This study used transcriptomic profiling of rodent GnRH neurons and exome sequencing from two human patients with gonadotropin-releasing hormone deficiency (GD) to identify candidate disease genes. The central result was the discovery that loss-of-function variants in the autism-linked gene *NLGN3* were found in two unrelated GD patients and that NLGN3 protein promotes neurite growth in GnRH cells, suggesting a shared genetic mechanism between GD and autism.