VAX1 Gene: Ventral Anterior Homeobox 1
Key regulator of craniofacial development and forebrain patterning
Gene Information Card
| Symbol | VAX1 |
|---|---|
| Full Name | ventral anterior homeobox 1 |
| Gene Type | protein-coding |
| Chromosomal Location | 10q25.3 |
| NCBI Gene ID | 11023 ncbi.nlm.nih.gov/gene/11023 |
| Ensembl ID | ENSG00000148704 |
| UniProt ID | Q5SQQ9 |
| OMIM ID | 604294 |
| HGNC ID | 12660 |
| Aliases | MCOPCB6, VAX-1 |
Description
VAX1 (ventral anterior homeobox 1) is a homeobox-containing transcription factor essential for proper development of the forebrain, eyes, and craniofacial structures. It acts as a repressor of dorsal telencephalic identity and is critical for optic fissure closure and palate formation. Mutations in VAX1 are associated with microphthalmia, coloboma, and cleft palate.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Microphthalmia with coloboma and cleft palate (MCOPCB6) | Loss-of-function mutations disrupt VAX1-mediated repression of dorsal forebrain genes, impairing optic fissure closure and palatal fusion. | ClinVar, OMIM |
| Non-syndromic cleft lip with or without cleft palate | Regulatory variants affecting VAX1 expression alter craniofacial morphogenesis pathways. | NCBI Gene, ClinVar |
| Coloboma (isolated) | Heterozygous missense variants reduce DNA-binding affinity, leading to incomplete optic fissure closure. | ClinVar |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain (cerebral cortex) | 0.0 | Not detected |
| Eye (retina) | 0.0 | Not detected |
| Testis | 0.0 | Not detected |
| Thyroid | 0.0 | Not detected |
| Adipose tissue | 0.0 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| H9 (embryonic stem cells) | 0.0 | Differentiated derivatives may express VAX1; undifferentiated cells show no expression |
| SH-SY5Y (neuroblastoma) | 0.0 | No detectable expression in standard culture |
| HeLa (cervical carcinoma) | 0.0 | Not expressed |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.697C>T (p.Arg233*) | Nonsense | Rare | Premature truncation; loss of homeodomain and transcriptional repressor function |
| c.2T>C (p.Met1?) | Missense (initiator codon) | Rare | Loss of translation initiation; complete loss of protein |
| c.476G>A (p.Arg159Gln) | Missense | Rare | Reduced DNA-binding affinity; associated with coloboma |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations (e.g., p.Arg233*) lead to truncated protein lacking the homeodomain, abolishing DNA binding and transcriptional repression.
Gain of Function (GOF)
No gain-of-function mutations reported in VAX1.
Dominant Negative (DN)
Heterozygous missense variants (e.g., p.Arg159Gln) may interfere with wild-type VAX1 function by competing for target DNA sites, though dominant-negative effect is not fully established.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Forebrain development (ventral identity specification)
• Optic fissure closure (retinoic acid signaling)
• Craniofacial morphogenesis (BMP and SHH pathways)
Protein Summary
VAX1 is a 294-amino-acid homeodomain-containing transcription factor that localizes to the nucleus. It functions primarily as a transcriptional repressor, binding to specific DNA sequences via its homeodomain to silence dorsal forebrain genes. The protein is critical for ventral forebrain patterning, optic fissure closure, and palatal fusion. Structural analysis reveals a conserved homeodomain (residues 158–217) responsible for DNA recognition. No post-translational modifications have been experimentally validated in UniProt.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| VAX1 Knockout HEK293 Cell Line | EDJ-KQ7250 | Human | 11023 | Details Get a Quote |
| VAX1 Knockout HeLa Cell Line | EDJ-KQ55547 | Human | 11023 | Details Get a Quote |
| VAX1 Knockout A-549 Cell Line | EDJ-KQ64041 | Human | 11023 | Details Get a Quote |
| VAX1 Knockout HCT 116 Cell Line | EDJ-KQ72491 | Human | 11023 | Details Get a Quote |
