An increased burden of rare copy number variants (CNVs), structural variations of the genome, has been associated with neurodevelopmental and psychiatric disorders, including intellectual disability, autism spectrum disorders and schizophrenia. Given their relatively high penetrance, a significant impact on brain structure and function is anticipated but studies within brain structure are still relatively scarce. This panel of senior and early-career researchers brings together exciting multidisciplinary evidence on the impact of some of these rare variants using different imaging modalities (MRI, rs-fMRI, DTI, TEM) and functional measures in both human and animals. Results on the effects of 1q21.1, 15q11.2, and other rare CNVs on brain structure using big data from large collaborative efforts will be presented. Next, we will focus on mirror effects associated with 16p11.2 and 22q11.2 in functional connectivity (FC) and how these deletion-FC-signatures are specifically enriched in a large idiopathic autism sample. Next, mirror effects of 16p11.2 CNVs on sexual development will be explored by looking at 16p11.2 CNV carriers, patient cells, and animal models. Finally, using a novel Cyfip1 haploinsufficiency rat line, we will address how this gene in 15q11.2 BP1-BP2 affects white matter microstructure, which starts to unravel the cellular mechanisms contributing to 15q11.2 associated phenotypes.