Targeted Resequencing of 29 Candidate Genes and Mouse Expression Studies Implicate ZIC3 and FOXF1 in Human VATER/VACTERL Association

Hum Mutat. 2015 Dec;36(12):1150-4. doi: 10.1002/humu.22859. Epub 2015 Sep 14.


The VATER/VACTERL association describes the combination of congenital anomalies including vertebral defects, anorectal malformations, cardiac defects, tracheoesophageal fistula with or without esophageal atresia, renal malformations, and limb defects. As mutations in ciliary genes were observed in diseases related to VATER/VACTERL, we performed targeted resequencing of 25 ciliary candidate genes as well as disease-associated genes (FOXF1, HOXD13, PTEN, ZIC3) in 123 patients with VATER/VACTERL or VATER/VACTERL-like phenotype. We detected no biallelic mutation in any of the 25 ciliary candidate genes; however, identified an identical, probably disease-causing ZIC3 missense mutation (p.Gly17Cys) in four patients and a FOXF1 de novo mutation (p.Gly220Cys) in a further patient. In situ hybridization analyses in mouse embryos between E9.5 and E14.5 revealed Zic3 expression in limb and prevertebral structures, and Foxf1 expression in esophageal, tracheal, vertebral, anal, and genital tubercle tissues, hence VATER/VACTERL organ systems. These data provide strong evidence that mutations in ZIC3 or FOXF1 contribute to VATER/VACTERL.

Keywords: FOXF1; VATER/VACTERL association; ZIC3; cilia.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Anal Canal / abnormalities*
  • Animals
  • Anus, Imperforate / diagnosis
  • Anus, Imperforate / genetics*
  • Cilia / genetics
  • Computational Biology / methods
  • DNA Mutational Analysis
  • Esophagus / abnormalities*
  • Female
  • Forkhead Transcription Factors / genetics*
  • Forkhead Transcription Factors / metabolism
  • Genetic Association Studies*
  • Genotype
  • Heart Defects, Congenital / diagnosis
  • Heart Defects, Congenital / genetics*
  • High-Throughput Nucleotide Sequencing
  • Homeodomain Proteins / genetics*
  • Homeodomain Proteins / metabolism
  • Humans
  • Immunohistochemistry
  • Kidney / abnormalities*
  • Limb Deformities, Congenital / diagnosis
  • Limb Deformities, Congenital / genetics*
  • Male
  • Mice
  • Mutation
  • Phenotype
  • Radius / abnormalities*
  • Spine / abnormalities*
  • Trachea / abnormalities*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism


  • FOXF1 protein, human
  • Forkhead Transcription Factors
  • Foxf1 protein, mouse
  • Homeodomain Proteins
  • Transcription Factors
  • ZIC3 protein, human
  • Zic3 protein, mouse

Supplementary concepts

  • VACTERL association
  • VATER association