	CLIP-seq
MIRT2369667	hsa-miR-4755-3p	CLIP-seq
MIRT2149222	hsa-miR-506	CLIP-seq
MIRT1495320	hsa-miR-509-3-5p	CLIP-seq
MIRT1495321	hsa-miR-509-5p	CLIP-seq
MIRT2369668	hsa-miR-512-3p	CLIP-seq
MIRT2149223	hsa-miR-513a-5p	CLIP-seq
MIRT2369669	hsa-miR-519d	CLIP-seq
MIRT2369670	hsa-miR-520a-3p	CLIP-seq
MIRT2369671	hsa-miR-520b	CLIP-seq
MIRT2369672	hsa-miR-520c-3p	CLIP-seq
MIRT2369673	hsa-miR-520d-3p	CLIP-seq
MIRT2369674	hsa-miR-520e	CLIP-seq
MIRT2369675	hsa-miR-520g	CLIP-seq
MIRT2369676	hsa-miR-520h	CLIP-seq
MIRT2369677	hsa-miR-544b	CLIP-seq
MIRT2369678	hsa-miR-93	CLIP-seq
MIRT2369679	hsa-miR-940	CLIP-seq
MIRT2463585	hsa-miR-1255a	CLIP-seq
MIRT2463586	hsa-miR-1255b	CLIP-seq
MIRT2463587	hsa-miR-1265	CLIP-seq
MIRT2463588	hsa-miR-2392	CLIP-seq

Show/Hide all(57)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000255	Process	Allantoin metabolic process	IDA	1619276
GO:0000255	Process	Allantoin metabolic process	IEA
GO:0004854	Function	Xanthine dehydrogenase activity	IBA
GO:0004854	Function	Xanthine dehydrogenase activity	IDA	8670112
GO:0004854	Function	Xanthine dehydrogenase activity	IEA
GO:0004855	Function	Xanthine oxidase activity	IDA	8670112, 17301077
GO:0004855	Function	Xanthine oxidase activity	IEA
GO:0005506	Function	Iron ion binding	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005576	Component	Extracellular region	IEA
GO:0005615	Component	Extracellular space	HDA	16502470
GO:0005615	Component	Extracellular space	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005777	Component	Peroxisome	IEA
GO:0005829	Component	Cytosol	IDA	1619276
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006147	Process	Guanine catabolic process	IEA
GO:0006148	Process	Inosine catabolic process	IDA	1619276
GO:0006148	Process	Inosine catabolic process	IEA
GO:0006149	Process	Deoxyinosine catabolic process	IDA	1619276
GO:0006149	Process	Deoxyinosine catabolic process	IEA
GO:0006154	Process	Adenosine catabolic process	IEA
GO:0006157	Process	Deoxyadenosine catabolic process	IEA
GO:0006161	Process	Deoxyguanosine catabolic process	IEA
GO:0006196	Process	AMP catabolic process	IDA	1619276
GO:0006196	Process	AMP catabolic process	IEA
GO:0006204	Process	IMP catabolic process	IDA	1619276
GO:0006204	Process	IMP catabolic process	IEA
GO:0007595	Process	Lactation	IEA
GO:0009114	Process	Hypoxanthine catabolic process	IDA	1619276
GO:0009114	Process	Hypoxanthine catabolic process	IEA
GO:0009115	Process	Xanthine catabolic process	IBA
GO:0009115	Process	Xanthine catabolic process	IDA	8670112, 17301077
GO:0009115	Process	Xanthine catabolic process	IEA
GO:0016226	Process	Iron-sulfur cluster assembly	IEA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0016529	Component	Sarcoplasmic reticulum	IEA
GO:0030856	Process	Regulation of epithelial cell differentiation	IEA
GO:0042803	Function	Protein homodimerization activity	IPI	17301077
GO:0043546	Function	Molybdopterin cofactor binding	IDA	17301077
GO:0043546	Function	Molybdopterin cofactor binding	IEA
GO:0043605	Process	Amide catabolic process	IEA
GO:0046038	Process	GMP catabolic process	IEA
GO:0046055	Process	DGMP catabolic process	IEA
GO:0046059	Process	DAMP catabolic process	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050660	Function	Flavin adenine dinucleotide binding	IDA	17301077
GO:0050660	Function	Flavin adenine dinucleotide binding	IEA
GO:0051536	Function	Iron-sulfur cluster binding	IEA
GO:0051537	Function	2 iron, 2 sulfur cluster binding	IDA	17301077
GO:0051537	Function	2 iron, 2 sulfur cluster binding	IEA
GO:0070674	Function	Hypoxanthine dehydrogenase activity	IDA	1619276
GO:0070674	Function	Hypoxanthine dehydrogenase activity	IEA
GO:0070675	Function	Hypoxanthine oxidase activity	IEA
GO:0071949	Function	FAD binding	IEA

MIM	HGNC	e!Ensembl
607633	12805	ENSG00000158125

Protein

UniProt ID

P47989

Protein name

Xanthine dehydrogenase/oxidase [Includes: Xanthine dehydrogenase (XD) (EC 1.17.1.4); Xanthine oxidase (XO) (EC 1.17.3.2) (Xanthine oxidoreductase) (XOR)]

Protein function

Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (i

PDB

2CKJ , 2E1Q

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00111	Fer2	8 → 78	2Fe-2S iron-sulfur cluster binding domain	Domain
PF01799	Fer2_2	87 → 161	[2Fe-2S] binding domain	Domain
PF00941	FAD_binding_5	228 → 412	FAD binding domain in molybdopterin dehydrogenase	Family
PF03450	CO_deh_flav_C	419 → 523	CO dehydrogenase flavoprotein C-terminal domain	Domain
PF01315	Ald_Xan_dh_C	588 → 694	Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain	Domain
PF02738	Ald_Xan_dh_C2	699 → 1237	Molybdopterin-binding domain of aldehyde dehydrogenase	Family

Tissue specificity

TISSUE SPECIFICITY: Detected in milk (at protein level). {ECO:0000269|Ref.12}.

Sequence

MTADKLVFFVNGRKVVEKNADPETTLLAYLRRKLGLSGTKLGCGEGGCGACTVMLSKYDR
LQNKIVHFSANACLAPICSLHHVAVTTVEGIGSTKTRLHPVQERIAKSHGSQCGFCTPGI
VMSMYTLLRNQPEPTMEEIENAFQGNLCRCTGYRPILQGFRTFARDGGCCGGDGNNPNCC
MNQKKDHSVSLSPSLFKPEEFTPLDPTQEPIFPPELLRLKDTPRKQLRFEGERVTWIQAS
TLKELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPMIVCPAWIPELNSVEHGPDGISFG
AACPLSIVEKTLVDAVAKLPAQKTEVFRGVLEQLRWFAGKQVKSVASVGGNIITASPISD
LNPVFMASGAKLTLVSRGTRRTVQMDHTFFPGYRKTLLSPEEILLSIEIPYSREGEYFSA
FKQASRREDDIAKVTSGMRVLFKPGTTEVQELALCYGGMANRTISALKTTQRQLSKLWKE
ELLQDVCAGLAEELHLPPDAPGGMVDFRCTLTLSFFFKFYLTVLQKLGQENLEDKCGKLD
PTFASATLLFQKDPPADVQLFQEVPKGQSEEDMVGRPLPHLAADMQASGEAVYCDDIPRY
ENELSLRLVTSTRAHAKIKSIDTSEAKKVPGFVCFISADDVPGSNITGICNDETVFAKDK
VTCVGHIIGAVVADTPEHTQRAAQGVKITYEELPAIITIEDAIKNNSFYGPELKIEKGDL
KKGFSEADNVVSGEIYIGGQEHFYLETHCTIAVPKGEAGEMELFVSTQNTMKTQSFVAKM
LGVPANRIVVRVKRMGGGFGGKETRSTVVSTAVALAAYKTGRPVRCMLDRDEDMLITGGR
HPFLARYKVGFMKTGTVVALEVDHFSNVGNTQDLSQSIMERALFHMDNCYKIPNIRGTGR
LCKTNLPSNTAFRGFGGPQGMLIAECWMSEVAVTCGMPAEEVRRKNLYKEGDLTHFNQKL
EGFTLPRCWEECLASSQYHARKSEVDKFNKENCWKKRGLCIIPTKFGISFTVPFLNQAGA
LLHVYTDGSVLLTHGGTEMGQGLHTKMVQVASRALKIPTSKIYISETSTNTVPNTSPTAA
SVSADLNGQAVYAACQTILKRLEPYKKKNPSGSWEDWVTAAYMDTVSLSATGFYRTPNLG
YSFETNSGNPFHYFSYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAF
VQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIPIEFRVSLLRDCPNKKAIYASKAV
GEPPLFLAASIFFAIKDAIRAARAQHTGNNVKELFRLDSPATPEKIRNACVDKFTTLCVT
GVPENCKPWSVRV

Sequence length

1333

Interactions

View interactions

	KEGG		Reactome
	Purine metabolism Caffeine metabolism Drug metabolism - other enzymes Metabolic pathways Nucleotide metabolism Peroxisome		Purine catabolism Butyrophilin (BTN) family interactions

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Xanthinuria	xanthinuria type ii	rs119460972, rs751921838, rs376882470, rs760186813, rs1558674294, rs773456900	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Gout	Gout	N/A	N/A	GWAS

Show/Hide Text Mining Associations (44)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	22678977, 36778128
Alcoholism	Stimulate	28839105
Aneuploidy	Associate	16935971
Breast Neoplasms	Associate	16935971, 23443115, 25416100
Carcinoma Renal Cell	Associate	35693733
Cardiovascular Abnormalities	Associate	37415141
Cerebral Infarction	Associate	38228698
Cerebrovascular Disorders	Associate	19175688
Colonic Neoplasms	Associate	34564978
Diabetes Mellitus	Stimulate	19175688
Diabetes Mellitus Type 1	Associate	19175688
Diabetic Cardiomyopathies	Associate	19175688
Drug Related Side Effects and Adverse Reactions	Associate	30927276, 35693733
Essential Hypertension	Associate	26239312
Genetic Diseases Inborn	Associate	9153281
Glioma	Associate	29414774
Gout	Associate	35154100, 38228698
Heart Diseases	Associate	19175688
Hypertension	Associate	26239312
Hyperuricemia	Associate	35154100
Hypoxia	Stimulate	12637268
Inflammation	Associate	28839105, 40147728
Inflammation	Stimulate	30104401
Ischemia	Associate	1616255
Ischemic Attack Transient	Associate	38228698
Kidney Diseases	Associate	37415141
Lung Neoplasms	Associate	22678977
Meningioma	Associate	19505917, 20406964
Molybdenum cofactor deficiency	Associate	12385777
Molybdenum cofactor deficiency	Inhibit	9634514
Molybdenum Cofactor Deficiency Complementation Group B	Associate	33502714
Multiple Organ Failure	Associate	37415141
Myocardial Infarction	Associate	38228698
Neoplasm Metastasis	Associate	22678977
Neoplasms	Inhibit	16935971
Neoplasms	Associate	18772145, 22678977, 30104401, 36778128
Neoplastic Syndromes Hereditary	Associate	22821105
Neutropenia	Associate	30927276
Pancreatic Neoplasms	Associate	32537471
Respiratory Distress Syndrome	Associate	28839105, 37415141
Sepsis	Associate	37415141
Stomach Neoplasms	Associate	16935971
Tissue Adhesions	Associate	40147728
Xanthinuria Type I	Associate	35491177, 9153281

XDH (xanthine dehydrogenase)