Mutations of the GnRH receptor have been recognized as a cause of familial gonadotropin deficiency. We here identify and functionally characterize a novel human GnRH receptor variant bearing an Ala(171)Thr substitution located at transmembrane helix 4 (TMH4). The affected kindred displays severe hypogonadotropic hypogonadism. After in vitro expression in human embryonic kidney 293T cells, the Ala(171)Thr mutant GnRH receptor exhibited a lack of phospholipase C activity in signal transduction. Specific receptor binding of (125)I-labeled GnRH ligand was undetectable in Ala(171)Thr GnRH receptor-transfected cells. Molecular modeling and dynamic simulation of the Ala(171)Thr GnRH receptor suggests the introduction of a stable hydrogen bond between residue Thr(171) and Tyr(119) side-chains at a distance of 2 A. Although spatially distant from the GnRH ligand-binding site, this hydrogen bond impedes conformational mobility of the TMH3 and TMH4 domains required for sequential ligand binding and receptor activation, thus stabilizing the GnRH receptor in its inactive conformation. Receptor structure modeling and functional data provide a comprehensive molecular view of how mutation Ala(171)Thr causes a complete loss of GnRH receptor function.