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. Epub 2019 May 16.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Protein Complex 2 / genetics*
  • Adaptor Protein Complex mu Subunits / genetics*
  • Adolescent
  • Animals
  • Brain Diseases / etiology*
  • Brain Diseases / pathology
  • Child
  • Child, Preschool
  • Clathrin / genetics
  • Clathrin / metabolism*
  • Endocytosis*
  • Epilepsy / etiology*
  • Epilepsy / pathology
  • Exome Sequencing
  • Female
  • Humans
  • Infant
  • Mice
  • Mice, Knockout
  • Mutation, Missense*
  • Neurodevelopmental Disorders / etiology*
  • Neurodevelopmental Disorders / pathology

Substances

  • Adaptor Protein Complex 2
  • Adaptor Protein Complex mu Subunits
  • Clathrin
  • adaptor protein complex 2, mu 2 subunit