<b><i>Introduction:</i></b> Gonadotropin-releasing hormone (GnRH) deficiency causes hypogonadotropic hypogonadism (HH), a rare genetic disorder that impairs sexual reproduction. HH can be due to defective GnRH-secreting neuron development or function and may be associated with other clinical signs in overlapping genetic syndromes. With most of the cases being idiopathic, genetics underlying HH is still largely unknown. <b><i>Objective:</i></b> To assess the contribution of mutated Semaphorin 3G (<i>SEMA3G</i>) in the onset of a syndromic form of HH, characterized by intellectual disability and facial dysmorphic features. <b><i>Method:</i></b> By combining homozygosity mapping with exome sequencing, we identified a novel variant in the <i>SEMA3G</i> gene. We then applied mouse as a model organism to examine <i>SEMA3G</i>expression and its functional requirement in vivo. Further, we applied homology modelling in silico and cell culture assays in vitro to validate the pathogenicity of the identified gene variant. <b><i>Results:</i></b> We found that (i) SEMA3G is expressed along the migratory route of GnRH neurons and in the developing pituitary, (ii) SEMA3G affects GnRH neuron development, but is redundant in the adult hypothalamic-pituitary-gonadal axis, and (iii) mutated SEMA3G alters binding properties in silico and in vitro to its PlexinA receptors and attenuates its effect on the migration of immortalized GnRH neurons. <b><i>Conclusion:</i></b> In silico, in vitro, and in vivo models revealed that SEMA3G regulates GnRH neuron migration and that its mutation affecting receptor selectivity may be responsible for the HH-related defects.