KDM5B (Lysine Demethylase 5B)
A histone demethylase regulating gene expression, implicated in cancer and development.
Gene Information Card
| Symbol | KDM5B |
|---|---|
| Full Name | Lysine Demethylase 5B |
| Gene Type | protein-coding |
| Chromosomal Location | 1q32.1 |
| NCBI Gene ID | 10765 ncbi.nlm.nih.gov/gene/10765 |
| Ensembl ID | ENSG00000117139 |
| UniProt ID | Q9UGL1 |
| OMIM ID | 605393 |
| HGNC ID | 18039 |
| Aliases | PLU-1, RBBP2H1, JARID1B, CT31 |
Description
KDM5B encodes a histone demethylase that specifically demethylates di- and tri-methylated lysine 4 of histone H3 (H3K4me2/me3), a mark associated with active gene transcription. By removing these methyl groups, KDM5B acts as a transcriptional repressor. It is involved in various cellular processes including cell proliferation, differentiation, and stem cell maintenance. KDM5B is frequently overexpressed in several cancers and has been implicated in tumorigenesis and drug resistance.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Cancer (breast, prostate, lung, etc.) | Overexpression of KDM5B promotes cell proliferation, epithelial-to-mesenchymal transition, and drug resistance by repressing tumor suppressor genes. | Multiple studies (e.g., PMID: 22158049, 25494235) show elevated KDM5B expression in tumors and correlation with poor prognosis. |
| Intellectual disability | Loss-of-function mutations in KDM5B are associated with autosomal dominant intellectual disability. | ClinVar and OMIM list pathogenic variants in KDM5B linked to neurodevelopmental disorders. |
| Autism spectrum disorder | De novo mutations in KDM5B have been identified in individuals with autism. | Exome sequencing studies (e.g., PMID: 25232744) report KDM5B variants in ASD cohorts. |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Breast | 8.2 | Low |
| Lung | 10.1 | Medium |
| Liver | 6.4 | Low |
| Testis | 15.3 | High |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| MCF7 (breast cancer) | 18.5 | High expression |
| A549 (lung cancer) | 12.3 | Moderate |
| HEK293 (embryonic kidney) | 9.8 | Low |
| K562 (leukemia) | 14.2 | Moderate |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| p.Arg99* | Nonsense | Rare | Loss of function, associated with intellectual disability |
| p.Leu437Pro | Missense | Rare | Likely damaging, reported in autism |
| p.Gly464Arg | Missense | Rare | Uncertain significance, found in cancer |
Mutation functional classification
Loss of Function (LOF)
Loss-of-function mutations (e.g., nonsense, frameshift) reduce demethylase activity, leading to increased H3K4 methylation and altered gene expression, contributing to neurodevelopmental phenotypes.
Gain of Function (GOF)
Gain-of-function mutations are rare; overexpression of wild-type KDM5B is more common in cancer, acting as an oncogene by repressing tumor suppressors.
Dominant Negative (DN)
Dominant-negative effects have been proposed for some missense mutations that retain DNA binding but lose catalytic activity, interfering with normal KDM5B function.
View complete mutation data：
Gene Ontology (GO)
| • histone demethylase activity (H3-K4 specific) | • metal ion binding |
| • chromatin binding | • transcription corepressor activity |
| • nucleus | • regulation of transcription |
| • DNA-templated |
Pathways
• Chromatin organization
• Epigenetic regulation of gene expression
• Cancer pathways (e.g.
• PI3K/AKT
• p53)
Protein Summary
KDM5B is a 1544-amino acid protein containing a JmjC domain responsible for demethylase activity, a JmjN domain, ARID domain, and PHD fingers. It binds to histone H3 and removes methyl groups from H3K4me2/me3, thereby repressing transcription. KDM5B interacts with transcription factors and chromatin remodelers. Its expression is cell-cycle regulated and it plays roles in development and cancer.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| KDM5B Knockout HEK293 Cell Line | EDJ-KQ1016 | Human | 10765 | Details Get a Quote |
| KDM5B Knockout A-549 Cell Line | EDJ-KQ20088 | Human | 10765 | Details Get a Quote |
| KDM5B Knockout HeLa Cell Line | EDJ-KQ20090 | Human | 10765 | Details Get a Quote |
| KDM5B Knockout HCT 116 Cell Line | EDJ-KQ18763 | Human | 10765 | Details Get a Quote |
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