Purpose Idiopathic hypogonadotropic hypogonadism (IHH) is characterized by impaired reproductive maturation, and approximately half of all cases lack an identified genetic cause. We investigated the genetic basis of IHH in two large cohorts to identify novel disease-causing genes.

Methods We analyzed exome and genome sequencing data from 1,822 patients with IHH from two independent cohorts. Rare variants were filtered using pedigree-informed inheritance models. PLEKHA6 expression in the postmortem human hypothalamus were tested at the mRNA and protein level. Functional studies assessed kisspeptin secretion in cell-based assays.

Results We identified 18 distinct PLEKHA6 variants in 24 patients from 20 unrelated families (1.3% of cohort). Variants segregated with disease under autosomal recessive and autosomal dominant (with variable penetrance) inheritance patterns. PLEKHA6 was robustly expressed in the hypothalamus and showed clear colocalization with neurokinin B, which served as the marker for the GnRH pulse generator. Functional studies demonstrated that patient variants significantly impaired kisspeptin secretion.

Conclusion PLEKHA6 is a novel IHH gene and the first reported regulator of kisspeptin secretion from the kisspeptin-neurokinin B-dynorphin (KNDy) neurons, which have recently been established as the GnRH pulse generator. These findings establish impaired kisspeptin release as a new disease mechanism in IHH and highlight the critical role of neuropeptide trafficking in reproductive function.

Stephanie Seminara has a financial interest in SeNa Therapeutics, which is developing treatments for reproductive disorders. Dr. Seminara s interests were reviewed and are managed by MGH and Mass General Brigham in accordance with their conflict-of-interest policies. The rest of the authors declare no conflicts of interest.

S.B.S. is supported by grants P50HD104224 (National Center for Translational Research in Reproduction and Infertility) and R37HD043341 from the Eunice Kennedy Shriver National Institute of Child Health and Development and grant R01FD007843 from the FDA. She is also supported by the Gates Foundation.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Human experimental protocols were approved by the ethics committee of the Cukurova University Faculty of Medicine and the institutional review board of Mass General Brigham for the Pediatric Endocrinology cohort and the institutional review board of Mass General Brigham for the Harvard Reproductive Endocrine Unit cohort.

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Anonymized genetic variant data will be deposited in ClinVar. Additional data supporting the findings of this study are available from the corresponding author upon reasonable request.

https://www.ncbi.nlm.nih.gov/clinvar/