Multiomic approaches identify a rare CCG repeat expansion in BCLAF3 in neurodevelopmental disorders

BACKGROUND: Tandem repeat expansions have been implicated in various neurological conditions. Here, we present a novel hypermethylated CCG repeat expansion on Xp22 in the 5'UTR of BCLAF3 in males with neurodevelopmental disorders. METHODS: We used patient-derived fibroblasts and neuronal models from a family with BCLAF3 repeat expansions to generate multiomic data and investigate downstream molecular consequences of the repeat expansion. To identify additional affected individuals with BCLAF3 repeat expansions, we screened methylation arrays (n = 12,375) and short-read genomes (n = 15,963) from probands with neurodevelopmental presentations. We also characterized BCLAF3 repeat expansions in the general population using long-read sequencing data (n = 793) and population-level short-read sequencing data (n = 410,076). RESULTS: Long-read sequencing validated hypermethylation of expanded repeats. Patient-derived cells showed repressed BCLAF3 RNA and protein expression. We show that the BCLAF3 CCG repeat expansion constitutes a previously uncharacterized fragile site (FRAXG) that shifts the surrounding chromatin compartment from open euchromatin to closed heterochromatin. Using our multiomic screening approaches, we identified three additional unrelated males and one related male cousin with long-read sequencing validated (n = 2) or short-read sequencing predicted (n = 2) repeat expansions. In one family, the BCLAF3 repeats segregate with more severe phenotypes than expected for the primary diagnoses. Long-read sequencing in three carrier mothers showed skewed X-inactivation against the repeat expansion, highlighting the potential deleterious effect of an allele with an expansion. Expansions were absent in long-read sequencing data from control populations. Assessment of the BCLAF3 repeat expansion in the UK Biobank indicates that it may be ~ 20X rarer than FMR1 repeat expansions. CONCLUSIONS: CCG repeat expansions in the 5'UTR of BCLAF3 likely constitute a novel genetic etiology associated with X-linked neurodevelopmental phenotypes in males. Future work will be essential to delineate the phenotypic spectrum and determine a disease pathomechanism.

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Publication Details

Journal
Genome Medicine
Published
2026-07-22
DOI
https://doi.org/10.1186/s13073-026-01729-4
Primary Topic
Congenital heart defects research
Type
article
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article

Multiomic approaches identify a rare CCG repeat expansion in BCLAF3 in neurodevelopmental disorders

Kristina Ibáñez, Emily Bonkowski, Bharati Jadhav, Soham Sengupta et al.
Genome Medicine
Congenital heart defects research
article

Multiomic approaches identify a rare CCG repeat expansion in BCLAF3 in neurodevelopmental disorders

Kristina Ibáñez, Emily Bonkowski, Bharati Jadhav, Soham Sengupta, Bida Gu, Jenny Lord, Evan E. Eichler, Mark Chaisson, Heather C. Mefford, Christy W. LaFlamme, Siddharth Banka, Danny E. Miller, Athena R. Olszewski, Mira Kharbanda, Andrew J. Sharp, Sanjay M. Sisodiya, Nicola Whiffin, Harriet Dashnow, Sophia B Gibson, Arianna Tucci, Helen M. Stuart, A Hosokawa, Bekim Sadikovic, Henry Houlden, Johanna M. van Hagen, Lynette G. Sadleir, Jiadong Lin, Andrew R. Webster, Sourav Ghosh, Chris Clarkson, Virginia Valentine, Edith P. Almanza Fuerte, Marc Valentine, Mariëlle Alders, Taralynn Mack, Alexandra Martin-Geary, Jin-Yuan Wang, Shondra M. Pruett-Miller, Richa Bajpai
article en

Abstract

BACKGROUND: Tandem repeat expansions have been implicated in various neurological conditions. Here, we present a novel hypermethylated CCG repeat expansion on Xp22 in the 5'UTR of BCLAF3 in males with neurodevelopmental disorders. METHODS: We used patient-derived fibroblasts and neuronal models from a family with BCLAF3 repeat expansions to generate multiomic data and investigate downstream molecular consequences of the repeat expansion. To identify additional affected individuals with BCLAF3 repeat expansions, we screened methylation arrays (n = 12,375) and short-read genomes (n = 15,963) from probands with neurodevelopmental presentations. We also characterized BCLAF3 repeat expansions in the general population using long-read sequencing data (n = 793) and population-level short-read sequencing data (n = 410,076). RESULTS: Long-read sequencing validated hypermethylation of expanded repeats. Patient-derived cells showed repressed BCLAF3 RNA and protein expression. We show that the BCLAF3 CCG repeat expansion constitutes a previously uncharacterized fragile site (FRAXG) that shifts the surrounding chromatin compartment from open euchromatin to closed heterochromatin. Using our multiomic screening approaches, we identified three additional unrelated males and one related male cousin with long-read sequencing validated (n = 2) or short-read sequencing predicted (n = 2) repeat expansions. In one family, the BCLAF3 repeats segregate with more severe phenotypes than expected for the primary diagnoses. Long-read sequencing in three carrier mothers showed skewed X-inactivation against the repeat expansion, highlighting the potential deleterious effect of an allele with an expansion. Expansions were absent in long-read sequencing data from control populations. Assessment of the BCLAF3 repeat expansion in the UK Biobank indicates that it may be ~ 20X rarer than FMR1 repeat expansions. CONCLUSIONS: CCG repeat expansions in the 5'UTR of BCLAF3 likely constitute a novel genetic etiology associated with X-linked neurodevelopmental phenotypes in males. Future work will be essential to delineate the phenotypic spectrum and determine a disease pathomechanism.

Genome Medicine
Broad Institute (US), University of Southern California (US), Western University (CA), Seattle Children's Hospital (US), St. Jude Children's Research Hospital (US), Moorfields Eye Hospital NHS Foundation Trust (GB), Centre for Human Genetics (GB), Howard Hughes Medical Institute (US), Colorado School of Public Health (US), Queen Mary University of London (GB), University of Washington (US), University of Utah (US), London Health Sciences Centre (CA), Open Data Institute (GB), University Hospital Southampton NHS Foundation Trust (GB), University of Manchester (GB), Epilepsy Research UK (GB), University of Oxford (GB), St Mary's Hospital (GB), Manchester University NHS Foundation Trust (GB), St Mary's Hospital (GB), Evolutionary Genomics (United States) (US), Child Health and Development Institute (US), Brotman Baty Institute (US), William Harvey Research Institute (GB), Broad Center (US), National Hospital for Neurology and Neurosurgery (GB), Genomics (United Kingdom) (GB), Amsterdam University Medical Centers (NL), University College London (GB), Epilepsy Society (GB), University of Colorado Anschutz Medical Campus (US), University of Otago (NZ), Vrije Universiteit Amsterdam (NL), University of Amsterdam (NL), University of Sheffield (GB), Icahn School of Medicine at Mount Sinai (US)
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Congenital heart defects research
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