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Coursimault J, Goldenberg A, Nicolas G, Saugier-Veber P, Coutant S, Vincent A, Pouliquen D, Feltin C, Aref-Eshghi E, Sadikovic B, Lecoquierre F. Contribution of DNA methylation profiling to the reclassification of a variant of uncertain significance in the KDM5C gene. Eur J Med Genet 2022; 65:104556. [PMID: 35781022 DOI: 10.1016/j.ejmg.2022.104556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/21/2022] [Accepted: 06/27/2022] [Indexed: 11/03/2022]
Abstract
KDM5C encodes a demethylase of the histone H3 lysine 4 residue, involved in chromatin regulation and gene expression. Hemizygous KDM5C pathogenic variants cause X-linked intellectual disability of Claes-Jensen type. Because of its mode of inheritance and the low specificity of the clinical phenotype, interpretation of variants can be difficult, hence the need for functional studies and biomarkers specific to this disorder. We present the case of a male patient with intellectual disability, behavioral abnormalities and subtle dysmorphic features, in which genetic investigation identified a hemizygous novel missense KDM5C variant of uncertain significance (VUS), inherited from his asymptomatic mother and present in his paucisymptomatic sister. We assessed the global genomic DNA methylation status from a whole blood sample of the proband. Global DNA methylation profiling specifically identified the recently discovered epi-signature of Claes-Jensen syndrome. This result served as a biomarker which independently highlighted KDM5C as the cause of the disorder in this patient. Because of the X-linked mode of inheritance, variant reclassification had a high impact on genetic counseling in this family. This example highlights the value of global methylome profiling in situations of variants of uncertain significance in genes with a known specific epi-signature.
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Affiliation(s)
- Juliette Coursimault
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Anne Vincent
- Reference Centre for Learning Disorders, Rouen University Hospital, F-76031 Rouen Cedex, France; Department of Neonatology and Paediatric Intensive Care, Rouen University Hospital, F-76031 Cedex, France
| | | | - Cécile Feltin
- Institut de Psychiatrie - Centre Hospitalier du Rouvray, Sotteville-lès-Rouen, France
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Canada and Verspeeten Clinical Genome Centre, London Health Sciences, London, Ontario, Canada
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France.
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