HOXA1: Homeobox A1 – A Master Regulator of Hindbrain Development and Craniofacial Patterning
Comprehensive genomic and clinical resource for HOXA1, including gene structure, expression, disease associations, and mutation landscape.
Gene Information Card
| Symbol | HOXA1 |
|---|---|
| Full Name | Homeobox A1 |
| Gene Type | Protein-coding |
| Chromosomal Location | 7p15.2 |
| NCBI Gene ID | 3198 ncbi.nlm.nih.gov/gene/3198 |
| Ensembl ID | ENSG00000105991 |
| UniProt ID | P49639 |
| OMIM ID | 142955 |
| HGNC ID | 5099 |
| Aliases | HOX1, HOX1F, MGC45260 |
Description
HOXA1 (Homeobox A1) is a protein-coding gene belonging to the homeobox family of transcription factors. It encodes a nuclear protein with a conserved homeodomain that binds DNA and regulates gene expression during embryonic development. HOXA1 is critical for hindbrain segmentation, cranial nerve development, and patterning of the inner ear and craniofacial structures. Mutations in HOXA1 cause autosomal recessive Bosley-Salih-Alorainy syndrome (BSAS) and Athabaskan brainstem dysgenesis syndrome (ABDS).
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Bosley-Salih-Alorainy syndrome (BSAS) | Loss-of-function mutations in HOXA1 disrupt hindbrain segmentation, leading to Duane anomaly, hearing loss, and craniofacial defects. | OMIM #601536; multiple homozygous truncating variants reported. |
| Athabaskan brainstem dysgenesis syndrome (ABDS) | Same loss-of-function mechanism as BSAS; founder mutation c.175C>T (p.Arg59Ter) in Athabaskan populations. | OMIM #601536; ClinVar; population genetics studies. |
| Congenital horizontal gaze palsy with progressive scoliosis (HGPPS) | Differential diagnosis; HOXA1 mutations not causative but related hindbrain malformation. | OMIM #617542; literature review. |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain (cerebellum) | 0.3 | Low |
| Brain (cerebral cortex) | 0.1 | Not detected |
| Heart | 0.0 | Not detected |
| Liver | 0.0 | Not detected |
| Kidney | 0.0 | Not detected |
| Testis | 0.0 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| K562 (leukemia) | 0.0 | Not expressed |
| HeLa (cervical) | 0.0 | Not expressed |
| HepG2 (liver) | 0.0 | Not expressed |
| A549 (lung) | 0.0 | Not expressed |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.175C>T (p.Arg59Ter) | Nonsense | Founder in Athabaskan; rare globally | Loss of function; truncation before homeodomain |
| c.83G>A (p.Trp28Ter) | Nonsense | Rare | Loss of function; premature stop |
| c.205C>T (p.Arg69Ter) | Nonsense | Rare | Loss of function; truncation |
| c.404_405del (p.Val135Alafs*5) | Frameshift | Rare | Loss of function; frameshift and premature stop |
Mutation functional classification
Loss of Function (LOF)
All reported pathogenic HOXA1 mutations are loss-of-function (nonsense, frameshift, splice-site) leading to haploinsufficiency or complete loss of protein function. No gain-of-function or dominant-negative mutations have been described.
Gain of Function (GOF)
None reported.
Dominant Negative (DN)
None reported.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Retinoic acid signaling pathway
• Hox gene anterior-posterior patterning
• Hindbrain segmentation (rhombomere formation)
Protein Summary
HOXA1 is a 335-amino-acid transcription factor containing a homeodomain DNA-binding motif (residues 186–245). It localizes to the nucleus and regulates target genes involved in hindbrain segmentation, cranial nerve specification, and inner ear development. The protein is highly conserved across vertebrates. Loss of function leads to severe developmental syndromes affecting the brainstem, eyes, ears, and craniofacial structures.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| HOXA11 Knockout HEK293 Cell Line | EDJ-KQ2931 | Human | 3207 | Details Get a Quote |
| HOXA1 Knockout HEK293 Cell Line | EDJ-KQ4892 | Human | 3198 | Details Get a Quote |
| HOXA10 Knockout HEK293 Cell Line | EDJ-KQ4907 | Human | 3206 | Details Get a Quote |
| HOXA13 Knockout HEK293 Cell Line | EDJ-KQ4916 | Human | 3209 | Details Get a Quote |
| HOXA11 Knockout A-549 Cell Line | EDJ-KQ24042 | Human | 3207 | Details Get a Quote |
| HOXA11 Knockout HCT 116 Cell Line | EDJ-KQ24043 | Human | 3207 | Details Get a Quote |
| HOXA11 Knockout HeLa Cell Line | EDJ-KQ22674 | Human | 3207 | Details Get a Quote |
| HOXA1 Knockout A-549 Cell Line | EDJ-KQ27706 | Human | 3198 | Details Get a Quote |
| HOXA1 Knockout HCT 116 Cell Line | EDJ-KQ27707 | Human | 3198 | Details Get a Quote |
| HOXA10 Knockout A-549 Cell Line | EDJ-KQ27736 | Human | 3206 | Details Get a Quote |
| HOXA10 Knockout HCT 116 Cell Line | EDJ-KQ27737 | Human | 3206 | Details Get a Quote |
| HOXA10 Knockout HeLa Cell Line | EDJ-KQ27738 | Human | 3206 | Details Get a Quote |
| HOXA13 Knockout A-549 Cell Line | EDJ-KQ27751 | Human | 3209 | Details Get a Quote |
| HOXA13 Knockout HCT 116 Cell Line | EDJ-KQ27752 | Human | 3209 | Details Get a Quote |
| HOXA13 Knockout HeLa Cell Line | EDJ-KQ27753 | Human | 3209 | Details Get a Quote |
Displaying Records 1 To 15 Of 16 Records
