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van der Sluijs PJ, Alders M, Dingemans AJM, Parbhoo K, van Bon BW, Dempsey JC, Doherty D, den Dunnen JT, Gerkes EH, Milller IM, Moortgat S, Regier DS, Ruivenkamp CAL, Schmalz B, Smol T, Stuurman KE, Vincent-Delorme C, de Vries BBA, Sadikovic B, Hickey SE, Rosenfeld JA, Maystadt I, Santen GWE. A Case Series of Familial ARID1B Variants Illustrating Variable Expression and Suggestions to Update the ACMG Criteria. Genes (Basel) 2021; 12:genes12081275. [PMID: 34440449 PMCID: PMC8393241 DOI: 10.3390/genes12081275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023] Open
Abstract
ARID1B is one of the most frequently mutated genes in intellectual disability (~1%). Most variants are readily classified, since they are de novo and are predicted to lead to loss of function, and therefore classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines for the interpretation of sequence variants. However, familial loss-of-function variants can also occur and can be challenging to interpret. Such variants may be pathogenic with variable expression, causing only a mild phenotype in a parent. Alternatively, since some regions of the ARID1B gene seem to be lacking pathogenic variants, loss-of-function variants in those regions may not lead to ARID1B haploinsufficiency and may therefore be benign. We describe 12 families with potential loss-of-function variants, which were either familial or with unknown inheritance and were in regions where pathogenic variants have not been described or are otherwise challenging to interpret. We performed detailed clinical and DNA methylation studies, which allowed us to confidently classify most variants. In five families we observed transmission of pathogenic variants, confirming their highly variable expression. Our findings provide further evidence for an alternative translational start site and we suggest updates for the ACMG guidelines for the interpretation of sequence variants to incorporate DNA methylation studies and facial analyses.
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Affiliation(s)
- Pleuntje J. van der Sluijs
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (P.J.v.d.S.); (C.A.L.R.)
| | - Mariëlle Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Alexander J. M. Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.J.M.D.); (B.B.A.d.V.)
| | - Kareesma Parbhoo
- Division of Genetic & Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA; (K.P.); (B.S.); (S.E.H.)
| | - Bregje W. van Bon
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Jennifer C. Dempsey
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; (J.C.D.); (D.D.)
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; (J.C.D.); (D.D.)
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Johan T. den Dunnen
- Human Genetics and Clinical Genetics, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands;
| | - Erica H. Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands;
| | - Ilana M. Milller
- Rare Disease Institute, Children’s National Hospital, Washington, DC 20010, USA; (I.M.M.); (D.S.R.)
| | - Stephanie Moortgat
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, 6041 Gosselies, Belgium; (S.M.); (I.M.)
| | - Debra S. Regier
- Rare Disease Institute, Children’s National Hospital, Washington, DC 20010, USA; (I.M.M.); (D.S.R.)
| | - Claudia A. L. Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (P.J.v.d.S.); (C.A.L.R.)
| | - Betsy Schmalz
- Division of Genetic & Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA; (K.P.); (B.S.); (S.E.H.)
| | - Thomas Smol
- EA7364 RADEME, Institut de Génétique Médicale, Université de Lille, CHU de Lille, F-59000 Lille, France;
| | - Kyra E. Stuurman
- Erasmus MC, Department of Clinical Genetics, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | | | - Bert B. A. de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.J.M.D.); (B.B.A.d.V.)
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre and London Health Sciences Centre, Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Scott E. Hickey
- Division of Genetic & Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA; (K.P.); (B.S.); (S.E.H.)
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
- Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, 6041 Gosselies, Belgium; (S.M.); (I.M.)
| | - Gijs W. E. Santen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (P.J.v.d.S.); (C.A.L.R.)
- Correspondence:
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Pagliaroli L, Trizzino M. The Evolutionary Conserved SWI/SNF Subunits ARID1A and ARID1B Are Key Modulators of Pluripotency and Cell-Fate Determination. Front Cell Dev Biol 2021; 9:643361. [PMID: 33748136 PMCID: PMC7969888 DOI: 10.3389/fcell.2021.643361] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
Organismal development is a process that requires a fine-tuned control of cell fate and identity, through timely regulation of lineage-specific genes. These processes are mediated by the concerted action of transcription factors and protein complexes that orchestrate the interaction between cis-regulatory elements (enhancers, promoters) and RNA Polymerase II to elicit transcription. A proper understanding of these dynamics is essential to elucidate the mechanisms underlying developmental diseases. Many developmental disorders, such as Coffin-Siris Syndrome, characterized by growth impairment and intellectual disability are associated with mutations in subunits of the SWI/SNF chromatin remodeler complex, which is an essential regulator of transcription. ARID1B and its paralog ARID1A encode for the two largest, mutually exclusive, subunits of the complex. Mutations in ARID1A and, especially, ARID1B are recurrently associated with a very wide array of developmental disorders, suggesting that these two SWI/SNF subunits play an important role in cell fate decision. In this mini-review we therefore discuss the available scientific literature linking ARID1A and ARID1B to cell fate determination, pluripotency maintenance, and organismal development.
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Affiliation(s)
- Luca Pagliaroli
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
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