Whole exome sequencing in the UK Biobank reveals risk gene SLC2A1 and biological insights for major depressive disorder

Abstract

Nearly two hundred common-variant depression risk loci have been identified by genome-wide association studies (GWAS). However, the impact of rare coding variants on depression remains poorly understood. Here, we present the largest to date exome analysis of depression based on 320,356 UK Biobank participants. We show that the burden of rare disruptive coding variants in loss-of-function intolerant genes is significantly associated with depression risk. Among 30 genes with false discovery rate (FDR) <0.1, SLC2A1, a blood-brain barrier glucose transporter underlying GLUT1 deficiency syndrome, reached exome-wide significance (P = 2.96e-7). Gene-set enrichment supports neuron projection development and muscle activities as implicated in depression. Integrating exomes with polygenic risk revealed additive contributions from common and rare variants to depression risk. The burden of rare disruptive coding variants for depression overlapped with that of developmental disorder, autism and schizophrenia. Our study provides novel insight into the contribution of rare coding variants on depression and genetic relationships across developmental and psychiatric disorders.