KDM3A (Lysine Demethylase 3A)
A histone demethylase regulating gene expression, spermatogenesis, and cancer progression.
Gene Information Card
| Symbol | KDM3A |
|---|---|
| Full Name | Lysine Demethylase 3A |
| Gene Type | Protein-coding |
| Chromosomal Location | 2p11.2 |
| NCBI Gene ID | 55818 ncbi.nlm.nih.gov/gene/55818 |
| Ensembl ID | ENSG00000115548 |
| UniProt ID | Q9Y4C1 |
| OMIM ID | 611512 |
| HGNC ID | 20979 |
| Aliases | JMJD1A, JHMD2A, KIAA0742, FLJ14340 |
Description
KDM3A (lysine demethylase 3A) encodes a JmjC-domain-containing histone demethylase that specifically demethylates mono- and dimethylated histone H3 lysine 9 (H3K9me1/me2), a repressive chromatin mark. By removing these methyl groups, KDM3A activates transcription of target genes involved in spermatogenesis, metabolism, and stem cell maintenance. The gene is located on chromosome 2p11.2 and is widely expressed in adult tissues. Dysregulation of KDM3A is implicated in various cancers and developmental disorders.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Cancer (multiple types) | Overexpression promotes oncogene transcription (e.g., MYC, CCND1) via H3K9 demethylation at promoter regions. | COSMIC; NCBI Gene; ClinVar |
| Male infertility | KDM3A knockout in mice leads to defective spermatogenesis and reduced fertility; human variants may impair sperm maturation. | OMIM; NCBI Gene |
| Obesity / Metabolic syndrome | KDM3A regulates metabolic genes (e.g., PPARγ, UCP1); altered expression linked to adipogenesis and energy balance. | NCBI Gene; UniProt |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 28.5 | High |
| Brain (cerebellum) | 12.3 | Medium |
| Heart | 9.8 | Medium |
| Liver | 6.2 | Low |
| Kidney | 7.1 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 15.4 | Embryonic kidney cells; high expression |
| HeLa | 11.2 | Cervical cancer cells; moderate expression |
| K562 | 8.9 | Leukemia cells; moderate expression |
| MCF7 | 6.5 | Breast cancer cells; low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1234C>T (p.Arg412Trp) | Missense | <0.1% | Unknown functional impact; reported in COSMIC |
| c.567_568insA (p.Glu190fs) | Frameshift | <0.1% | Predicted loss of function; rare in population |
| c.2345G>A (p.Arg782Gln) | Missense | <0.1% | Found in cancer samples; potential gain of function |
Mutation functional classification
Loss of Function (LOF)
Frameshift or nonsense mutations that truncate the JmjC domain abolish demethylase activity.
Gain of Function (GOF)
Missense mutations in the catalytic domain may increase demethylase activity, promoting oncogenic transcription.
Dominant Negative (DN)
Not well characterized; mutations that disrupt dimerization or substrate binding could interfere with wild-type function.
View complete mutation data：
Gene Ontology (GO)
| • histone H3K9 demethylase activity | • transcription coactivator activity |
| • chromatin binding | • nucleus |
| • spermatogenesis | • regulation of gene expression |
Pathways
• Chromatin modifying enzymes
• Transcriptional regulation by histone demethylation
• Spermatogenesis
Protein Summary
KDM3A is a 1321-amino-acid nuclear protein containing a JmjC domain responsible for demethylating H3K9me1/me2. It acts as a transcriptional coactivator by removing repressive histone marks, thereby facilitating RNA polymerase II recruitment. The protein is essential for male germ cell development and metabolic gene regulation. Its overexpression in tumors correlates with poor prognosis, making it a potential therapeutic target.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| KDM3A Knockout HEK293 Cell Line | EDJ-KQ2029 | Human | 55818 | Details Get a Quote |
| KDM3A Knockout A-549 Cell Line | EDJ-KQ22069 | Human | 55818 | Details Get a Quote |
| KDM3A Knockout HCT 116 Cell Line | EDJ-KQ22070 | Human | 55818 | Details Get a Quote |
| KDM3A Knockout HeLa Cell Line | EDJ-KQ20770 | Human | 55818 | Details Get a Quote |
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