Gene Gene information from NCBI Gene database.
Entrez ID 84678
Gene name Lysine demethylase 2B
Gene symbol KDM2B
Synonyms (NCBI Gene)
CXXC2FBXL10Fbl10JHDM1BPCCX2
Chromosome 12
Chromosome location 12q24.31
Summary 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.
1
SNP ID Visualize variation Clinical significance Consequence
rs782304760 C>T Likely-pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
216
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 (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
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 IEA
GO:0003677 Function DNA binding NAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
609078 13610 ENSG00000089094
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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 associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
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Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
KDM2B-related disorder Likely pathogenic rs2502086109, rs2500838817 RCV004554910
RCV004555115
KDM2B-related syndrome Likely pathogenic; Pathogenic rs1555292064 RCV005242565
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute myeloid leukemia Benign rs78494968 RCV005903670
Cervical cancer Benign rs201930981 RCV005936874
Global developmental delay Likely benign rs782304760 RCV000491693
Hypotonia Likely benign rs782304760 RCV000491693
Associations from Text MiningDisease associations identified through Pubtator
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