Loss-of-function (LOF) (i.e., nonsense, splice site, and frameshift) variants that lead to disruption of gene function are likely to contribute to the etiology of neuropsychiatric disorders. Here, we perform a systematic investigation of the role of both de novo and inherited LOF variants in schizophrenia using exome sequencing data from 231 case and 34 control trios. We identify two de novo LOF variants in the SETD1A gene, which encodes a subunit of histone methyltransferase, a finding unlikely to have occurred by chance, and provide evidence for a more general role of chromatin regulators in schizophrenia risk. Transmission pattern analyses reveal that LOF variants are more likely to be transmitted to affected individuals than controls. This is especially true for private LOF variants in genes intolerant to functional genetic variation. These findings highlight the contribution of LOF mutations to the genetic architecture of schizophrenia and provide important insights into disease pathogenesis. •De novo LOF variants in SETD1A histone methyltransferase implicate the gene in SCZ•Genes with damaging de novo variants in SCZ are enriched for chromatin regulators•Rare LOF variants contribute to the inherited component of SCZ risk•A key role for private LOF variants in genes intolerant to functional variation Takata et al. perform systematic survey of de novo and inherited loss-of-function mutations in schizophrenia and reveal two de novo loss-of-function mutations in the same gene, SETD1A, and a relative overtransmission of rare loss-of-function variants in genes intolerant to functional variation.