{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T17:40:46Z","timestamp":1768412446607,"version":"3.49.0"},"reference-count":24,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2024,11,10]],"date-time":"2024-11-10T00:00:00Z","timestamp":1731196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Portuguese Foundation for Science and Technology","award":["PTDC\/SAU-GMG\/098419\/2008"],"award-info":[{"award-number":["PTDC\/SAU-GMG\/098419\/2008"]}]},{"name":"Portuguese Foundation for Science and Technology","award":["UIDB\/00709\/2020"],"award-info":[{"award-number":["UIDB\/00709\/2020"]}]},{"name":"Portuguese Foundation for Science and Technology","award":["2020.04924.BD"],"award-info":[{"award-number":["2020.04924.BD"]}]},{"name":"Portuguese Foundation for Science and Technology","award":["CEECINST\/00016\/2021\/CP2828\/CT0002"],"award-info":[{"award-number":["CEECINST\/00016\/2021\/CP2828\/CT0002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Kallmann syndrome is a rare disorder characterized by hypogonadotropic hypogonadism and an impaired sense of smell (anosmia or hyposmia) caused by congenital defects in the development of the gonadotropin-releasing hormone (GnRH) and olfactory neurons. Mutations in several genes have been associated with Kallmann syndrome. However, genetic testing of this disorder often reveals variants of uncertain significance (VUS) that remain uninterpreted without experimental validation. The aim of this study was to analyze the functional consequences of a heterozygous missense VUS in the CHD7 gene (c.4354G&gt;T, p.Val1452Leu), in a patient with Kallmann syndrome with reversal of hypogonadism. The variant, located in the first nucleotide of exon 19, was analyzed using minigene assays to determine its effect on ribonucleic acid (RNA) splicing. These showed that the variant generates two different transcripts: a full-length transcript with the missense change (p.Val1452Leu), and an abnormally spliced transcript lacking exon 19. The latter results in an in-frame deletion (p.Val1452_Lys1511del) that disrupts the helicase C-terminal domain of the CHD7 protein. The variant was reclassified as likely pathogenic. These findings demonstrate that missense variants can exert more extensive effects beyond simple amino acid substitutions and underscore the critical role of functional analyses in VUS reclassification and genetic diagnosis.<\/jats:p>","DOI":"10.3390\/ijms252212061","type":"journal-article","created":{"date-parts":[[2024,11,11]],"date-time":"2024-11-11T03:52:07Z","timestamp":1731297127000},"page":"12061","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Kallmann Syndrome: Functional Analysis of a CHD7 Missense Variant Shows Aberrant RNA Splicing"],"prefix":"10.3390","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6280-2664","authenticated-orcid":false,"given":"Josianne Nunes","family":"Carri\u00e7o","sequence":"first","affiliation":[{"name":"CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilh\u00e3, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6659-1200","authenticated-orcid":false,"given":"Catarina In\u00eas","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilh\u00e3, Portugal"}]},{"given":"Jos\u00e9 Maria","family":"Arag\u00fc\u00e9s","sequence":"additional","affiliation":[{"name":"Servi\u00e7o de Endocrinologia, Diabetes e Metabolismo, Hospital de Santa Maria, Centro Hospitalar Universit\u00e1rio Lisboa Norte, 1649-028 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9326-8900","authenticated-orcid":false,"given":"Manuel Carlos","family":"Lemos","sequence":"additional","affiliation":[{"name":"CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilh\u00e3, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/nrendo.2015.112","article-title":"Expert consensus document: European Consensus Statement on congenital hypogonadotropic hypogonadism\u2014Pathogenesis, diagnosis and treatment","volume":"11","author":"Boehm","year":"2015","journal-title":"Nat. Rev. Endocrinol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1210\/er.2018-00116","article-title":"Clinical Management of Congenital Hypogonadotropic Hypogonadism","volume":"40","author":"Young","year":"2019","journal-title":"Endocr. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/s00439-020-02148-0","article-title":"Molecular genetic diagnostics of hypogonadotropic hypogonadism: From panel design towards result interpretation in clinical practice","volume":"140","author":"Butz","year":"2021","journal-title":"Hum. Genet."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"101599","DOI":"10.1016\/j.beem.2021.101599","article-title":"Genetics of congenital central hypogonadism","volume":"36","author":"Grinspon","year":"2021","journal-title":"Best Pract. Res. Clin. Endocrinol. Metab."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"111334","DOI":"10.1016\/j.mce.2021.111334","article-title":"Genetics of hypogonadotropic Hypogonadism-Human and mouse genes, inheritance, oligogenicity, and genetic counseling","volume":"534","author":"Louden","year":"2021","journal-title":"Mol. Cell. Endocrinol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"994","DOI":"10.7326\/M21-4109","article-title":"The Challenge of Genetic Variants of Uncertain Clinical Significance : A Narrative Review","volume":"175","author":"Burke","year":"2022","journal-title":"Ann. Intern. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1016\/j.tig.2015.05.009","article-title":"Functional Insights into Chromatin Remodelling from Studies on CHARGE Syndrome","volume":"31","author":"Basson","year":"2015","journal-title":"Trends Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/ng1407","article-title":"Mutations in a new member of the chromodomain gene family cause CHARGE syndrome","volume":"36","author":"Vissers","year":"2004","journal-title":"Nat. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/j.ajhg.2008.09.005","article-title":"Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome","volume":"83","author":"Kim","year":"2008","journal-title":"Am. J. Hum. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"E2138","DOI":"10.1210\/jc.2014-2110","article-title":"The prevalence of CHD7 missense versus truncating mutations is higher in patients with Kallmann syndrome than in typical CHARGE patients","volume":"99","author":"Marcos","year":"2014","journal-title":"J. Clin. Endocrinol. Metab."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1597","DOI":"10.1038\/s41598-018-38178-y","article-title":"High frequency of CHD7 mutations in congenital hypogonadotropic hypogonadism","volume":"9","author":"Goncalves","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1038\/nrg2164","article-title":"Splicing in disease: Disruption of the splicing code and the decoding machinery","volume":"8","author":"Wang","year":"2007","journal-title":"Nat. Rev. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s13353-019-00493-z","article-title":"Correction to: Splicing mutations in human genetic disorders: Examples, detection, and confirmation","volume":"60","author":"Abramowicz","year":"2019","journal-title":"J. Appl. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"4396","DOI":"10.1093\/nar\/gkr026","article-title":"AG-dependent 3\u2019-splice sites are predisposed to aberrant splicing due to a mutation at the first nucleotide of an exon","volume":"39","author":"Fu","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3812","DOI":"10.1093\/nar\/gkg509","article-title":"SIFT: Predicting amino acid changes that affect protein function","volume":"31","author":"Ng","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"eadg7492","DOI":"10.1126\/science.adg7492","article-title":"Accurate proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","author":"Cheng","year":"2023","journal-title":"Science"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1056\/NEJMoa066494","article-title":"Reversal of idiopathic hypogonadotropic hypogonadism","volume":"357","author":"Raivio","year":"2007","journal-title":"N. Engl. J. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/S2213-8587(24)00028-7","article-title":"Classes and predictors of reversal in male patients with congenital hypogonadotropic hypogonadism: A cross-sectional study of six international referral centres","volume":"12","author":"Dwyer","year":"2024","journal-title":"Lancet Diabetes Endocrinol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nmeth0810-575","article-title":"MutationTaster evaluates disease-causing potential of sequence alterations","volume":"7","author":"Schwarz","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","article-title":"The mutational constraint spectrum quantified from variation in 141,456 humans","volume":"581","author":"Karczewski","year":"2020","journal-title":"Nature"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/978-1-62703-980-2_18","article-title":"Cell-based splicing of minigenes","volume":"1126","author":"Smith","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: Homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/22\/12061\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:29:34Z","timestamp":1760113774000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/22\/12061"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,10]]},"references-count":24,"journal-issue":{"issue":"22","published-online":{"date-parts":[[2024,11]]}},"alternative-id":["ijms252212061"],"URL":"https:\/\/doi.org\/10.3390\/ijms252212061","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,10]]}}}