In two independent EA patients, we identified a four-base intronic deletion at chr5:140806031 covering 18 genes of the protocadherin (Pcdhs) families A and B, while the locus is also the exonic region for noncoding RNA, HGB8P. PCDHs are critical for the formation and function of neural circuits, including dendrite arborization, axon outgrowth and targeting, synaptogenesis, and synapse elimination, and epigenetic regulation of clustered PCDHs has been shown to play roles in brain developments. The gene discussed is PCDH11X; the disease is Esophageal atresia.