The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability

By meta-analyzing rare coding variants in whole-exome sequences of 4,133 schizophrenia cases and 9,274 controls, de novo mutations in 1,077 trios, and copy number variants from 6,882 cases and 11,255 controls, we show that individuals with schizophrenia carry a significant burden of rare damaging variants in 3,488 genes previously identified as having a near-complete depletion of loss-of-function variants. In schizophrenia patients who also have intellectual disability, this burden is concentrated in risk genes associated with neurodevelopmental disorders. After excluding known neurodevelopmental disorder risk genes, a significant rare variant burden persists in other loss-of-function intolerant genes, and while this effect is notably stronger in schizophrenia patients with intellectual disability, it is also seen in patients who do not have intellectual disability. Together, our results show that rare damaging variants contribute to the risk of schizophrenia both with and without intellectual disability, and support an overlap of genetic risk between schizophrenia and other neurodevelopmental disorders.