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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
33
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
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
View all (10 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental delay Likely pathogenic rs2146060644 RCV002274350
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder Likely pathogenic rs2146018043 RCV002277638
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma Adenocarcinoma BEFREE 24481461
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 27630338
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma CTD_human_DG 19270706
★☆☆☆☆
Found in Text Mining only
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 33909202 Associate
★☆☆☆☆
Found in Text Mining only
Asthma Asthma Pubtator 33688506 Associate
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 20682797, 21445275, 25725194, 30266800, 30418174, 30459150, 31390833
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 20682797, 23723241, 25725194 Associate
★☆☆☆☆
Found in Text Mining only
Carcinogenesis Carcinogenesis Pubtator 30683841, 31647098 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 27487123 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma of lung Lung carcinoma BEFREE 21930796, 27630338
★☆☆☆☆
Found in Text Mining only