SummaryKallmann syndrome (KS) is a genetically heterogeneous condition characterized by hypogonadotropic hypogonadism with coexisting anosmia or hyposmia along with potential other phenotypic abnormalities depending on the specific genetic mutation involved. Several genetic mutations have been described to cause KS. TheANOS1(KAL1)gene is responsible for 8% of mutations causing KS. A 17-year-old male presented to our clinic with delayed puberty and hyposmia, along with a family history suggestive of hypogonadism in his maternal uncle. Genetic testing for KS revealed complete exon 3 deletion in theANOS1gene. To the best of our knowledge, this specific mutation has not been previously described in the literature.Learning pointsMissense and frameshift mutations in theKAL1orANOS1gene located in the X chromosome are responsible for 8% of all known genetic mutations of Kallmann syndrome.Exon 3 deletion is one of theANOS1gene is a novel mutation, not reported before.Targeted gene sequencing for hypogonadotropic hypogonadism can be employed based on the phenotypic presentation.