Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
84678
Gene name Gene Name - the full gene name approved by the HGNC.
Lysine demethylase 2B
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
KDM2B
Synonyms (NCBI Gene) Gene synonyms aliases
CXXC2, FBXL10, Fbl10, JHDM1B, PCCX2
Chromosome Chromosome number
12
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
12q24.31
Summary Summary of gene provided in NCBI Entrez Gene.
This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), w
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs782304760 C>T Likely-pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT024040 hsa-miR-1-3p Microarray 18668037
MIRT042973 hsa-miR-324-3p CLASH 23622248
MIRT629261 hsa-miR-216a-5p HITS-CLIP 23824327
MIRT631070 hsa-miR-5197-5p HITS-CLIP 23824327
MIRT631069 hsa-miR-652-3p HITS-CLIP 23824327
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II ISS
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
GO:0003677 Function DNA binding NAS
GO:0003712 Function Transcription coregulator activity IBA 21873635
GO:0005515 Function Protein binding IPI 16943429, 24981860, 26496610, 27505670, 27705803
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
609078 13610 ENSG00000089094
Protein
UniProt ID Q8NHM5
Protein name Lysine-specific demethylase 2B (EC 1.14.11.27) (CXXC-type zinc finger protein 2) (F-box and leucine-rich repeat protein 10) (F-box protein FBL10) (F-box/LRR-repeat protein 10) (JmjC domain-containing histone demethylation protein 1B) (Jumonji domain-conta
Protein function Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H
PDB 4O64 , 5JH5 , 6BVA , 8HCU
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13621 Cupin_8 23 336 Cupin-like domain Domain
PF17811 JHD 333 418 Jumonji helical domain Domain
PF02008 zf-CXXC 605 651 CXXC zinc finger domain Domain
PF16866 PHD_4 656 723 PHD-finger Domain
PF00646 F-box 1050 1107 F-box domain Domain
Sequence
MAGPQMGGSAEDHPPRKRHAAEKQKKKTVIYTKCFEFESATQRPIDRQRYDENEDLSDVE
EIVSVRGFSLEEKLRSQLYQGDFVHAMEGKDFNYEYVQREALRVPLIFREKDGLGIKMPD
PDFTVRDVKLLVGSRRLVDVMDVNTQKGTEMSMSQFVRYYETPEAQRDKLYNVISLEFSH
TKLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNAIAEMKYPKVKKYCLMSVKGCFTD
FHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSGKQSDIFLGDRVERCQRIEL
KQGYTFFIPSGWIHAVYTPVDSLVFGGNILHS
FNVPMQLRIYEIEDRTRVQPKFRYPFYY
EMCWYVLERYVYCVTQRSHLTQEYQRESMLIDAPRKPSIDGFSSDSWLEMEEEACDQQ
PQ
EEEEKDEEGEGRDRAPKPPTDGSTSPTSTPSEDQEALGKKPKAPALRFLKRTLSNESEES
VKSTTLAVDYPKTPTGSPATEVSAKWTHLTEFELKGLKALVEKLESLPENKKCVPEGIED
PQALLEGVKNVLKEHADDDPSLAITGVPVVTWPKKTPKNRAVGRPKGKLGPASAVKLAAN
RTTAGARRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTA
VCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECP
KCN
HAGKTGKQKRGPGFKYASNLPGSLLKEQKMNRDNKEGQEPAKRRSECEEAPRRRSDE
HSKKVPPDGLLRRKSDDVHLRKKRKYEKPQELSGRKRASSLQTSPGSSSHLSPRPPLGSS
LSPWWRSSLTYFQQQLKPGKEDKLFRKKRRSWKNAEDRMALANKPLRRFKQEPEDELPEA
PPKTRESDHSRSSSPTAGPSTEGAEGPEEKKKVKMRRKRRLPNKELSRELSKELNHEIQR
TENSLANENQQPIKSEPESEGEEPKRPPGICERPHRFSKGLNGTPRELRHQLGPSLRSPP
RVISRPPPSVSPPKCIQMERHVIRPPPISPPPDSLPLDDGAAHVMHREVWMAVFSYLSHQ
DLCVCMRVCRTWNRWCCDKRLWTRIDL
NHCKSITPLMLSGIIRRQPVSLDLSWTNISKKQ
LSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRTLDVQWVEGLKDAQMRDLLSPPTD
NRPGQMDNRSKLRNIVELRLAGLDITDASLRLIIRHMPLLSKLHLSYCNHVTDQSINLLT
AVGTTTRDSLTEINLSDCNKVTDQCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSV
SVQFGQVEEKLLQKLS
Sequence length 1336
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG   Reactome
  Polycomb repressive complex   HDMs demethylate histones
Associated diseases Disease information provided by ClinVar, GenCC, and GWAS databases.
Causal
Disease term Disease name dbSNP ID References
Developmental delay Global developmental delay rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291
View all (32 more)
Infantile spasms Infantile Spasm rs387906686, rs1553579488, rs1553567561
Schizophrenia Schizophrenia rs13447324, rs387906932, rs387906933, rs863223354, rs863223355, rs776061422, rs863223349, rs748809996, rs759748655, rs863223353, rs863223350, rs863223356, rs781821239, rs863223348, rs863223346
View all (12 more)
21743468
Unknown
Disease term Disease name Evidence References Source
Neurodevelopmental Disorders neurodevelopmental disorder GenCC
Diabetes Diabetes GWAS
Hypertension Hypertension GWAS
Associations from Text Mining
Disease Name Relationship Type References
Acute Kidney Injury Associate 37773725
Breast Neoplasms Associate 24853546, 30060056
Burkitt Lymphoma Associate 30996097
Carcinogenesis Associate 26725323
Carcinoma Squamous Cell Stimulate 34783291
Colonic Neoplasms Associate 29772566, 32175798
Disease Associate 35306360
Down Syndrome Associate 25701644
Drug Related Side Effects and Adverse Reactions Stimulate 37773725
Epstein Barr Virus Infections Associate 30996097