21 22 23 variants in ARC and NMDAR post-synaptic complexes and schizophrenia. Larger 48 samples are required to identify specific genes and variants driving these associations. 49 50 Author Summary 51 52Common and rare genetic variations are known to play a substantial role in the 53 development of schizophrenia. Recently, sequencing studies have started to highlight 54 specific sets of genes that are enriched for rare variation in schizophrenia, such as the 55 synaptic gene sets ARC and NMDAR, as well as voltage-gated sodium and calcium 56 channels. To confirm the role of these gene sets in schizophrenia, and identify specific 57 risk genes, we sequenced 187 genes in a new sample of 5,207 schizophrenia cases and 58 4,991 controls. We find an excess of protein truncating mutations with a frequency 59 <0.1% in all 187 targeted genes, and provide novel evidence that mutations altering 60 amino acids conserved across sodium channel proteins are risk factors for 61 schizophrenia. Through meta-analysing our new data with previously published 62 sequencing data sets, for a total of 11,319 cases, 15,854 controls and 1,136 trios, we 63 increase the evidence for association between rare coding variants and schizophrenia 64 in voltage-gated sodium channels, as well as in synaptic gene sets ARC and NMDAR. 65 Although no individual gene was associated with schizophrenia, these findings 66 suggest larger studies will identify the specific genes driving these associations. 67 68 Introduction 69 70 Schizophrenia is a highly heritable polygenic disorder [1]. Collectively, common 71 alleles contribute up to half of the genetic variance in schizophrenia liability [2, 3], 72 4 and 145 distinct loci have currently been associated with the disorder at genome-wide 73 levels of significance in the most recent genome-wide association study [4]. 74Schizophrenia risk is also conferred by rare mutations including copy number variants 75 (CNVs) [5, 6] and rare coding variants (RCVs) [7, 8], each of which sometimes occur 76 as de novo mutations [9, 10]. 77Studies of RCVs have the potential to inform schizophrenia pathogenesis 78 since they can pinpoint specific functional variants in individual genes. However, to 79 date, only two genes, SETD1A [11] and RBM12 [12], have been strongly implicated. 80A major limiting factor, as for studies of common variants, is that for complex 81 disorders, large samples are generally required to obtain robust results in case-control 82[13] studies. To date, the largest published sequencing studies of schizophrenia have 83 involved around 5,000 cases, 9,000 controls and 1,000 parent-proband trios [7, 11], 84 which are an order of magnitude smaller than recently published schizophrenia SNP 85 genotyping studies of common risk alleles (e.g. 40,675 cases and 64,643 controls [4]). 86 Nevertheless, whole exome sequencing studies have provided important clues to the 87 pathophysiology of schizophrenia. For example, proband-parent trio based studies 88 have shown de novo RCVs to be significantly enriched among ...