Congenital heart defects (CHD) are associated with the recurrent 10q22q23 deletion syndrome and with partially overlapping distal 10q23.2.q23.31 microdeletions. We report on a de novo intragenic deletion of the BMPR1A gene in a normally developing adolescent boy with short stature, delayed puberty, facial dysmorphism and an atrioventricular septal defect. Based on this finding, complemented with computational prioritization data and molecular evidence in literature, the critical region for CHD on 10q23 can be downsized to a single gene, BMPR1A. Although loss-of-function mutations in BMPR1A typically result in juvenile polyposis syndrome, none of the patients with the typical 10q22q23 microdeletion syndrome, comprising this gene, were reported to have juvenile polyposis thus far. We reason that, even in the absence of juvenile polyposis syndrome, sequencing and copy number analysis of BMPR1A should be considered in patients with (atrioventricular) septal defects, especially when associated with facial dysmorphism and anomalous growth.