In this study we identify a new gene for subependymal and subcortical heterotopia, revealing a de novo Disks large-associated protein 4 (DLGAP4) frameshift variation in a patient with unilateral heterotopia and polymicrogyria, resembling the EML1 phenotype. Here, DLGAP4 is linked to Non-syndromic cerebral malformation due to abnormal neuronal migration.