Homeobox genes are expressed during embryonic development in a spatially and temporally regulated manner to control the developing body of an embryo along the anterior-posterior axis.  These genes are found in clusters named A, B, C, and D on four separate chromosomes, and they encode a group of transcription factors.  The HOXA1 gene belongs to the “A” cluster on chromosome 7 and it encodes a DNA-binding transcription factor, with potential roles in regulating gene expression, morphogenesis, and differentiation.  The specific role of this transcription factor is thought to revolve around ensuring the correct placement of hindbrain segments in the proper location along the anterior-posterior axis during development.

Many clinically relevant mutations were identified in the HOXA1 gene.  Loss of function mutations in HOXA1 gene were implicated in two clinically overlapping autosomal recessive syndromes; the Bosley-Salih-Alorainy Syndrome (BSAS) and the Athabascan Brainstem Dysgenesis Syndrome (ABDS).