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The two common OFC phenotypes are cleft lip with\/without cleft palate (CL\/P) and cleft palate only (CPO). In this study, we searched for penetrant CL\/P genes, by evaluating de novo copy number variants (CNV) from an exome sequencing dataset of 50 nonsyndromic patient-parent trios. We detected a heterozygous 86\u2009kb de novo deletion affecting exons 4\u201311 of <jats:italic>ZFHX4<\/jats:italic>, a gene previously associated with OFC. Genetic and phenotypic data from our in-house and the AGORA cohort (710 and 229 individuals with nonsyndromic CL\/P) together with literature and database reviews demonstrate that <jats:italic>ZFHX4<\/jats:italic> variants can lead to both nonsyndromic and syndromic forms not only of CL\/P but also CPO. Expression analysis in published single-cell RNA-sequencing data (mouse embryo, zebrafish larva) at relevant time-points support an important role of <jats:italic>Zfhx4<\/jats:italic>\/<jats:italic>zfhx4<\/jats:italic> in craniofacial development. To characterize the role of <jats:italic>zfhx4<\/jats:italic> in zebrafish craniofacial development, we knocked out\/down the zebrafish orthologue. Cartilage staining of the <jats:italic>zfhx4<\/jats:italic> CRISPR F0 knockout and morpholino knockdown at 4 days post-fertilization showed an underdeveloped and abnormally shaped ethmoid plate and cartilaginous jaw (resembling micrognathia). While there is evidence for the dominant inheritance of <jats:italic>ZFHX4<\/jats:italic> variants in OFC, we here present a patient with a possible recessive inheritance. In conclusion, <jats:italic>ZFHX4<\/jats:italic> has a highly heterogeneous phenotypic spectrum and variable mode of inheritance. Our data highlight that <jats:italic>ZFHX4<\/jats:italic> should be considered in genetic testing in patients with nonsyndromic clefting.<\/jats:p>","DOI":"10.1038\/s41431-024-01775-9","type":"journal-article","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T21:51:31Z","timestamp":1734645091000},"page":"595-606","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models"],"prefix":"10.1038","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9836-554X","authenticated-orcid":false,"given":"Nina","family":"Ishorst","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0128-6263","authenticated-orcid":false,"given":"Selina","family":"H\u00f6lzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4993-1378","authenticated-orcid":false,"given":"Carola","family":"Greve","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00d6znur","family":"Yilmaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Lindenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Lambertz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitriy","family":"Drichel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Berina","family":"Zametica","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrico","family":"Mingardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeshurun C.","family":"Kalanithy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khadija","family":"Channab","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duygu","family":"Kibris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina","family":"Henne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franziska","family":"Degenhardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Siewert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Dixon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa","family":"Kruse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9250-027X","authenticated-orcid":false,"given":"Edwin","family":"Ongkosuwito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0139-8239","authenticated-orcid":false,"given":"Katta M.","family":"Girisha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5700-7789","authenticated-orcid":false,"given":"Shruti","family":"Pande","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Nowak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregor","family":"Hagelueken","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7718-5002","authenticated-orcid":false,"given":"Matthias","family":"Geyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carine","family":"Carels","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9519-966X","authenticated-orcid":false,"given":"Iris A. 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Furthermore, K.U.L. is a co-founder of LAMPseq Diagnostics GmbH. Although past and current clients might include biotech, life science, and pharma companies, the services are not related to the presented work and all authors are unaware of any possible competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Written informed consent was obtained from all participants, or the respective parents\/legal guardians, prior to inclusion. The study was approved by the ethics committee of the Medical Faculty of the University of Bonn (ethics approval number 295\/14, last dated June 20th, 2022). Animal husbandry and experimental setups were in accordance with European Legislation for the Protection of Animals used for Scientific Purposes (Directive 2010\/62\/EU). National law exempts all zebrafish experiments conducted at larval stages up to 5 dpf, before larvae begin to feed, from ethical approval.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}