2. Academic Validation
  3. A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy

A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy

  • Am J Hum Genet. 2019 Jun 6;104(6):1060-1072. doi: 10.1016/j.ajhg.2019.04.001.
Ingo Helbig 1,  Tania Lopez-Hernandez 2,  Oded Shor 3,  Peter Galer 4,  Shiva Ganesan 4,  Manuela Pendziwiat 5,  Annika Rademacher 5,  Colin A Ellis 6,  Nadja Hümpfer 7,  Niklas Schwarz 8,  Simone Seiffert 8,  Joseph Peeden 9,  Joseph Shen 10,  Katalin Štěrbová 11,  Trine Bjørg Hammer 12,  Rikke S Møller 13,  Deepali N Shinde 14,  Sha Tang 14,  Lacey Smith 15,  Annapurna Poduri 16,  Roland Krause 17,  Felix Benninger 3,  Katherine L Helbig 4,  Volker Haucke 7,  Yvonne G Weber 18,  EuroEPINOMICS-RES Consortium,  GRIN Consortium
Affiliations

Affiliations

  • 1 Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA. Electronic address: [email protected].
  • 2 Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany.
  • 3 Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
  • 4 Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
  • 5 Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.
  • 6 Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
  • 7 Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany.
  • 8 Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany.
  • 9 East Tennessee Children's Hospital, University of Tennessee Department of Medicine, Knoxville, TN 37916, USA.
  • 10 Division of Genetics, Department of Pediatrics, University of California San Francisco, Fresno, CA 93701, USA.
  • 11 Department of Child Neurology, Charles University 2nd Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic.
  • 12 Danish Epilepsy Centre Filadelfia, 4293 Dianalund, Denmark.
  • 13 Danish Epilepsy Centre Filadelfia, 4293 Dianalund, Denmark; Institute for Regional Health Services, University of Southern Denmark, 5230 Odense, Denmark.
  • 14 Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA.
  • 15 Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA.
  • 16 Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.
  • 17 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg.
  • 18 Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; Department of Neurosurgery, University of Tübingen, 72076 Tübingen, Germany.
PMID: 31104773 DOI: 10.1016/j.ajhg.2019.04.001
Abstract

The developmental and epileptic encephalopathies (DEEs) are heterogeneous disorders with a strong genetic contribution, but the underlying genetic etiology remains unknown in a significant proportion of individuals. To explore whether statistical support for genetic etiologies can be generated on the basis of phenotypic features, we analyzed whole-exome sequencing data and phenotypic similarities by using Human Phenotype Ontology (HPO) in 314 individuals with DEEs. We identified a de novo c.508C>T (p.Arg170Trp) variant in AP2M1 in two individuals with a phenotypic similarity that was higher than expected by chance (p = 0.003) and a phenotype related to epilepsy with myoclonic-atonic seizures. We subsequently found the same de novo variant in two individuals with neurodevelopmental disorders and generalized epilepsy in a cohort of 2,310 individuals who underwent diagnostic whole-exome sequencing. AP2M1 encodes the μ-subunit of the adaptor protein complex 2 (AP-2), which is involved in clathrin-mediated endocytosis (CME) and synaptic vesicle recycling. Modeling of protein dynamics indicated that the p.Arg170Trp variant impairs the conformational activation and thermodynamic entropy of the AP-2 complex. Functional complementation of both the μ-subunit carrying the p.Arg170Trp variant in human cells and astrocytes derived from AP-2μ conditional knockout mice revealed a significant impairment of CME of transferrin. In contrast, stability, expression levels, membrane recruitment, and localization were not impaired, suggesting a functional alteration of the AP-2 complex as the underlying disease mechanism. We establish a recurrent pathogenic variant in AP2M1 as a cause of DEEs with distinct phenotypic features, and we implicate dysfunction of the early steps of endocytosis as a disease mechanism in epilepsy.

Keywords

Human Phenotype Ontology; clathrin-mediated endocytosis; computational phenotypes; developmental and epileptic encephalopathy; neurodevelopmental disorders; synaptic transmission.

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