Association study of PHOX2B as a candidate gene for Hirschsprung's disease

Gut. 2003 Apr;52(4):563-7. doi: 10.1136/gut.52.4.563.


Background: Hirschsprung's disease (HSCR) is a congenital disorder characterised by an absence of ganglion cells in the nerve plexuses of the lower digestive tract. Manifestation of the disease has been linked to mutations in genes that encode the crucial signals for the development of the enteric nervous system-the RET and EDNRB signalling pathways. The Phox2b gene is involved in neurogenesis and regulates Ret expression in mice, in which disruption of the Phox2b results in a HSCR-like phenotype.

Aims: To investigate the contribution of PHOX2B to the HSCR phenotype.

Methods: Using polymerase chain reaction amplification and direct sequencing, we screened PHOX2B coding regions and intron/exon boundaries for mutations and polymorphisms in 91 patients with HSCR and 71 ethnically matched controls. Seventy five HSCR patients with no RET mutations were independently considered. Haplotype and genotype frequencies were compared using the standard case control statistic.

Results: Sequence analysis revealed three new polymorphisms: two novel single nucleotide polymorphisms (A-->G(1364); A-->C(2607)) and a 15 base pair deletion (DEL(2609)). Statistically significant differences were found for A-->G(1364). Genotypes comprising allele G were underrepresented in patients (19% v 36%; chi(2)=9.30; p=0.0095 and 22% v 36%; chi(2)=7.38; p=0.024 for patients with no RET mutations). Pairwise linkage disequilibrium (LD) analysis revealed no LD between physically close polymorphisms indicating a hot spot for recombination in exon 3.

Conclusion: The PHOX2B A-->G(1364) polymorphism is associated with HSCR. Whether it directly contributes to disease susceptibility or represents a marker for a locus in LD with PHOX2B needs further investigation. Our findings are in accordance with the involvement of PHOX2B in the signalling pathways governing the development of enteric neurones.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Case-Control Studies
  • DNA Mutational Analysis
  • Genetic Predisposition to Disease*
  • Genotype
  • Haplotypes
  • Hirschsprung Disease / genetics*
  • Homeodomain Proteins / genetics*
  • Humans
  • Linkage Disequilibrium
  • Molecular Sequence Data
  • Nerve Tissue Proteins / genetics
  • Polymerase Chain Reaction / methods
  • Polymorphism, Genetic
  • Transcription Factors / genetics*


  • Homeodomain Proteins
  • NBPhox protein
  • Nerve Tissue Proteins
  • Transcription Factors

Associated data

  • GENBANK/AB015671
  • GENBANK/AF117979