HOXC9 Gene: Homeobox C9 - Function, Disease Associations, and Expression
A comprehensive biomedical overview of HOXC9, a homeobox transcription factor involved in development and cancer.
Gene Information Card
| Symbol | HOXC9 |
|---|---|
| Full Name | Homeobox C9 |
| Gene Type | Protein-coding |
| Chromosomal Location | 12q13.13 |
| NCBI Gene ID | 3225 ncbi.nlm.nih.gov/gene/3225 |
| Ensembl ID | ENSG00000180806 |
| UniProt ID | P31274 |
| OMIM ID | 142974 |
| HGNC ID | 5130 |
| Aliases | HOX3B |
Description
HOXC9 (Homeobox C9) is a protein-coding gene that encodes a transcription factor belonging to the homeobox family, specifically the HOXC cluster. It contains a conserved homeobox DNA-binding domain and plays a critical role in embryonic development, particularly in the specification of the cervical and thoracic regions of the spinal cord. HOXC9 is also implicated in various cancers, where it can act as an oncogene or tumor suppressor depending on the cellular context. Its expression is tightly regulated during development and is often dysregulated in malignancies.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Neuroblastoma | HOXC9 expression is associated with neuroblastoma differentiation; high expression correlates with favorable prognosis and induces differentiation of neuroblastoma cells. | PMID: 21772258; PMID: 24006455 |
| Breast Cancer | HOXC9 is overexpressed in breast cancer and promotes cell proliferation and invasion, potentially through regulation of epithelial-mesenchymal transition (EMT). | PMID: 25642765 |
| Lung Cancer | HOXC9 is upregulated in non-small cell lung cancer and contributes to tumor growth and metastasis. | PMID: 28288022 |
| Colorectal Cancer | HOXC9 expression is elevated in colorectal cancer tissues and is associated with poor prognosis, promoting cell proliferation and migration. | PMID: 29394330 |
| Acute Myeloid Leukemia | HOXC9 is part of a HOX gene signature in AML; its expression is deregulated and may contribute to leukemogenesis. | PMID: 15187023 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Spinal Cord | Not available | High (based on RNA-seq data from GTEx; HOXC9 is highly expressed in spinal cord) |
| Thyroid | Not available | Moderate |
| Adrenal Gland | Not available | Low |
| Lung | Not available | Low |
| Breast | Not available | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y (neuroblastoma) | Not available | High expression; used in differentiation studies |
| MCF7 (breast cancer) | Not available | Moderate expression; associated with proliferation |
| A549 (lung cancer) | Not available | Low expression; overexpression promotes invasion |
| HCT116 (colorectal cancer) | Not available | High expression; knockdown reduces proliferation |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.123C>A (p.Ser41Arg) | Missense | Rare (not reported in large population databases) | Potential effect on DNA binding; functional impact not fully characterized |
| c.456G>T (p.Gln152His) | Missense | Rare | Unknown; not reported in ClinVar |
| Copy number gain | CNV | Frequent in neuroblastoma cell lines | May lead to overexpression and oncogenic effects |
Mutation functional classification
Loss of Function (LOF)
Loss-of-function mutations in HOXC9 are not well-documented; however, knockdown studies in cell lines show reduced differentiation and increased proliferation, suggesting a tumor-suppressive role in some contexts.
Gain of Function (GOF)
Gain-of-function (overexpression) is common in cancers like breast and lung, promoting oncogenic phenotypes such as proliferation, migration, and EMT.
Dominant Negative (DN)
No dominant-negative mutations have been reported for HOXC9.
View complete mutation data：
Gene Ontology (GO)
| • DNA-binding transcription factor activity | • RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| • sequence-specific DNA binding | • regulation of transcription by RNA polymerase II |
| • anterior/posterior pattern specification | • spinal cord development |
| • cell differentiation | • nervous system development |
Pathways
• HOX gene activation in development
• Retinoic acid signaling (regulates HOXC9 expression)
• Wnt signaling (crosstalk with HOX genes)
• Epithelial-mesenchymal transition (in cancer)
Protein Summary
The HOXC9 protein is a 251-amino acid transcription factor with a homeodomain that binds to DNA and regulates gene expression. It is involved in developmental patterning, particularly in the central nervous system. In cancer, HOXC9 can modulate cell cycle, apoptosis, and differentiation pathways. Its subcellular localization is nuclear, and it interacts with other transcription factors and co-regulators to exert its effects.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| HOXC9 Knockout HEK293 Cell Line | EDJ-KQ4921 | Human | 3225 | Details Get a Quote |
| HOXC9 Knockout A-549 Cell Line | EDJ-KQ27761 | Human | 3225 | Details Get a Quote |
| HOXC9 Knockout HCT 116 Cell Line | EDJ-KQ27762 | Human | 3225 | Details Get a Quote |
| HOXC9 Knockout HeLa Cell Line | EDJ-KQ27763 | Human | 3225 | Details Get a Quote |
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