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Recent studies have implicated SMARCC1, a component of the BRG1-associated factor (BAF) chromatin remodelling complex, as a candidate congenital hydrocephalus gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, congenital hydrocephalus-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo. Here, we aimed to assess the prevalence of SMARCC1 variants in an expanded patient cohort, describe associated clinical and radiographic phenotypes, and assess the impact of Smarcc1 depletion in a novel Xenopus tropicalis model of congenital hydrocephalus.<\/jats:p>\n               <jats:p>To do this, we performed a genetic association study using whole-exome sequencing from a cohort consisting of 2697 total ventriculomegalic trios, including patients with neurosurgically-treated congenital hydrocephalus, that total 8091 exomes collected over 7 years (2016\u201323). A comparison control cohort consisted of 1798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents were sourced from the Simons Simplex Collection. Enrichment and impact on protein structure were assessed in identified variants. Effects on the human fetal brain transcriptome were examined with RNA-sequencing and Smarcc1 knockdowns were generated in Xenopus and studied using optical coherence tomography imaging, in situ hybridization and immunofluorescence. SMARCC1 surpassed genome-wide significance thresholds, yielding six rare, protein-altering de novo variants localized to highly conserved residues in key functional domains. Patients exhibited hydrocephalus with aqueductal stenosis; corpus callosum abnormalities, developmental delay, and cardiac defects were also common. Xenopus knockdowns recapitulated both aqueductal stenosis and cardiac defects and were rescued by wild-type but not patient-specific variant SMARCC1. Hydrocephalic SMARCC1-variant human fetal brain and Smarcc1-variant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2. These results suggest de novo variants in SMARCC1 cause a novel human BAFopathy we term \u2018SMARCC1-associated developmental dysgenesis syndrome\u2019, characterized by variable presence of cerebral ventriculomegaly, aqueductal stenosis, developmental delay and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodelling complex for human brain morphogenesis and provide evidence for a \u2018neural stem cell\u2019 paradigm of congenital hydrocephalus pathogenesis.<\/jats:p>\n               <jats:p>These results highlight utility of trio-based whole-exome sequencing for identifying pathogenic variants in sporadic congenital structural brain disorders and suggest whole-exome sequencing may be a valuable adjunct in clinical management of congenital hydrocephalus patients.<\/jats:p>","DOI":"10.1093\/brain\/awad405","type":"journal-article","created":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T10:50:19Z","timestamp":1703069419000},"page":"1553-1570","source":"Crossref","is-referenced-by-count":18,"title":["A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus"],"prefix":"10.1093","volume":"147","author":[{"given":"Amrita K","family":"Singh","sequence":"first","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5458-6129","authenticated-orcid":false,"given":"Garrett","family":"Allington","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"},{"name":"Department of Genetics, Yale University , New Haven, CT 06510 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Viviano","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Yale University , New Haven, CT 06510 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"McGee","sequence":"additional","affiliation":[{"name":"GeneDx , Gaithersburg, MD 20877 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emre","family":"Kiziltug","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaojie","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Genetics, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neuroscience, Yale University , New Haven, CT 06510 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shujuan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"},{"name":"Departments of Genetics and Pediatrics, Washington University School of Medicine , St Louis, MO 63110 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kedous Y","family":"Mekbib","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P","family":"Shohfi","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phan Q","family":"Duy","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"},{"name":"Department of Neuroscience, Yale University , New Haven, CT 06510 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr","given":"Tyrone","family":"DeSpenza","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"},{"name":"Department of Neuroscience, Yale University , New Haven, CT 06510 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charuta G","family":"Furey","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin C","family":"Reeves","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02115 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9 M M","family":"Sousa","sequence":"additional","affiliation":[{"name":"Waisman Center, University of Wisconsin-Madison , Madison, WI 53705 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriana","family":"Cherskov","sequence":"additional","affiliation":[{"name":"Department of Neuroscience, Yale University , New 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A","family":"Rizvi","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy , London, WC1N 1AX , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth L","family":"Alper","sequence":"additional","affiliation":[{"name":"Division of Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02142 , USA"},{"name":"Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center , Boston, MA 02215 , USA"},{"name":"Department of Medicine, Harvard Medical School , Boston, MA 02115 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nenad","family":"Sestan","sequence":"additional","affiliation":[{"name":"Department of Genetics, Yale University , New Haven, CT 06510 , USA"},{"name":"Department of Pediatrics, Yale University , New Haven, CT 06510 , 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Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences , Kingston, Ontario , Canada"},{"name":"Department of Radiology, Diagnostic Medicine Institute, Geisinger , Danville, PA, 17822 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5777-7262","authenticated-orcid":false,"given":"Sheng Chih","family":"Jin","sequence":"additional","affiliation":[{"name":"Departments of Genetics and Pediatrics, Washington University School of Medicine , St Louis, MO 63110 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Kruszka","sequence":"additional","affiliation":[{"name":"GeneDx , Gaithersburg, MD 20877 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2999-0429","authenticated-orcid":false,"given":"Engin","family":"Deniz","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Yale 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