PAX6 Gene: Paired Box 6
Master Regulator of Eye and Central Nervous System Development
Gene Information Card
| Symbol | PAX6 |
|---|---|
| Full Name | Paired Box 6 |
| Gene Type | Protein coding |
| Chromosomal Location | 11p13 |
| NCBI Gene ID | 5080 ncbi.nlm.nih.gov/gene/5080 |
| Ensembl ID | ENSG00000007372 |
| UniProt ID | P26367 |
| OMIM ID | 607108 |
| HGNC ID | 8620 |
| Aliases | AN, AN2, D11S812E, MGDA, WAGR |
Description
PAX6 (Paired Box 6) is a homeobox-containing transcription factor that acts as a master regulator of eye, central nervous system, and pancreatic development. It binds DNA via its paired domain and homeodomain, controlling the expression of genes involved in ocular morphogenesis, neurogenesis, and cell differentiation. Heterozygous loss-of-function mutations cause aniridia, while compound heterozygosity or homozygous mutations lead to severe ocular and brain malformations.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Aniridia | Heterozygous loss-of-function mutations (nonsense, frameshift, deletions) reduce PAX6 protein dosage, disrupting iris and retinal development. | ClinVar, OMIM #106210 |
| Peters anomaly | Missense mutations in the paired domain impair DNA binding, leading to anterior segment dysgenesis. | ClinVar, OMIM #604229 |
| WAGR syndrome | Contiguous gene deletion of 11p13 including PAX6 and WT1 causes Wilms tumor, aniridia, genitourinary anomalies, and intellectual disability. | OMIM #194072 |
| Foveal hypoplasia | PAX6 haploinsufficiency results in underdevelopment of the fovea, causing nystagmus and reduced visual acuity. | ClinVar, OMIM #136520 |
| Autism spectrum disorder | Rare PAX6 missense variants have been associated with neurodevelopmental phenotypes, though mechanism is not fully defined. | NCBI Gene, PubMed |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Cerebral cortex | 12.5 | Medium |
| Retina | 45.2 | High |
| Pancreas | 8.3 | Low |
| Cerebellum | 6.1 | Low |
| Spinal cord | 9.8 | Medium |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| ARPE-19 (retinal pigment epithelium) | 35.0 | High expression |
| SH-SY5Y (neuroblastoma) | 18.2 | Moderate expression |
| HeLa (cervical carcinoma) | 2.1 | Low expression |
| HepG2 (hepatocellular carcinoma) | 1.5 | Very low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.607C>T (p.Arg203*) | Nonsense | Common in aniridia | Loss of function; premature truncation |
| c.103-2A>G | Splice site | Rare | Aberrant splicing; loss of function |
| c.140A>G (p.Asn47Ser) | Missense | Rare in Peters anomaly | Impaired DNA binding; dominant negative |
| Whole gene deletion | Structural | Common in WAGR | Haploinsufficiency of PAX6 and WT1 |
Mutation functional classification
Loss of Function (LOF)
Nonsense, frameshift, and splice-site mutations that reduce PAX6 protein levels or abolish DNA binding, leading to aniridia and foveal hypoplasia.
Gain of Function (GOF)
Not well documented; PAX6 duplications are rare and associated with mild phenotypes, but no clear gain-of-function mechanism is established.
Dominant Negative (DN)
Missense mutations in the paired domain (e.g., p.Asn47Ser) that produce a protein capable of interfering with wild-type PAX6 function, causing Peters anomaly.
View complete mutation data：
Gene Ontology (GO)
Pathways
• PAX6 in eye development (Reactome: R-HSA-5617472)
• Transcriptional regulation by PAX6 (KEGG: hsa04350)
Protein Summary
PAX6 is a 422-amino acid transcription factor containing two DNA-binding domains: an N-terminal paired domain and a central homeodomain, plus a C-terminal transactivation domain. It forms homodimers and heterodimers with other transcription factors to regulate target genes such as SOX2, FOXE3, and CRYAA. The protein is highly conserved across species and essential for eye morphogenesis, neurogenesis, and pancreatic islet development.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PAX6 Knockout HEK293 Cell Line | EDJ-KQ5409 | Human | 5080 | Details Get a Quote |
| PAX6 Knockout A-549 Cell Line | EDJ-KQ28573 | Human | 5080 | Details Get a Quote |
| PAX6 Knockout HCT 116 Cell Line | EDJ-KQ28574 | Human | 5080 | Details Get a Quote |
| PAX6 Knockout HeLa Cell Line | EDJ-KQ28575 | Human | 5080 | Details Get a Quote |
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