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

Ingo Helbig*, Tania Lopez-Hernandez, Oded Shor, Peter Galer, Shiva Ganesan, Manuela Pendziwiat, Annika Rademacher, Colin A. Ellis, Nadja Hümpfer, Niklas Schwarz, Simone Seiffert, Joseph Peeden, Joseph Shen, Katalin Štěrbová, Trine Bjørg Hammer, Rikke S. Møller, Deepali N. Shinde, Sha Tang, Lacey Smith, Annapurna PoduriRoland Krause, Felix Benninger, Katherine L. Helbig, Volker Haucke, Yvonne G. Weber, Rudi Balling, Nina Barisic, Stéphanie Baulac, Hande Caglayan, Dana Craiu, Peter De Jonghe, Christel Depienne, Renzo Guerrini, Helle Hjalgrim, Dorota Hoffman-Zacharska, Johanna Jähn, Karl Martin Klein, Bobby P.C. Koeleman, Vladimir Komarek, Eric Leguern, Anna Elina Lehesjoki, Johannes R. Lemke, Holger Lerche, Tarja Linnankivi, Carla Marini, Patrick May, Hiltrud Muhle, Deb K. Pal, Aarno Palotie, Felix Rosenow, the EuroEPINOMICS-RES Consortium, the GRIN Consortium

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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.

TidsskriftAmerican Journal of Human Genetics
Udgave nummer6
Sider (fra-til)1060-1072
StatusUdgivet - 6. jun. 2019

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