Neuroligin-3 is a member of the neuroligin family of neuronal cell surface proteins. Neuroligins may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene, but their full length sequences have not been determined.

NLGN3 encodes an 828-amino acid protein that shares 98.5% sequence identity with rat NL3. Northern blot analysis detected a 2.4-kb NLGN3 transcript in pancreas, a 7.5-kb transcript in skeletal and cardiac muscle, and a 4-kb transcript throughout the adult human central nervous system and fetal brain.