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Original research
De novo variants in SIAH1, encoding an E3 ubiquitin ligase, are associated with developmental delay, hypotonia and dysmorphic features
  1. Julien Buratti1,
  2. Lei Ji2,
  3. Boris Keren1,
  4. Youngha Lee3,
  5. Stephanie Booke4,
  6. Serkan Erdin5,6,
  7. Soo Yeon Kim7,
  8. Timothy Blake Palculict8,
  9. Vardiella Meiner9,
  10. Jong Hee Chae7,
  11. Christopher Geoffrey Woods10,
  12. Allison Tam4,
  13. Delphine Héron11,
  14. Feng Cong2,
  15. Tamar Harel9
  1. 1Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
  2. 2Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
  3. 3Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
  4. 4Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA
  5. 5Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
  6. 6Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
  7. 7Department of Pediatrics, Seoul National University Children’s Hospital, Seoul, Republic of Korea
  8. 8GeneDx, Gaithersburg, MD, USA
  9. 9Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
  10. 10Cambridge Institute for Medical Research, Department of Medical Genetics, Univeristy of Cambridge, Cambridge, UK
  11. 11Département de Génétique et Centre de Référence "déficiences intellectuelles de causes rares", AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
  1. Correspondence to Dr Tamar Harel, Hadassah-Hebrew University Medical Center, Jerusalem, Israel; tamarhe{at}hadassah.org.il

Abstract

Background Ubiquitination has a central role in numerous biological processes, including cell development, stress responses and ageing. Perturbed ubiquitination has been implicated in human diseases ranging from cancer to neurodegenerative diseases. SIAH1 encodes a RING-type E3 ubiquitin ligase involved in protein ubiquitination. Among numerous other roles, SIAH1 regulates metabotropic glutamate receptor signalling and affects neural cell fate. Moreover, SIAH1 positively regulates Wnt signalling through ubiquitin-mediated degradation of Axin and accumulation of β-catenin.

Methods Trio exome sequencing followed by Sanger validation was undertaken in five individuals with syndromic developmental delay. Three-dimensional structural modelling was used to predict pathogenicity of affected residues. Wnt stimulatory activity was measured by luciferase reporter assays and Axin degradation assays in HEK293 cells transfected with wild-type and mutant SIAH1 expression plasmids.

Results We report five unrelated individuals with shared features of developmental delay, infantile hypotonia, dysmorphic features and laryngomalacia, in whom exome sequencing identified de novo monoallelic variants in SIAH1. In silico protein modelling suggested alteration of conserved functional sites. In vitro experiments demonstrated loss of Wnt stimulatory activity with the SIAH1 mutants, suggesting variant pathogenicity.

Conclusion Our results lend support to SIAH1 as a candidate Mendelian disease gene for a recognisable syndrome, further strengthening the connection between SIAH1 and neurodevelopmental disorders. Furthermore, the results suggest that dysregulation of the Wnt/β-catenin pathway may be involved in the pathogenesis.

  • SIAH1
  • E3 ubiquitin ligase
  • Wnt signaling
  • exome sequencing
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Footnotes

  • Contributors SB, SYK, JHC, CGW, AT, DH and TH provided detailed clinical data. JB, BK, YL, TBP, VM and TH were involved in data analysis and provided molecular genetic data. SE provided three-dimensional modelling. LJ and FC planned and performed the functional studies. TH supervised the study and wrote the manuscript with input from all authors. All authors read and approved the final version of the manuscript.

  • Funding CGW acknowledges the Cambridge NIHR Biomedical Research Centre award 2017-2022.

  • Competing interests TBP is an employee of GeneDx.

  • Patient consent for publication Parental/guardian consent obtained.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data availability statement All data relevant to the study are included in the article or uploaded as supplementary information.

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