Gene Gene information from NCBI Gene database.
Entrez ID 23030
Gene name Lysine demethylase 4B
Gene symbol KDM4B
Synonyms (NCBI Gene)
JMJD2BMRD65TDRD14B
Chromosome 19
Chromosome location 19p13.3
miRNA miRNA information provided by mirtarbase database.
244
miRTarBase ID miRNA Experiments Reference
MIRT018784 hsa-miR-335-5p Microarray 18185580
MIRT040426 hsa-miR-615-3p CLASH 23622248
MIRT038564 hsa-miR-106b-3p CLASH 23622248
MIRT037961 hsa-miR-505-5p CLASH 23622248
MIRT1084488 hsa-miR-1178 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
20
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin IBA
GO:0005634 Component Nucleus IBA
GO:0005634 Component Nucleus IEA
GO:0005654 Component Nucleoplasm TAS
GO:0006325 Process Chromatin organization IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
609765 29136 ENSG00000127663
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O94953
Protein name Lysine-specific demethylase 4B (EC 1.14.11.66) (JmjC domain-containing histone demethylation protein 3B) (Jumonji domain-containing protein 2B) ([histone H3]-trimethyl-L-lysine(9) demethylase 4B)
Protein function Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9
PDB 4LXL , 4UC4 , 7JM5 , 9H44
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02375 JmjN 16 50 jmjN domain Family
PF02373 JmjC 176 292 JmjC domain, hydroxylase Domain
PF13831 PHD_2 754 789 Family
PF13832 zf-HC5HC2H_2 795 906 Domain
PF18104 Tudor_2 922 956 Jumonji domain-containing protein 2A Tudor domain Domain
PF18104 Tudor_2 980 1014 Jumonji domain-containing protein 2A Tudor domain Domain
Sequence
MGSEDHGAQNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQTY
DDIDDVVIPAPIQQVVTGQSGLFTQYNIQKKAMTVGEYRRLANSEKYCTPRHQDFDDLER
KYWKNLTFVSPIYGADISGSLYDDDVAQWNIGSLRTILDMVERECGTIIEGVNTPYLYFG
MWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFPGSSQGCDAFLR
HKMTLISPIILKKYGIPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNF
ATLRWIDY
GKVATQCTCRKDMVKISMDVFVRILQPERYELWKQGKDLTVLDHTRPTALTSPELSSWSA
SRASLKAKLLRRSHRKRSQPKKPKPEDPKFPGEGTAGAALLEEAGGSVKEEAGPEVDPEE
EEEEPQPLPHGREAEGAEEDGRGKLRPTKAKSERKKKSFGLLPPQLPPPPAHFPSEEALW
LPSPLEPPVLGPGPAAMEESPLPAPLNVVPPEVPSEELEAKPRPIIPMLYVVPRPGKAAF
NQEHVSCQQAFEHFAQKGPTWKEPVSPMELTGPEDGAASSGAGRMETKARAGEGQAPSTF
SKLKMEIKKSRRHPLGRPPTRSPLSVVKQEASSDEEASPFSGEEDVSDPDALRPLLSLQW
KNRAASFQAERKFNAAAARTEPYCAICTLFYPYCQALQTEKEAPIASLGKGCPATLPSKS
RQKTRPLIPEMCFTSGGENTEPLPANSYIGDDGTSPLIACGKCCLQVHASCYGIRPELVN
EGWTCSRCA
AHAWTAECCLCNLRGGALQMTTDRRWIHVICAIAVPEARFLNVIERHPVDI
SAIPEQRWKLKCVYCRKRMKKVSGACIQCSYEHCSTSFHVTCAHAAGVLMEPDDWPYVVS
ITCLKH
KSGGHAVQLLRAVSLGQVVITKNRNGLYYRCRVIGAASQTCYEVNFDDGSYSDN
LYPESITSRDCVQLGPPSEGELVELRWTDGNLYKAKFISSVTSHIYQVEFEDGSQLTVKR
GDIFTLEEELPKRVRSRLSLSTGAPQEPAFSGEEAKAAKRPRVGTPLATEDSGRSQDYVA
FVESLLQVQGRPGAPF
Sequence length 1096
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    HDMs demethylate histones
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
Estrogen-dependent gene expression
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
68
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Intellectual developmental disorder, autosomal dominant 65 Pathogenic; Likely pathogenic rs2145822607, rs2146074788, rs2146057065, rs746714213, rs1231991589, rs2512133290, rs2512571434, rs748669919, rs2512166678, rs2512151147, rs2512130849, rs2039680672, rs2512537089, rs2512571628, rs151146933 RCV001420723
RCV001420724
RCV001420725
RCV001800248
RCV002227606
RCV002465450
RCV002468851
RCV002776564
RCV003120333
RCV003123257
RCV003322698
RCV003447849
RCV003986086
RCV003992142
RCV001420726
Neurodevelopmental delay Likely pathogenic rs2146060644 RCV002274350
Neurodevelopmental disorder Likely pathogenic rs2146018043 RCV002277638
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Cholangiocarcinoma Benign rs148314771 RCV005911630
Developmental disorder Uncertain significance rs780782889 RCV003764460
Familial cancer of breast Benign rs2613739, rs148314771 RCV005915273
RCV005911626
KDM4B-related disorder Conflicting classifications of pathogenicity; Uncertain significance; Likely benign rs143239564, rs936726492, rs150616189, rs2512147429, rs960371558, rs747372978, rs1397820479, rs2512234473, rs781760371, rs769976056, rs144327370, rs369236395, rs374489612, rs1029259660, rs202201915
View all (2 more)
RCV003900909
RCV003963787
RCV003402596
RCV003406095
RCV003394508
RCV003412349
RCV003412409
RCV003392972
RCV003420982
RCV003946568
RCV003908909
RCV003938958
RCV003896876
RCV003902168
RCV003902054
RCV003934302
RCV003962254
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Arthritis Rheumatoid Associate 33909202
Asthma Associate 33688506
Breast Neoplasms Associate 20682797, 23723241, 25725194
Carcinogenesis Associate 30683841, 31647098
Carcinoma Hepatocellular Associate 27487123
Carcinoma Non Small Cell Lung Associate 26722485
Carcinoma Renal Cell Associate 36952476
Colorectal Neoplasms Associate 26511091
Glioblastoma Associate 38093312
Hereditary Breast and Ovarian Cancer Syndrome Associate 21502505