max=300 words): 283 28 Article body: 3,950 ABSTRACT 34The contactin-associated protein-like 2 (CNTNAP2) gene is a member of the neurexin 35 superfamily. CNTNAP2 was implicated in the cortical dysplasia-focal epilepsy (CDFE) 36 syndrome, a recessive disease characterized by intellectual disability, epilepsy, language 37 4 58 AUTHOR SUMMARY 59 Genetic mutations that disrupt both copies of the CNTNAP2 gene lead to severe disease, 60 characterized by profound intellectual disability, epilepsy, language difficulties and autistic 61 traits. Researchers hypothesized that this gene may also be involved in autism given some 62 overlapping clinical features with this disease. Indeed, several large DNA deletions affecting 63 one of the two copies of CNTNAP2 were found in some patients with autism, and later also in 64 patients with schizophrenia, bipolar disorder, ADHD and epilepsy, suggesting that this gene 65 was involved in several psychiatric or neurologic diseases. Other studies considered genetic 66 sequence variations that are common in the general population, and suggested that two such 67 sequence variations in CNTNAP2 predispose to psychiatric diseases by influencing the 68 functionality and connectivity of the brain. In the current study, we report the deletion of one 69 copy of CNTNAP2 in a patient with bipolar disorder from an extended family where five 70 relatives were affected with this condition. To better understand the involvement of CNTNAP2 71 in risk of mental illness, we performed several genetic analyses using a series of large publically 72 available or in-house datasets, comprising many thousands of patients and controls. Despite 73 the previous consideration of CNTNAP2 as a strong candidate gene for autism or schizophrenia, 74 we show that neither common, deletion nor ultra-rare variants in CNTNAP2 are likely to play 75 a major role in risk of psychiatric diseases. 76 77 78 79 80 81 82 5 83 84The contactin-associated protein-like 2 (CNTNAP2) is located on chromosome 7q35-36.1, and 85 consists of 24 exons spanning 2.3Mb, making it one of the largest protein coding genes in the 86 human genome. This gene encodes the CASPR2 protein, related to the neurexin superfamily, 87 which localises with potassium channels at the juxtaparanodal regions of the Ravier nodes in 88 myelinated axons, playing a crucial role in the clustering of potassium channels required for 89 conduction of axon potentials [1]. CNTNAP2 is expressed in the spinal cord, prefrontal and 90 frontal cortex, striatum, thalamus and amygdala; this pattern of expression is preserved 91 throughout the development and adulthood [2, 3]. Its function is related to neuronal migration, 92 dendritic arborisation and synaptic transmission [4]. The crucial role of CNTNAP2 in the 93 human brain became clear when Strauss et al, reported homozygous mutations in Old Order 94 Amish families segregating with a severe Mendelian condition, described as cortical dysplasia-95 focal epilepsy (CDFE) syndrome (OMIM 610042) [5]. In 2009, additional patie...