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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51780
Gene name	Lysine demethylase 3B
Gene symbol	KDM3B
Synonyms (NCBI Gene)	5qNCAC5orf7DIJOSJMJD1BNET22
Chromosome	5
Chromosome location	5q31.2

Show/Hide all (1)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1554131871	C>T	Likely-pathogenic	Coding sequence variant, stop gained

213

Show/Hide all (213)

miRTarBase ID	miRNA	Experiments	Reference
MIRT027294	hsa-miR-101-3p	Sequencing	20371350
MIRT028029	hsa-miR-93-5p	Sequencing	20371350
MIRT050442	hsa-miR-23a-3p	CLASH	23622248
MIRT049079	hsa-miR-92a-3p	CLASH	23622248
MIRT045875	hsa-miR-128-3p	CLASH	23622248
MIRT045145	hsa-miR-186-5p	CLASH	23622248
MIRT036998	hsa-miR-877-3p	CLASH	23622248
MIRT036652	hsa-miR-935	CLASH	23622248
MIRT530287	hsa-miR-454-5p	PAR-CLIP	22012620
MIRT530286	hsa-miR-519d-5p	PAR-CLIP	22012620
MIRT530285	hsa-miR-5695	PAR-CLIP	22012620
MIRT530284	hsa-miR-6826-3p	PAR-CLIP	22012620
MIRT530283	hsa-miR-515-5p	PAR-CLIP	22012620
MIRT530282	hsa-miR-519e-5p	PAR-CLIP	22012620
MIRT530281	hsa-miR-8070	PAR-CLIP	22012620
MIRT530280	hsa-miR-3679-3p	PAR-CLIP	22012620
MIRT530287	hsa-miR-454-5p	PAR-CLIP	22012620
MIRT530286	hsa-miR-519d-5p	PAR-CLIP	22012620
MIRT530285	hsa-miR-5695	PAR-CLIP	22012620
MIRT530284	hsa-miR-6826-3p	PAR-CLIP	22012620
MIRT530283	hsa-miR-515-5p	PAR-CLIP	22012620
MIRT530282	hsa-miR-519e-5p	PAR-CLIP	22012620
MIRT530281	hsa-miR-8070	PAR-CLIP	22012620
MIRT530280	hsa-miR-3679-3p	PAR-CLIP	22012620
MIRT1084379	hsa-miR-101	CLIP-seq
MIRT1084380	hsa-miR-1205	CLIP-seq
MIRT1084381	hsa-miR-1233	CLIP-seq
MIRT1084382	hsa-miR-1237	CLIP-seq
MIRT1084383	hsa-miR-1248	CLIP-seq
MIRT1084384	hsa-miR-1262	CLIP-seq
MIRT1084385	hsa-miR-1276	CLIP-seq
MIRT1084386	hsa-miR-129-3p	CLIP-seq
MIRT1084387	hsa-miR-139-5p	CLIP-seq
MIRT1084388	hsa-miR-144	CLIP-seq
MIRT1084389	hsa-miR-149	CLIP-seq
MIRT1084390	hsa-miR-185	CLIP-seq
MIRT1084391	hsa-miR-186	CLIP-seq
MIRT1084392	hsa-miR-1909	CLIP-seq
MIRT1084393	hsa-miR-200b	CLIP-seq
MIRT1084394	hsa-miR-200c	CLIP-seq
MIRT1084395	hsa-miR-3065-5p	CLIP-seq
MIRT1084396	hsa-miR-3135b	CLIP-seq
MIRT1084397	hsa-miR-3173-5p	CLIP-seq
MIRT1084398	hsa-miR-3175	CLIP-seq
MIRT1084399	hsa-miR-3179	CLIP-seq
MIRT1084400	hsa-miR-326	CLIP-seq
MIRT1084401	hsa-miR-330-5p	CLIP-seq
MIRT1084402	hsa-miR-338-3p	CLIP-seq
MIRT1084403	hsa-miR-339-5p	CLIP-seq
MIRT1084404	hsa-miR-3609	CLIP-seq
MIRT1084405	hsa-miR-3652	CLIP-seq
MIRT1084406	hsa-miR-3673	CLIP-seq
MIRT1084407	hsa-miR-3688-3p	CLIP-seq
MIRT1084408	hsa-miR-3689a-3p	CLIP-seq
MIRT1084409	hsa-miR-3689c	CLIP-seq
MIRT1084410	hsa-miR-3978	CLIP-seq
MIRT1084411	hsa-miR-421	CLIP-seq
MIRT1084412	hsa-miR-429	CLIP-seq
MIRT1084413	hsa-miR-4306	CLIP-seq
MIRT1084414	hsa-miR-4426	CLIP-seq
MIRT1084415	hsa-miR-4430	CLIP-seq
MIRT1084416	hsa-miR-4432	CLIP-seq
MIRT1084417	hsa-miR-4494	CLIP-seq
MIRT1084418	hsa-miR-4505	CLIP-seq
MIRT1084419	hsa-miR-4511	CLIP-seq
MIRT1084420	hsa-miR-4512	CLIP-seq
MIRT1084421	hsa-miR-4530	CLIP-seq
MIRT1084422	hsa-miR-4644	CLIP-seq
MIRT1084423	hsa-miR-4647	CLIP-seq
MIRT1084424	hsa-miR-4662b	CLIP-seq
MIRT1084425	hsa-miR-4690-3p	CLIP-seq
MIRT1084426	hsa-miR-4693-3p	CLIP-seq
MIRT1084427	hsa-miR-4701-3p	CLIP-seq
MIRT1084428	hsa-miR-4716-3p	CLIP-seq
MIRT1084429	hsa-miR-4723-5p	CLIP-seq
MIRT1084430	hsa-miR-4728-5p	CLIP-seq
MIRT1084431	hsa-miR-4733-5p	CLIP-seq
MIRT1084432	hsa-miR-4757-5p	CLIP-seq
MIRT1084433	hsa-miR-4761-5p	CLIP-seq
MIRT1084434	hsa-miR-4802-3p	CLIP-seq
MIRT1084435	hsa-miR-499-5p	CLIP-seq
MIRT1084436	hsa-miR-499a-5p	CLIP-seq
MIRT1084437	hsa-miR-545	CLIP-seq
MIRT1084438	hsa-miR-548ag	CLIP-seq
MIRT1084439	hsa-miR-548ah	CLIP-seq
MIRT1084440	hsa-miR-548ai	CLIP-seq
MIRT1084441	hsa-miR-548b-3p	CLIP-seq
MIRT1084442	hsa-miR-561	CLIP-seq
MIRT1084443	hsa-miR-596	CLIP-seq
MIRT1084444	hsa-miR-605	CLIP-seq
MIRT1084445	hsa-miR-642a	CLIP-seq
MIRT1084446	hsa-miR-670	CLIP-seq
MIRT1084447	hsa-miR-760	CLIP-seq
MIRT1084448	hsa-miR-766	CLIP-seq
MIRT1084449	hsa-miR-767-3p	CLIP-seq
MIRT1084450	hsa-miR-892b	CLIP-seq
MIRT1084451	hsa-miR-943	CLIP-seq
MIRT1084380	hsa-miR-1205	CLIP-seq
MIRT1084390	hsa-miR-185	CLIP-seq
MIRT1084392	hsa-miR-1909	CLIP-seq
MIRT1084396	hsa-miR-3135b	CLIP-seq
MIRT2021414	hsa-miR-3671	CLIP-seq
MIRT1084410	hsa-miR-3978	CLIP-seq
MIRT1084413	hsa-miR-4306	CLIP-seq
MIRT1084422	hsa-miR-4644	CLIP-seq
MIRT2021415	hsa-miR-4764-5p	CLIP-seq
MIRT2021416	hsa-miR-607	CLIP-seq
MIRT2021417	hsa-miR-617	CLIP-seq
MIRT1084379	hsa-miR-101	CLIP-seq
MIRT1084380	hsa-miR-1205	CLIP-seq
MIRT2252885	hsa-miR-1207-3p	CLIP-seq
MIRT2252886	hsa-miR-1224-3p	CLIP-seq
MIRT2252887	hsa-miR-1226	CLIP-seq
MIRT2252888	hsa-miR-1260	CLIP-seq
MIRT2252889	hsa-miR-1260b	CLIP-seq
MIRT2252890	hsa-miR-1280	CLIP-seq
MIRT2252891	hsa-miR-1289	CLIP-seq
MIRT2252892	hsa-miR-1304	CLIP-seq
MIRT2252893	hsa-miR-1343	CLIP-seq
MIRT2252894	hsa-miR-139-3p	CLIP-seq
MIRT1084387	hsa-miR-139-5p	CLIP-seq
MIRT2252895	hsa-miR-140-3p	CLIP-seq
MIRT2252896	hsa-miR-141	CLIP-seq
MIRT1084388	hsa-miR-144	CLIP-seq
MIRT1084389	hsa-miR-149	CLIP-seq
MIRT2252897	hsa-miR-1827	CLIP-seq
MIRT1084390	hsa-miR-185	CLIP-seq
MIRT1084392	hsa-miR-1909	CLIP-seq
MIRT2252898	hsa-miR-1915	CLIP-seq
MIRT2252899	hsa-miR-1976	CLIP-seq
MIRT2252900	hsa-miR-199a-5p	CLIP-seq
MIRT2252901	hsa-miR-199b-5p	CLIP-seq
MIRT2252902	hsa-miR-200a	CLIP-seq
MIRT1084393	hsa-miR-200b	CLIP-seq
MIRT1084394	hsa-miR-200c	CLIP-seq
MIRT2252903	hsa-miR-2110	CLIP-seq
MIRT2252904	hsa-miR-2355-5p	CLIP-seq
MIRT2252905	hsa-miR-2467-3p	CLIP-seq
MIRT1084396	hsa-miR-3135b	CLIP-seq
MIRT2252906	hsa-miR-3198	CLIP-seq
MIRT1084400	hsa-miR-326	CLIP-seq
MIRT2252907	hsa-miR-329	CLIP-seq
MIRT1084401	hsa-miR-330-5p	CLIP-seq
MIRT2252908	hsa-miR-3613-5p	CLIP-seq
MIRT2252909	hsa-miR-361-5p	CLIP-seq
MIRT2252910	hsa-miR-362-3p	CLIP-seq
MIRT1084405	hsa-miR-3652	CLIP-seq
MIRT1084406	hsa-miR-3673	CLIP-seq
MIRT2252911	hsa-miR-3678-3p	CLIP-seq
MIRT2252912	hsa-miR-3690	CLIP-seq
MIRT2252913	hsa-miR-3941	CLIP-seq
MIRT2252914	hsa-miR-4254	CLIP-seq
MIRT2252915	hsa-miR-4257	CLIP-seq
MIRT2252916	hsa-miR-4271	CLIP-seq
MIRT2252917	hsa-miR-4276	CLIP-seq
MIRT1084412	hsa-miR-429	CLIP-seq
MIRT2252918	hsa-miR-4294	CLIP-seq
MIRT2252919	hsa-miR-4302	CLIP-seq
MIRT1084413	hsa-miR-4306	CLIP-seq
MIRT2252920	hsa-miR-4309	CLIP-seq
MIRT1084415	hsa-miR-4430	CLIP-seq
MIRT1084417	hsa-miR-4494	CLIP-seq
MIRT2252921	hsa-miR-4501	CLIP-seq
MIRT1084418	hsa-miR-4505	CLIP-seq
MIRT2252922	hsa-miR-4640-5p	CLIP-seq
MIRT2252923	hsa-miR-4643	CLIP-seq
MIRT1084422	hsa-miR-4644	CLIP-seq
MIRT2252924	hsa-miR-4645-5p	CLIP-seq
MIRT2252925	hsa-miR-4673	CLIP-seq
MIRT1084426	hsa-miR-4693-3p	CLIP-seq
MIRT2252926	hsa-miR-4717-3p	CLIP-seq
MIRT2252927	hsa-miR-4725-3p	CLIP-seq
MIRT2252928	hsa-miR-4726-5p	CLIP-seq
MIRT2252929	hsa-miR-4733-3p	CLIP-seq
MIRT2252930	hsa-miR-494	CLIP-seq
MIRT1084436	hsa-miR-499a-5p	CLIP-seq
MIRT2252931	hsa-miR-522	CLIP-seq
MIRT2252932	hsa-miR-576-3p	CLIP-seq
MIRT1084443	hsa-miR-596	CLIP-seq
MIRT2252933	hsa-miR-603	CLIP-seq
MIRT2021417	hsa-miR-617	CLIP-seq
MIRT1084447	hsa-miR-760	CLIP-seq
MIRT2252934	hsa-miR-885-3p	CLIP-seq
MIRT1084450	hsa-miR-892b	CLIP-seq
MIRT1084451	hsa-miR-943	CLIP-seq
MIRT2452335	hsa-miR-1305	CLIP-seq
MIRT2021414	hsa-miR-3671	CLIP-seq
MIRT2452336	hsa-miR-500a	CLIP-seq
MIRT1084444	hsa-miR-605	CLIP-seq
MIRT2021416	hsa-miR-607	CLIP-seq
MIRT2452335	hsa-miR-1305	CLIP-seq
MIRT2555906	hsa-miR-3125	CLIP-seq
MIRT2555907	hsa-miR-3622a-5p	CLIP-seq
MIRT2021414	hsa-miR-3671	CLIP-seq
MIRT2555908	hsa-miR-3692	CLIP-seq
MIRT2555909	hsa-miR-3916	CLIP-seq
MIRT2555910	hsa-miR-4275	CLIP-seq
MIRT2555911	hsa-miR-4423-3p	CLIP-seq
MIRT2555912	hsa-miR-4436b-5p	CLIP-seq
MIRT2252921	hsa-miR-4501	CLIP-seq
MIRT2555913	hsa-miR-4503	CLIP-seq
MIRT2252924	hsa-miR-4645-5p	CLIP-seq
MIRT2252925	hsa-miR-4673	CLIP-seq
MIRT2252929	hsa-miR-4733-3p	CLIP-seq
MIRT2452336	hsa-miR-500a	CLIP-seq
MIRT1084444	hsa-miR-605	CLIP-seq
MIRT2021416	hsa-miR-607	CLIP-seq
MIRT2555910	hsa-miR-4275	CLIP-seq
MIRT2252921	hsa-miR-4501	CLIP-seq
MIRT2555913	hsa-miR-4503	CLIP-seq
MIRT2252924	hsa-miR-4645-5p	CLIP-seq
MIRT2252925	hsa-miR-4673	CLIP-seq
MIRT2252929	hsa-miR-4733-3p	CLIP-seq

Show/Hide all (17)

GO ID	Ontology	Definition	Evidence
GO:0000118	Component	Histone deacetylase complex	IBA
GO:0000785	Component	Chromatin	IBA
GO:0003712	Function	Transcription coregulator activity	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0031490	Function	Chromatin DNA binding	IBA
GO:0032454	Function	Histone H3K9 demethylase activity	IBA
GO:0032454	Function	Histone H3K9 demethylase activity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:0140683	Function	Histone H3K9me/H3K9me2 demethylase activity	IEA

MIM	HGNC	e!Ensembl
609373	1337	ENSG00000120733

Q7LBC6

Protein name

Lysine-specific demethylase 3B (EC 1.14.11.65) (JmjC domain-containing histone demethylation protein 2B) (Jumonji domain-containing protein 1B) (Nuclear protein 5qNCA) ([histone H3]-dimethyl-L-lysine(9) demethylase 3B)

Protein function

Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activity. {ECO:0000269|PubMed:

PDB

4C8D , 5R7X , 5RAA , 5RAB , 5RAC , 5RAD , 5RAE , 5RAF , 5RAG , 5RAH , 5RAI , 5RAJ , 5RAK , 5RAL , 5RAM , 5RAN , 5RAO , 5RAP , 5RAQ , 5RAR , 5RAS , 5RAU , 5RAV , 5RAW , 5RAX , 5RAY , 5RAZ , 5RB0 , 5RB1 , 5RB2 , 5RB3 , 5RB4 , 5RB5 , 5RB6 , 5RB7 , 6RBJ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02373	JmjC	1594 → 1704	JmjC domain, hydroxylase	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous. Highly expressed in placenta, skeletal muscle, kidney, heart and liver. {ECO:0000269|PubMed:11087669, ECO:0000269|PubMed:11687974}.

Sequence

MADAAASPVGKRLLLLFADTAASASASAPAAAAASGDPGPALRTRAWRAGTVRAMSGAVP
QDLAIFVEFDGCNWKQHSWVKVHAEEVIVLLLEGSLVWAPREDPVLLQGIRVSIAQWPAL
TFTPLVDKLGLGSVVPVEYLLDRELRFLSDANGLHLFQMGTDSQNQILLEHAALRETVNA
LISDQKLQEIFSRGPYSVQGHRVKIYQPEGEEGWLYGVVSHQDSITRLMEVSVTESGEIK
SVDPRLIHVMLMDNSAPQSEGGTLKAVKSSKGKKKRESIEGKDGRRRKSASDSGCDPASK
KLKGDRGEVDSNGSDGGEASRGPWKGGNASGEPGLDQRAKQPPSTFVPQINRNIRFATYT
KENGRTLVVQDEPVGGDTPASFTPYSTATGQTPLAPEVGGAENKEAGKTLEQVGQGIVAS
AAVVTTASSTPNTVRISDTGLAAGTVPEKQKGSRSQASGENSRNSILASSGFGAPLPSSS
QPLTFGSGRSQSNGVLATENKPLGFSFGCSSAQEAQKDTDLSKNLFFQCMSQTLPTSNYF
TTVSESLADDSSSRDSFKQSLESLSSGLCKGRSVLGTDTKPGSKAGSSVDRKVPAESMPT
LTPAFPRSLLNARTPENHENLFLQPPKLSREEPSNPFLAFVEKVEHSPFSSFASQASGSS
SSATTVTSKVAPSWPESHSSADSASLAKKKPLFITTDSSKLVSGVLGSALTSGGPSLSAM
GNGRSSSPTSSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLKTFSNVFGRHSGGFLSSP
ADFSQENKAPFEAVKRFSLDERSLACRQDSDSSTNSDLSDLSDSEEQLQAKTGLKGIPEH
LMGKLGPNGERSAELLLGKSKGKQAPKGRPRTAPLKVGQSVLKDVSKVKKLKQSGEPFLQ
DGSCINVAPHLHKCRECRLERYRKFKEQEQDDSTVACRFFHFRRLIFTRKGVLRVEGFLS
PQQSDPDAMNLWIPSSSLAEGIDLETSKYILANVGDQFCQLVMSEKEAMMMVEPHQKVAW
KRAVRGVREMCDVCETTLFNIHWVCRKCGFGVCLDCYRLRKSRPRSETEEMGDEEVFSWL
KCAKGQSHEPENLMPTQIIPGTALYNIGDMVHAARGKWGIKANCPCISRQNKSVLRPAVT
NGMSQLPSINPSASSGNETTFSGGGGPAPVTTPEPDHVPKADSTDIRSEEPLKTDSSASN
SNSELKAIRPPCPDTAPPSSALHWLADLATQKAKEETKEAGSLRSVLNKESHSPFGLDSF
NSTAKVSPLTPKLFNSLLLGPTASNNKTEGSSLRDLLHSGPGKLPQTPLDTGIPFPPVFS
TSSAGVKSKASLPNFLDHIIASVVENKKTSDASKRACNLTDTQKEVKEMVMGLNVLDPHT
SHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGD
QDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPT
RFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLH
LDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKQRIHDGKEKPGALWHIYAAK
DAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDA
VFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHTNHEDKLQVKNII
YHAVKDAVGTLKAHESKLARS

Sequence length

1761

Interactions

View interactions

	KEGG		Reactome
	Thermogenesis		HDMs demethylate histones

110

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autism spectrum disorder	Likely pathogenic	rs2480236167	RCV003127406
Diets-Jongmans syndrome	Likely pathogenic; Pathogenic	rs2126962006, rs2127002980, rs201211181, rs2480217162, rs2480334700, rs2480231295, rs2480323492, rs2480209302, rs2480311448, rs1761904420, rs1762257015, rs1763530961, rs1762639635, rs377463473, rs1762477174, rs1334033128 View all (1 more)	RCV001814780 RCV002249086 RCV002285203 RCV002468724 RCV002664379 RCV003153194 RCV003233426 RCV003444079 RCV003459051 RCV001072132 RCV001072133 RCV001072134 RCV001072135 RCV001072136 RCV001250505 RCV001254084
KDM3B-related disorder	Likely pathogenic; Pathogenic	rs1561796122, rs1561792565	RCV004753550 RCV003402466
Neurodevelopmental delay	Likely pathogenic; Pathogenic	rs1561796122, rs2126959971	RCV002274348 RCV002274349
Neurodevelopmental disorder	Pathogenic	rs2126922810	RCV002277710
Rare genetic epilepsy	Pathogenic	rs2126998820	RCV001787026
Rare genetic intellectual disability	Pathogenic	rs2126998820	RCV001787026
See cases	Likely pathogenic	rs2127002980	RCV002287530

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Colon adenocarcinoma	Benign	rs187275789	RCV005927399
Developmental disorder	Conflicting classifications of pathogenicity; Likely benign; Uncertain significance	rs2126994153, rs2126987772, rs1464939653	RCV001843730 RCV001843776 RCV003763056
Gastric cancer	Benign	rs187275789	RCV005927400
Uterine carcinosarcoma	Benign	rs144228142	RCV005904577

Show/Hide Text Mining Associations (14)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Breast Neoplasms	Associate	23266085
Carcinoma Hepatocellular	Associate	37400994
Colorectal Neoplasms	Associate	32716961
Developmental Disabilities	Associate	30929739, 31694657
Facial Dysmorphism with Multiple Malformations	Associate	30929739
Growth Disorders	Associate	30929739
Intellectual Disability	Associate	30929739
Leukemia	Associate	22615488, 37326062
Neoplasms	Associate	30885698
Obsessive Compulsive Disorder	Associate	35020433
Precursor Cell Lymphoblastic Leukemia Lymphoma	Stimulate	22615488
Prostatic Neoplasms	Associate	31822799
Prostatic Neoplasms Castration Resistant	Associate	31822799
Wilms Tumor	Associate	30885698

KDM3B (lysine demethylase 3B)