Most of the time, this defect occurs spontaneously. Genetic disorders, and teratogens (viruses, metabolic imbalance, and industrial or pharmacological agents) have been associated as possible causes. Up to 50% (varies in studies) of cases are associated with chromosome 22q11 deletions (DiGeorge Syndrome). The neural crest, specifically a population known as the cardiac neural crest, directly contributes to the aorticopulmonary septum.^[1][2]

Microablation of the cardiac neural crest in developing chick embryos and genetic anomalies affecting this population of cells in rodents results in persistent truncus arteriosus.^[3][4][5]

Numerous perturbations affecting the cardiac neural crest have been associated with persistent truncus arteriosus, some of which include growth factors (fibroblast growth factor 8 and bone morphogenetic protein), transcription factors (T-box, Pax, Nkx2-5, GATA-6, and Forkhead), and gap junction proteins (Connexin). The cardiac neural crest also contributes the smooth muscle of the great arteries.