Significance Previous research has explored the association between behavioral disorders and dysfunction in corresponding neural networks. For example, autism spectrum disorder, Prader–Willi syndrome, and Dravet syndrome are characterized by behavioral deficits in the visuomotor integration system. To date, few investigations have combined brain connectomic–genetic data to investigate the biological basis of childhood neurodevelopment and clinical syndromes. The present study provides evidence of a link between expression of malfunctioning genes associated with these syndromes (i.e., TBR1, SCN1A, MAGEL2, and CACNB4) and cortical distribution across regions devoted to integrating visual and motor information (i.e., the lateral occipital cortex, OP4, and intraparietal sulcus). We suggest this altered gene expression may underlie brain network dysfunction which, in turn, leads to behavioral deficits.