Sequence variants in the HLX gene at chromosome 1q41-1q42 in patients with diaphragmatic hernia

Clin Genet. 2009 May;75(5):429-39. doi: 10.1111/j.1399-0004.2009.01182.x.


Congenital diaphragmatic hernia (CDH) is a common birth defect for which few causative genes have been identified. Several candidate regions containing genes necessary for normal diaphragm development have been identified, including a 4-5 Mb deleted region at chromosome 1q41-1q42 from which the causative gene(s) has/have not been cloned. We selected the HLX gene from this interval as a candidate gene for CDH, as the Hlx homozygous null mouse has been reported to have diaphragmatic defects and the gene was described as being expressed in the murine diaphragm. We re-sequenced HLX in 119 CDH patients and identified four novel single nucleotide substitutions that predict amino acid changes: p.S12F, p.S18L, p.D173Y and p.A235V. These sequence alterations were all present in patients with isolated CDH, although patients with both isolated CHD and CDH with additional anomalies were studied. The single-nucleotide substitutions were absent in more than 186 control chromosomes. In-situ hybridization studies confirmed expression of Hlx in the developing murine diaphragm at the site of the junction of the diaphragm and the liver. Although functional studies to determine if these novel sequence variants altered the inductive activity of Hlx on the alpha-smooth muscle actin and SM22alpha promoters showed no significant differences between the variants and wild-type Hlx, sequence variants in HLX may still be relevant in the pathogenesis of CDH in combination with additional genetic and environmental factors.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Chromosomes, Human, Pair 1 / genetics*
  • Embryo, Mammalian
  • Genetic Variation*
  • Hernia, Diaphragmatic / genetics*
  • Homeodomain Proteins / genetics*
  • Humans
  • In Situ Hybridization
  • Karyotyping
  • Mice
  • Molecular Sequence Data
  • Phenotype
  • Sequence Analysis, DNA
  • Transcription Factors / genetics*


  • HLX protein, human
  • Homeodomain Proteins
  • Transcription Factors