Congenital heart diseases (CHD) occur in nearly 1% of all live births and are the major cause of infant mortality and morbidity. Although an improved understanding of the genetic causes of CHD would provide insight into the underlying pathobiology, the genetic etiology of most CHD remains unknown. Here we show that mutations in the gene encoding the transcription factor GATA6 cause CHD characteristic of a severe form of cardiac outflow tract (OFT) defect, namely persistent truncus arteriosus (PTA). Two different GATA6 mutations were identified by systematic genetic analysis using DNA from patients with PTA. Genes encoding the neurovascular guiding molecule semaphorin 3C (SEMA3C) and its receptor plexin A2 (PLXNA2) appear to be regulated directly by GATA6, and both GATA6 mutant proteins failed to transactivate these genes. Transgenic analysis further suggests that, in the developing heart, the expression of SEMA3C in the OFT/subpulmonary myocardium and PLXNA2 in the cardiac neural crest contributing to the OFT is dependent on GATA transcription factors. Together, our data implicate mutations in GATA6 as genetic causes of CHD involving OFT development, as a result of the disruption of the direct regulation of semaphorin-plexin signaling.congenital heart disease ͉ persistent truncus arteriosus ͉ cardiac neural crest C ongenital heart diseases (CHD) constitute a major percentage of clinically significant birth defects with an estimated prevalence of 4-10 per 1,000 live infants (1). Cardiac outflow tract (OFT) defects are estimated to account for approximately 30% of CHD (2) and usually require an intervention during the first year of life. A variety of OFT defects results from disturbance of the morphogenetic patterning of the anterior pole of the heart, which is essential for the establishment of separate systemic and pulmonary circulations in higher vertebrates. Persistent truncus arteriosus (PTA), which is attributed to missing septation of the OFT, is recognized as the most severe phenotype of OFT defect, and is often associated with an unfavorable prognosis because complete surgical repair is not always possible (3). Although an improved understanding of possible genetic causes would provide insight into the pathogenesis of CHD and allow for better assessment of disease risk, prenatal diagnosis, and critical information for disease prevention, the etiology of most CHD, including OFT defects, remains unknown because of the multifactorial nature of the diseases (4-6).Based on animal studies, it appears that abnormal development of cardiac neural crest (CNC) cells, an ectoderm-derived cell lineage, contributes significantly to the pathology of OFT defects (7-12). During early embryogenesis, CNC cells arise from the dorsal neural tube and migrate ventrally as mesenchymal cells to populate the OFT, where they coalesce to form the aorticopulmonary septum, which divides the single truncus arteriosus (embryonic OFT) into the aorta and pulmonary artery, resulting in the establishment of separate systemic and pulmonary c...