Identification of high risk DISC1 structural variants with a 2% attributable risk for schizophrenia

The causes of schizophrenia remain elusive. In a large Scottish pedigree, a balanced translocation t(1;11) (q42.1;q14.3) disrupting the DISC1 and DISC2 genes segregates with major mental illness, including schizophrenia and unipolar depression. A frame-shift carboxyl-terminal deletion was reported in DISC1 in an American family, but subsequently found in two controls. A few common structural variants have been associated with less than a 2-fold increased risk for schizophrenia, but replication has not been uniform. No large scale case-control mutation study has been performed. We have analyzed the regions of likely functional significance in the DISC1 gene in 288 patients with schizophrenia and 288 controls (5 megabases of genomic sequence analyzed). Six patients with schizophrenia were heterozygous for ultra-rare missense variants not found in the 288 controls (p = 0.015) and shown to be ultra-rare by their absence in a pool of 10,000 control alleles. We conclude that ultra-rare structural variants in DISC1 are associated with an attributable risk of about 2% for schizophrenia. In addition, we confirm that two common structural variants (Q264R and S704C) elevate the risk for schizophrenia slightly (odds ratio 1.3, 95% CI: 1.0-1.7). DISC1 illustrates how common/moderate risk alleles suggested by the HapMap project might be followed up by resequencing to identify genes with high risk, low frequency alleles of clinical relevance.