Copy number variants reveal divergent genetic and diagnostic cortical signatures across psychiatric disorders.

Structural variants, including copy number variants (CNVs), confer substantial risk for neurodevelopmental and psychiatric disorders (NPDs), yet whether their cortical effects relate to those observed in the psychiatric conditions they predispose to remains unclear. Here, we present the first systematic comparison of cortical phenotypes across 18 NPD-associated CNVs and aneuploidies, disorder-associated common variants, and 8 psychiatric disorders. Rare CNVs preferentially affected total surface area (SA), with 11-fold larger effects than psychiatric diagnoses, while NPDs preferentially affected mean cortical thickness (CT), with most CT effects observed in medicated subgroups, suggesting non-genetic contributions. NPD-associated common variants showed enrichment in SA but not CT associations. Regionally, both rare and common genetic variants showed larger effects in sensorimotor regions, aligning with the sensorimotor-to-association cortical gradient as well as regional heritability estimates. In contrast, psychiatric diagnoses showed larger effects in association regions. Individual NPD-associated variants were evenly split between those increasing and decreasing surface area. This heterogeneity likely explains why aggregating variants using polygenic scores shows only weak associations with SA. Overall, cortical signatures of psychiatric diagnoses diverge from those associated with genetic risk. Genetic variants preferentially impact SA and sensorimotor regions through early developmental mechanisms, while psychiatric diagnoses are associated with CT and association regions likely reflecting medication, illness chronicity, and environmental factors.