Individuals with intellectual disability have an increased burden of de novo variants in cis-regulatory elements of glutamatergic neurons.

To understand the role of non-coding sequence variation in neurodevelopmental disorders, we studied 709,222 de novo variants (DNVs) using the genomes of 20,366 individuals. We found enrichment of DNVs at cis-regulatory elements (CREs) of all somatic cell types, attributable to the deamination of 5-methylcytosine at CG dinucleotide-dense CREs. In neurodivergent individuals with or without intellectual disability (ID), the DNVs were enriched at genes implicated in autism/ID at promoter-proximal CREs of brain cell types specifically. As the properties of the DNVs were not sufficiently distinctive to explain the phenotypic associations, we performed a multivariate category-wide association study (CWAS) that revealed enrichment of DNVs in CREs of glutamatergic neurons in individuals with ID, with a random forest analysis demonstrating an increased burden of these events in these individuals with ID. Our findings are consistent with a model of non-coding variants contributing to the oligogenic heritability of neurodevelopmental disorders.