. 2025 Jun 5;112(6):1388-1414.

doi: 10.1016/j.ajhg.2025.04.008. Epub 2025 May 13.

Loss of function of the zinc finger homeobox 4 gene, ZFHX4, underlies a neurodevelopmental disorder

María Del Rocío Pérez Baca¹, María Palomares-Bralo², Michiel Vanhooydonck¹, Lisa Hamerlinck¹, Eva D'haene¹, Sebastian Leimbacher¹, Eva Z Jacobs¹, Laurenz De Cock³, Erika D'haenens¹, Annelies Dheedene¹, Zoë Malfait¹, Lies Vantomme¹, Ananilia Silva⁴, Kathleen Rooney⁵, Xiaonan Zhao⁶, Amir Hossein Saeidian⁶, Nichole Marie Owen⁶, Fernando Santos-Simarro⁷, Roser Lleuger-Pujol⁸, Sixto García-Miñaúr², Itsaso Losantos-García⁹, Björn Menten¹, Gaia Gestri¹⁰, Nicola Ragge¹¹; ZFHX4 consortium; Bekim Sadikovic¹², Elke Bogaert¹, Kris Vleminckx¹³, Thomas Naert¹³, Delfien Syx¹, Bert Callewaert¹⁴, Sarah Vergult¹⁵

Collaborators, Affiliations

Collaborators

ZFHX4 consortium:
Abbey Scott, Alejandro Iglesias, Allyn McConkie-Rosell, Amy Kritzer, Ana Boto, Andi M Lewis, Andreas Tzschach, Annarita Nicosia, Anne O'Donnell-Luria, Angela Peron, Ann-Charlotte Thuresson, Anneke Vulto-van-Silfhout, Antonio Novelli, Astrid S Plomp, Balram Gangaram, Belén Gil-Fournier, Boris Keren, Casie Genetti, Chiara De Luca, Christian P Schaaf, Claire Beneteau, Daniela Graziani, Daryl A Scott, David A Koolen, David Geneviéve, Dorine Bax, Elizabeth J Leslie, Elizabeth Mizerik, Elizabeth Roeder, Emily Magness, Esther Nibbeling, Gaetan Lesca, Göran Annerén, Gregory M Enns, Hilde Van Esch, Himanshu Goel, Inés Quintela, Jan Cobben, Jennifer L Morrison, Jesus Eiris, Joan Stoler, Josephine Gao, Katharina Steindl, Katrina Dipple, Konstantinos Kolokotronis, Laurie H Seaver, Lynda Pollack, Mahdi Motazacker, Manuela Gasparri, Margje Sinnema, Maria Cristina Digilio, Marie T McDonald, Marisol Ibarra Ramírez, Martine Doco-Fenzy, Marzena Kucharczyk, Mathilde Nizon, Megan Boothe, Melanie C O'Leary, Melissa T Carter, Meredith Ross, Meredith Wilson, Merel Klaassens, Monia Ginevrino, Monica Hsiung Wojcik, Nathaniel Robin, Nicolas Chatron, Odile Boute, Pankaj Agrawal, Paolo Fontana, Paolo Zanoni, Pascal Joset, Pernille M Torring, Ping Yee Billie Au, Servi Stevens, Soraya Ramiro León, Stephanie Baskin, Stephanie Parker DiTroia, Sue-Faye Siow, Tanguy Demaret, Vasilica Plaiasu, Virginia Clowes, Xi Luo, Yvonne Hilhorst-Hofstee

Affiliations

¹ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
² CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain; ITHACA-European Reference Network, Madrid, Spain.
³ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
⁴ Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
⁵ Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada.
⁶ Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Genetics Laboratories, One Baylor Plaza, R806, Houston, TX 77030, USA.
⁷ Unit of Molecular Diagnostics and Clinical Genetics, Hospital Universitari Son Espases, Health Research Institute of the Balearic Islands (IdiSBa), Palma, Spain.
⁸ Hereditary Cancer Program, Catalan Institute of Oncology, Doctor Josep Trueta University Hospital, Precision Oncology Group (OncoGIR-Pro), Institut d'Investigació Biomèdica de Girona (IDIGBI), Girona, Spain.
⁹ Department of Biostatistics, Hospital Universitario La Paz, Madrid, Spain.
¹⁰ Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.
¹¹ Birmingham Women's and Children's NHS Foundation Trust, Clinical Genetics Unit, Birmingham Womens Hospital, Lavender House, Mindelsohn Way, Edgbaston, Birmingham B15 2TG, UK.
¹² Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada.
¹³ Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
¹⁴ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. Electronic address: bert.callewaert@ugent.be.
¹⁵ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. Electronic address: sarah.vergult@ugent.be.

PMID: 40367947
PMCID: PMC12256859 (available on 2025-12-05)
DOI: 10.1016/j.ajhg.2025.04.008

Loss of function of the zinc finger homeobox 4 gene, ZFHX4, underlies a neurodevelopmental disorder

María Del Rocío Pérez Baca et al. Am J Hum Genet. 2025.

. 2025 Jun 5;112(6):1388-1414.

doi: 10.1016/j.ajhg.2025.04.008. Epub 2025 May 13.

Authors

Collaborators

ZFHX4 consortium:
Abbey Scott, Alejandro Iglesias, Allyn McConkie-Rosell, Amy Kritzer, Ana Boto, Andi M Lewis, Andreas Tzschach, Annarita Nicosia, Anne O'Donnell-Luria, Angela Peron, Ann-Charlotte Thuresson, Anneke Vulto-van-Silfhout, Antonio Novelli, Astrid S Plomp, Balram Gangaram, Belén Gil-Fournier, Boris Keren, Casie Genetti, Chiara De Luca, Christian P Schaaf, Claire Beneteau, Daniela Graziani, Daryl A Scott, David A Koolen, David Geneviéve, Dorine Bax, Elizabeth J Leslie, Elizabeth Mizerik, Elizabeth Roeder, Emily Magness, Esther Nibbeling, Gaetan Lesca, Göran Annerén, Gregory M Enns, Hilde Van Esch, Himanshu Goel, Inés Quintela, Jan Cobben, Jennifer L Morrison, Jesus Eiris, Joan Stoler, Josephine Gao, Katharina Steindl, Katrina Dipple, Konstantinos Kolokotronis, Laurie H Seaver, Lynda Pollack, Mahdi Motazacker, Manuela Gasparri, Margje Sinnema, Maria Cristina Digilio, Marie T McDonald, Marisol Ibarra Ramírez, Martine Doco-Fenzy, Marzena Kucharczyk, Mathilde Nizon, Megan Boothe, Melanie C O'Leary, Melissa T Carter, Meredith Ross, Meredith Wilson, Merel Klaassens, Monia Ginevrino, Monica Hsiung Wojcik, Nathaniel Robin, Nicolas Chatron, Odile Boute, Pankaj Agrawal, Paolo Fontana, Paolo Zanoni, Pascal Joset, Pernille M Torring, Ping Yee Billie Au, Servi Stevens, Soraya Ramiro León, Stephanie Baskin, Stephanie Parker DiTroia, Sue-Faye Siow, Tanguy Demaret, Vasilica Plaiasu, Virginia Clowes, Xi Luo, Yvonne Hilhorst-Hofstee

Affiliations

¹ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
² CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain; ITHACA-European Reference Network, Madrid, Spain.
³ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
⁴ Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
⁵ Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada.
⁶ Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Genetics Laboratories, One Baylor Plaza, R806, Houston, TX 77030, USA.
⁷ Unit of Molecular Diagnostics and Clinical Genetics, Hospital Universitari Son Espases, Health Research Institute of the Balearic Islands (IdiSBa), Palma, Spain.
⁸ Hereditary Cancer Program, Catalan Institute of Oncology, Doctor Josep Trueta University Hospital, Precision Oncology Group (OncoGIR-Pro), Institut d'Investigació Biomèdica de Girona (IDIGBI), Girona, Spain.
⁹ Department of Biostatistics, Hospital Universitario La Paz, Madrid, Spain.
¹⁰ Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.
¹¹ Birmingham Women's and Children's NHS Foundation Trust, Clinical Genetics Unit, Birmingham Womens Hospital, Lavender House, Mindelsohn Way, Edgbaston, Birmingham B15 2TG, UK.
¹² Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada.
¹³ Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
¹⁴ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. Electronic address: bert.callewaert@ugent.be.
¹⁵ Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. Electronic address: sarah.vergult@ugent.be.

PMID: 40367947
PMCID: PMC12256859 (available on 2025-12-05)
DOI: 10.1016/j.ajhg.2025.04.008

Abstract

8q21.11 microdeletions involving ZFHX4 have previously been associated with a syndromic form of intellectual disability, hypotonia, unstable gait, and hearing loss. We report on 63 individuals-57 probands and 6 affected family members-with protein-truncating variants (n = 41), (micro)deletions (n = 21), or an inversion (n = 1) affecting ZFHX4. Probands display variable developmental delay and intellectual disability, distinctive facial characteristics, morphological abnormalities of the central nervous system, behavioral alterations, short stature, hypotonia, and occasionally cleft palate and anterior segment dysgenesis. The phenotypes associated with 8q21.11 microdeletions and ZFHX4 intragenic loss-of-function (LoF) variants largely overlap, although leukocyte-derived DNA shows a mild common methylation profile for (micro)deletions. ZFHX4 shows increased expression during human brain development and neuronal differentiation. Furthermore, ZFHX4-interacting factors identified via immunoprecipitation followed by mass spectrometry (IP-MS) suggest an important role for ZFHX4 in cellular pathways, especially during histone modifications, protein trafficking, signal transduction, cytosolic transport, and development. Additionally, using CUT&RUN, we observed that ZFHX4 binds the promoter of genes with crucial roles in embryonic, neuronal, and axonal development. Moreover, we investigated whether the disruption of zfhx4 causes craniofacial abnormalities in zebrafish. First-generation (F0) zfhx4 crispant zebrafish, a (mosaic) mutant for zfhx4 LoF variants, have significantly shorter Meckel's cartilage and smaller ethmoid plates compared to control zebrafish. Behavioral assays showed a decreased movement frequency in the zfhx4 crispant zebrafish in comparison with controls. Furthermore, structural abnormalities were found in the zebrafish hindbrain. In conclusion, our findings delineate a ZFHX4-associated neurodevelopmental disorder and suggest a role for zfhx4 in facial skeleton patterning, palatal development, and behavior.

Keywords: 8q21.11 microdeletion; ZFHX4; craniofacial development; methylation profile; neurodevelopmental disorder; neurogenesis; ocular anomalies; orofacial cleft; transcription factor; transcription regulation.

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Conflict of interest statement

Declaration of interests B.S. is a shareholder in Episign, Inc.

Update of

Loss-of-function of the Zinc Finger Homeobox 4 (ZFHX4) gene underlies a neurodevelopmental disorder.
María Del Rocío PB, Palomares Bralo M, Vanhooydonck M, Hamerlinck L, D'haene E, Leimbacher S, Jacobs EZ, De Cock L, D'haenens E, Dheedene A, Malfait Z, Vantomme L, Silva A, Rooney K, Santos-Simarro F, Lleuger-Pujol R, García-Miñaúr S, Losantos-García I, Menten B, Gestri G, Ragge N; ZFHX4 consortium; Sadikovic B, Bogaert E, Syx D, Callewaert B, Vergult S. María Del Rocío PB, et al. medRxiv [Preprint]. 2024 Aug 8:2024.08.07.24311381. doi: 10.1101/2024.08.07.24311381. medRxiv. 2024. Update in: Am J Hum Genet. 2025 Jun 5;112(6):1388-1414. doi: 10.1016/j.ajhg.2025.04.008. PMID: 39148819 Free PMC article. Updated. Preprint.

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Loss of function of the zinc finger homeobox 4 gene, ZFHX4, underlies a neurodevelopmental disorder

Collaborators

Affiliations

Loss of function of the zinc finger homeobox 4 gene, ZFHX4, underlies a neurodevelopmental disorder

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

Update of

References

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Molecular Biology Databases

Research Materials