Mutations in the paired-like homeobox 2b (PHOX2B) gene are associated with congenital central hypoventilation syndrome (CCHS), which is a rare condition in which both autonomic dysregulation with hypoventilation and an enteric neuropathy may occur. The majority of CCHS patients have a polyalanine repeat mutation (PARM) in PHOX2B, but a minority of patients have non-polyalanine repeat mutations (NPARM), some of which have been localized to exon 1. A PHOX2B-Y14X nonsense mutation previously generated in a human pluripotent stem cell (hPSC) line results in an N-terminus truncated product missing the first 17 or 20 amino acids, possibly due to translational reinitiation at an alternate ATG start site. This N-terminal truncation in the PHOX2B protein results in the loss of two key phosphorylation residues. Though the deletion does not affect the potential for PHOX2B(Y14X/Y14X) mutant hPSC to differentiate into enteric neural crest cells (ENCC) in culture, it impedes in vivo development of neurons in an in vivo model of human aganglionic small intestine.