Neurodevelopmental disorders (NDDs), including severe paediatric epilepsy, autism and intellectual disabilities are heterogeneous conditions in which clinical genetic testing can often identify a pathogenic variant. For many of them, genetic therapies will be tested in this or the coming years in clinical trials. In contrast to first-generation symptomatic treatments, the new disease-modifying precision medicines require a genetic test-informed diagnosis before a patient can be enrolled in a clinical trial. However, even in 2022, most identified genetic variants in NDD genes are 'variants of uncertain significance'. To safely enrol patients in precision medicine clinical trials, it is important to increase our knowledge about which regions in NDD-associated proteins can 'tolerate' missense variants and which ones are 'essential' and will cause a NDD when mutated. In addition, knowledge about functionally indispensable regions in the 3D structure context of proteins can also provide insights into the molecular mechanisms of disease variants. We developed a novel consensus approach that overlays evolutionary, and population based genomic scores to identify 3D essential sites (Essential3D) on protein structures. After extensive benchmarking of AlphaFold predicted and experimentally solved protein structures, we generated the currently largest expert curated protein structure set for 242 NDDs and identified 14 377 Essential3D sites across 189 gene disorders associated proteins. We demonstrate that the consensus annotation of Essential3D sites improves prioritization of disease mutations over single annotations. The identified Essential3D sites were enriched for functional features such as intermembrane regions or active sites and discovered key inter-molecule interactions in protein complexes that were otherwise not annotated. Using the currently largest autism, developmental disorders, and epilepsies exome sequencing studies including >360 000 NDD patients and population controls, we found that missense variants at Essential3D sites are 8-fold enriched in patients. In summary, we developed a comprehensive protein structure set for 242 NDDs and identified 14 377 Essential3D sites in these. All data are available at https://es-ndd.broadinstitute.org for interactive visual inspection to enhance variant interpretation and development of mechanistic hypotheses for 242 NDDs genes. The provided resources will enhance clinical variant interpretation and in silico drug target development for NDD-associated genes and encoded proteins.

Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA 02114 USA

Cologne Center for Genomics University of Cologne 50923 Köln Germany

Department of Software Engineering Faculty of Mathematics and Physics Charles University 110 00 Staré Město Czechia Czech Republic

Epilepsy Center Neurological Institute Cleveland Clinic Cleveland OH 44195 USA

Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland OH 44106 USA

Institute for Molecular Medicine Finland Centre of Excellence in Complex Disease Genetics University of Helsinki 00100 Helsinki Finland

Luxembourg Centre for Systems Biomedicine University of Luxembourg 4365 Esch sur Alzette Luxembourg

School of Health and Wellbeing College of Medical Veterinary and Life Sciences University of Glasgow Glasgow G12 8QQ UK

Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA 02142 USA

The Center for the Development of Therapeutics Broad Institute of MIT and Harvard Cambridge MA 02142 USA

The Paediatric Neurosciences Research Group Royal Hospital for Children Glasgow G12 8QQ UK

Universidad del Desarrollo Centro de Genética y Genómica Facultad de Medicina Clínica Alemana 7610658 Las Condes Santiago de Chile Chile

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Brain. 2023 Feb 13;146(2):411-412. doi: 10.1093/brain/awad011. PubMed

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Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures