Clinical presentation of congenital hypogonadotropic hypogonadism in males with delayed puberty according to genetic etiology: a systematic review and meta-analysis after reclassification of gene variants

STUDY QUESTION: Which phenotypes can be confidently linked to a genetic etiology in males with congenital hypogonadotropic hypogonadism (CHH) resulting in absent or arrested puberty? SUMMARY ANSWER: In this systematic review and reclassification of the disease-causing potential of gene variants using the recommendations of the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP), we found that absent or arrested puberty in males with CHH was linked to 93 genes, of which 29 were unequivocally disease-causing. WHAT IS KNOWN ALREADY: The number of genes and phenotype characterizations associated with CHH in males has rapidly increased since the advent of next-generation sequencing technologies; however, the quality of the evidence for the interpretation of the causal relationship of gene variants is limited due to the lack of systematic criteria applied to the assessment of the pathogenic potential of the variants. STUDY DESIGN, SIZE, DURATION: We performed a systematic review of original articles indexed in PubMed until 5 October 2022 and using the search terms '(('hypogonadotropic hypogonadism' OR Kallmann) AND (sequencing OR mutation OR variant))' limited to 'Humans' and 'English'. PARTICIPANTS/MATERIALS, SETTING, METHODS: After two investigators undertook the literature search independently, titles and abstracts of all records were reviewed by four of the authors to identify those articles to be included in the full-text review. Clinical data and the association with gene variants were extracted from males with delayed or arrested puberty due to CHH according to the article authors' criteria. Raw sequence variant information was used to reevaluate their pathogenic potential applying the ACMG/AMP guidelines for variant classification with InterVar. Subsequently, we considered the phenotype specificity criteria for sequence variant pathogenicity classification, based on curated genes associated with CHH, and classified patients into three categories: with monogenic disease-causing variants in genes associated with CHH, with variants in genes whose causality is unclear, and with variants that are not disease-causing. MAIN RESULTS AND THE ROLE OF CHANCE: From a total of 1083 records, we included 245 publications with 775 male patients with CHH resulting in absent or arrested puberty, carrying 1001 variants in 93 genes. Gene variants were detected by Sanger sequencing in 61.8% of the cases and by next-generation sequencing (NGS) technologies in the rest. After variant reclassification of causality, 278 individuals were not considered to have a bona fide disease-causing gene variant, and 497 patients were reclassified as carrying at least one disease-causing variant associated with CHH. They carried 503 different disease-causing variants in 29 genes. Spontaneous puberty was absent in 85.5% and arrested in 14.5% of the 497 individuals with CHH carrying bona fide disease-causing variants. In males with absent puberty (complete hypogonadotrophic hypogonadism), FGFR1 and ANOS1 were the most frequently affected genes, accounting for 53.5% of the disease-causing variants. In males with incomplete spontaneous puberty (partial hypogonadotrophic hypogonadism), variants in FGFR1, NR0B1, and GNRHR were found in 70.3% of the cases. Micropenis, cryptorchidism and/or low testicular volume, considered 'red flags' for the diagnosis of CHH, were found in less than 30% of males, with cryptorchidism being more frequently observed in association with variants in FGFR1, ANOS1, KISS1R, SOX10, and GNRH1, and micropenis being more prevalent in patients with variants in TACR3, KISS1R, or GNRH1. Clinical manifestations in non-reproductive organs were found in 39.8% of the patients with bona fide disease-causing variants. LIMITATIONS, REASONS FOR CAUTION: Because we included studies going back to the initial genetic reports of patients with CHH, results obtained by Sanger sequencing represent a significant proportion of the whole sample, which may be biased by the use of a candidate gene strategy. A subanalysis of cases studied by NGS modified the results only slightly. WIDER IMPLICATIONS OF THE FINDINGS: This comprehensive synthesis will help clinicians in the guidance of reverse phenotyping once the precise genetic diagnosis is established, and researchers in the design of functional studies to clarify the role of specific sequence variants in the etiology of male CHH. A genetic etiology of CHH in males with absent or arrested puberty should be considered even in the absence of micropenis, cryptorchidism, and/or low testicular volume. STUDY FUNDING/COMPETING INTEREST(S): This work was partially funded by grants PICT I-A-2018-02972 of Fondo de Promoción Científica y Técnica (FONCYT), PICT A-CAT III2021-73 of Fondo Argentino Sectorial (FONARSEC) and Proyectos de Redes Federales de Alto Impacto 2023 #3 of Ministerio de Ciencia, Tecnología e Innovación, Argentina. Competing interests: None declared. REGISTRATION NUMBER: None declared.