Coffin-Siris Syndrome and the BAF Complex: Genotype-Phenotype Study in 63 Patients
Open accessAbstract
De novo germline variants in several components of the SWI/SNF-like BAF complex can cause Coffin-Siris syndrome (CSS), Nicolaides-Baraitser syndrome (NCBRS), and nonsyndromic intellectual disability. We screened 63 patients with a clinical diagnosis of CSS for these genes (ARID1A, ARID1B, SMARCA2, SMARCA4, SMARCB1, and SMARCE1) and identified pathogenic variants in 45 (71%) patients. We found a high proportion of variants in ARID1B (68%). All four pathogenic variants in ARID1A appeared to be mosaic. By using all variants from the Exome Variant Server as test data, we were able to classify variants in ARID1A, ARID1B, and SMARCB1 reliably as being pathogenic or nonpathogenic. For SMARCA2, SMARCA4, and SMARCE1 several variants in the EVS remained unclassified, underlining the importance of parental testing. We have entered all variant and clinical information in LOVD-powered databases to facilitate further genotype-phenotype correlations, as these will become increasingly important because of the uptake of targeted and untargeted next generation sequencing in diagnostics. The emerging phenotype-genotype correlation is that SMARCB1 patients have the most marked physical phenotype and severe cognitive and growth delay. The variability in phenotype seems most marked in ARID1A and ARID1B patients. Distal limbs anomalies are most marked in ARID1A patients and least in SMARCB1 patients. Numbers are small however, and larger series are needed to confirm this correlation.
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Mutations in six BAF complex components (SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B) have been reported in patients with intellectual disability.
“Interestingly, mutations in patients with intellectual disability have been reported in six components of these complexes (SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B).”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [40]
The phenotype associated with mutations in these BAF component genes ranges from non-syndromic intellectual disability with hypotonia and speech delay to recognizable syndromes such as Coffin-Siris syndrome and Nicolaides-Baraitser syndrome.
“The phenotype associated with mutations in these genes ranges from non-syndromic intellectual disability with hypotonia and speech delay to recognizable syndromes such as the Coffin-Siris syndrome and Nicolaides-Baraitser syndrome.”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [40]
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- Authors
- Santen, G. W. E., Aten, E., Vulto-van Silfhout, A. T., Pottinger, C., van Bon, B. W. M., van Minderhout, I. J. H. M., Snowdowne, R., van der Lans, C. A. C., Boogaard, M., Linssen, M. M. L., Vijfhuizen, L., van der Wielen, M. J. R., Vollebregt, M. J. E., the Coffin-Siris consortium, Breuning, M. H., Kriek, M., van Haeringen, A., den Dunnen, J. T., Hoischen, A., Clayton-Smith, J., de Vries, B. B. A., Hennekam, R. C. M., van Belzen, M. J., Almureikhi, M., Baban, A., Barbosa, M., Ben-Omran, T., Berry, K., Bigoni, S., Boute, O., Brueton, L., van der Burgt, I., Canham, N., Chandler, K. E., Chrzanowska, K., Collins, A. L., de Toni, T., Dean, J., den Hollander, N. S., Flore, L. A., Fryer, A., Gardham, A., Graham, J. M., Harrison, V., Horn, D., Jongmans, M. C., Josifova, D., Kant, S. G., Kapoor, S., Kingston, H., Kini, U., Kleefstra, T., Krajewska-Walasek, M., Kramer, N., Maas, S. M., Maciel, P., Mancini, G. M. S., Maystadt, I., McKee, S., Milunsky, J. M., Nampoothiri, S., Newbury-Ecob, R., Nikkel, S. M., Parker, M. J., Pérez-Jurado, L. A., Robertson, S. P., Rooryck, C., Shears, D., Silengo, M., Singh, A., Smigiel, R., Soares, G., Splitt, M., Stewart, H., Sweeney, E., Tassabehji, M., Tuysuz, B., van Eerde, A. M., Vincent-Delorme, C., Wilson, L. C., & Yesil, G.
- Affiliations
- Leiden University Medical Center (NL)
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
- Glan Clwyd Hospital (GB)
- Center for Human and Clinical Genetics; Leiden University Medical Centre; Leiden The Netherlands
- Radboud University Medical Center (NL)
- Manchester Biomedical Research Centre; MAHSC, St Mary's Hospital; Manchester UK
- Amsterdam UMC Location University of Amsterdam (NL)
- Instituto Gulbenkian de Ciência (PT)
- University of Ferrara (IT)
- Université de Lille (FR)
- University of Manchester (GB)
- Boston Children's Hospital (US)
- Charité – Universitätsmedizin Berlin (DE)
- Radboud University Nijmegen (NL)
- Guy's and St Thomas' NHS Foundation Trust (GB)
- Leiden University (NL)
- Maulana Azad Medical College (IN)
- Cedars-Sinai Medical Center (US)
- University of Amsterdam (NL)
- Erasmus University Rotterdam (NL)
- Belfast Health and Social Care Trust (GB)
- Amrita Vishwa Vidyapeetham (IN)
- St. Michael's Hospital (CA)
- National Health Service (GB)
- University of Otago (NZ)
- Université de Bordeaux (FR)
- University of Turin (IT)
- University College London (GB)
- Corresponding author
- Santen, Gijs W.E.
- ORCID
- Santen, Gijs W.E.
- Aten, Emmelien
- Pottinger, Caroline
- Linssen, Margot M.L.
- Breuning, Martijn H.
- Hoischen, Alexander
- Hennekam, Raoul C.M.
- Baban, Anwar
- Barbosa, Mafalda
- Bigoni, Stefania
- Collins, Amanda L.
- Dean, John
- Gardham, Alice
- Graham, John M.
- Horn, Denise
- Jongmans, Marjolijn C.
- Josifova, Dragana
- Kant, Sarina G.
- Kini, Usha
- Kleefstra, Tjitske
- Maas, Saskia M.
- Mancini, Grazia M.S.
- Maystadt, Isabelle
- McKee, Shane
- Nampoothiri, Sheela
- Newbury-Ecob, Ruth
- Nikkel, Sarah M.
- Parker, Michael J.
- Robertson, Stephen P.
- Rooryck, Caroline
- Silengo, Margherita
- Singh, Ankur
- Soares, Gabriela
- Splitt, Miranda
- Stewart, Helen
- Tassabehji, May
- Wilson, Louise C.
- Venue
- Human Mutation
- Publisher
- Wiley
- Published
- 2013-08-30
- Volume
- 34
- Issue
- 11
- Pages
- 1519-1528
- ISSN
- 1059-7794 (ISSN-L)
- OpenAlex
- W2024699009
- Cited by
- 221
- References
- 35
- Citations by year
- 2026: 14 · 2025: 11 · 2024: 16 · 2023: 27 · 2022: 16 · 2021: 24 · 2020: 14 · 2019: 20 · 2018: 18 · 2017: 9 · 2016: 14 · 2015: 9 · 2014: 25 · 2013: 2
- FWCI
- 10.95
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- CINECA IRIS Institutial Research Information System (University of Genoa) (submittedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, cc-by-nc-nd)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- Santen
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, SWI/SNF complex, genotype-phenotype correlation, ARID1A, ARID1B, SMARCB1, SMARCA2, SMARCA4, SMARCE1, germline pathogenic variants, mosaicism, limb malformations, intellectual disability, growth delay, LOVD
- MeSH terms
- Abnormalities, Multiple, SMARCB1 Protein, Chromosomal Proteins, Non-Histone, DNA Helicases, DNA-Binding Proteins, Exons, Face, Hand Deformities, Congenital, Humans, Intellectual Disability, Micrognathism, Neck, Nuclear Proteins, Phenotype, Transcription Factors, Facies, Gene Order, Multiprotein Complexes, Genetic Association Studies
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