PAX9 Gene
Paired Box 9: A Key Regulator in Tooth Development and Craniofacial Patterning
Gene Information Card
| Symbol | PAX9 |
|---|---|
| Full Name | Paired Box 9 |
| Gene Type | Protein-coding |
| Chromosomal Location | 14q13.3 |
| NCBI Gene ID | 5083 ncbi.nlm.nih.gov/gene/5083 |
| Ensembl ID | ENSG00000107669 |
| UniProt ID | P55771 |
| OMIM ID | 167416 |
| HGNC ID | 8620 |
| Aliases | PAX-9, STHAG3 |
Description
PAX9 encodes a member of the paired box (PAX) family of transcription factors, characterized by a paired domain and a homeodomain. This protein is essential for embryonic development, particularly in the formation of teeth, craniofacial structures, and the thymus. PAX9 regulates the expression of genes involved in mesenchymal-epithelial interactions during organogenesis. Mutations in PAX9 are associated with selective tooth agenesis (oligodontia) and other craniofacial anomalies.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Selective Tooth Agenesis 3 (STHAG3) | Loss-of-function mutations in PAX9 disrupt tooth development by impairing mesenchymal signaling, leading to missing permanent and deciduous teeth. | ClinVar, OMIM |
| Oligodontia | Heterozygous mutations (e.g., frameshift, missense) reduce PAX9 DNA-binding ability, causing failure of tooth bud formation. | NCBI, OMIM |
| Craniofacial Abnormalities | PAX9 haploinsufficiency affects neural crest cell migration and patterning, contributing to facial dysmorphism. | UniProt, OMIM |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Salivary Gland | 12.5 | Medium |
| Thyroid | 10.2 | Medium |
| Esophagus | 8.1 | Medium |
| Lung | 6.3 | Low |
| Kidney | 4.7 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| A549 (Lung) | 5.2 | Low expression |
| HepG2 (Liver) | 3.8 | Low expression |
| MCF7 (Breast) | 2.1 | Not detected |
| K562 (Leukemia) | 1.5 | Not detected |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.175C>T (p.Arg59Trp) | Missense | Rare | Reduces DNA-binding affinity; associated with oligodontia |
| c.139G>A (p.Gly47Ser) | Missense | Rare | Impairs paired domain function; tooth agenesis |
| c.433_434delCT (p.Leu145fs) | Frameshift | Rare | Loss-of-function; premature truncation |
| c.2T>C (p.Met1Thr) | Missense | Rare | Disrupts translation initiation; severe oligodontia |
Mutation functional classification
Loss of Function (LOF)
Most PAX9 mutations are loss-of-function, leading to haploinsufficiency and reduced transcriptional activity, primarily causing tooth agenesis.
Gain of Function (GOF)
No gain-of-function mutations have been reported for PAX9.
Dominant Negative (DN)
Some missense mutations (e.g., p.Arg59Trp) may exert dominant-negative effects by interfering with wild-type PAX9 function.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Tooth development pathway (Reactome: R-HSA-5617472)
• PAX9 in craniofacial development (KEGG: hsa05204)
• Transcriptional regulation by PAX family (WikiPathways: WP2859)
Protein Summary
PAX9 is a 341-amino acid transcription factor containing a paired domain and a homeodomain. It binds DNA as a dimer and regulates target genes involved in cell proliferation and differentiation during organogenesis. The protein is predominantly nuclear and is critical for mesenchymal-epithelial signaling in tooth and craniofacial development. Structural studies show that the paired domain recognizes specific DNA sequences, and mutations in this region disrupt binding, leading to developmental defects.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PAX9 Knockout HEK293 Cell Line | EDJ-KQ5405 | Human | 5083 | Details Get a Quote |
| PAX9 Knockout A-549 Cell Line | EDJ-KQ28557 | Human | 5083 | Details Get a Quote |
| PAX9 Knockout HCT 116 Cell Line | EDJ-KQ28558 | Human | 5083 | Details Get a Quote |
| PAX9 Knockout HeLa Cell Line | EDJ-KQ28559 | Human | 5083 | Details Get a Quote |
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