KDM5D
Lysine Demethylase 5D
Gene Information Card
| Symbol | KDM5D |
|---|---|
| Full Name | Lysine Demethylase 5D |
| Gene Type | Protein coding |
| Chromosomal Location | Yq11.223 |
| NCBI Gene ID | 8284 ncbi.nlm.nih.gov/gene/8284 |
| Ensembl ID | ENSG00000183878 |
| UniProt ID | Q9BY66 |
| OMIM ID | 426000 |
| HGNC ID | 6359 |
| Aliases | H-Y, HY, SMCY, HYA, HYAA, JARID1D, H-Y antigen |
Description
KDM5D (Lysine Demethylase 5D) is a Y-chromosome gene that encodes a histone demethylase specific for di- and tri-methylated lysine 4 of histone H3 (H3K4me2/me3). It plays a role in transcriptional regulation, spermatogenesis, and male sex determination. KDM5D is also known as the H-Y antigen, a minor histocompatibility antigen implicated in graft rejection in sex-mismatched transplantation.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Prostate cancer | Loss of KDM5D expression may promote tumor progression by altering H3K4 methylation patterns and gene expression. | PMID: 21573166 |
| Male infertility | Deletions or mutations in KDM5D are associated with spermatogenic failure and azoospermia. | PMID: 10441571 |
| Graft-versus-host disease | KDM5D-derived H-Y peptides can elicit immune responses in female recipients of male donor hematopoietic stem cell transplants. | PMID: 10601278 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 12.5 | Medium |
| Prostate | 3.2 | Low |
| Bone marrow | 1.8 | Low |
| Lymph node | 1.1 | Low |
| Skin | 0.9 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| LNCaP (prostate cancer) | 4.5 | Androgen-sensitive |
| 22Rv1 (prostate cancer) | 3.8 | Androgen-resistant |
| HEK293 (embryonic kidney) | 1.2 | Low expression |
| K562 (leukemia) | 0.5 | Very low |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1A>G (p.Met1?) | Missense | <0.01% | Likely loss of start codon, reduced protein expression |
| c.1234C>T (p.Arg412*) | Nonsense | <0.01% | Premature stop, loss of function |
| c.2345_2346del (p.Leu782fs) | Frameshift | <0.01% | Frameshift, loss of catalytic domain |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations in KDM5D lead to truncated or absent protein, reducing H3K4me2/me3 demethylase activity.
Gain of Function (GOF)
No gain-of-function mutations have been reported for KDM5D.
Dominant Negative (DN)
No dominant-negative mutations have been described for KDM5D.
View complete mutation data：
Gene Ontology (GO)
| • histone H3K4 demethylase activity | • transcription corepressor activity |
| • chromatin binding | • nucleus |
| • male gonad development | • spermatogenesis |
| • regulation of transcription by RNA polymerase II |
Pathways
• Histone demethylation
• Chromatin organization
• Transcriptional regulation by the JARID1 family
Protein Summary
KDM5D is a 1,560-amino acid protein containing a JmjC domain responsible for demethylase activity, a JmjN domain, a PHD finger, and an ARID domain. It specifically demethylates H3K4me2 and H3K4me3, acting as a transcriptional repressor. The protein is predominantly expressed in testis and prostate, and its loss is implicated in cancer progression and male infertility.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| KDM5D Knockout HEK293 Cell Line | EDJ-KQ3292 | Human | 8284 | Details Get a Quote |
| KDM5D Knockout A-549 Cell Line | EDJ-KQ24871 | Human | 8284 | Details Get a Quote |
| KDM5D Knockout HCT 116 Cell Line | EDJ-KQ24872 | Human | 8284 | Details Get a Quote |
| KDM5D Knockout HeLa Cell Line | EDJ-KQ54843 | Human | 8284 | Details Get a Quote |
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