Extended Data Table 5. Association results for individual CNV regions.
Focused enrichment analysis of genes under schizophrenia-associated CNV regions. The top panel presents omnibus P-values testing all genes/regions (bold indicates significance after correction for the four tests, Pcorrected = 0.016 for NSstrict MAF < 0.1% variants). This enrichment arises solely from the 3q29 locus (middle panel; bold indicates significance after correction of the 44 tests performed, Pcorrected = 0.024 for 3q29). Genes and NSstrict case/control counts for the 3q29 region (lower panel).
| Group | Genes | Disruptive | NSstrict | ||
|---|---|---|---|---|---|
| Singletons | MAF < 0.1% | Singletons | MAF < 0.1% | ||
| CNV loci | All | 0.3279 | 0.4557 | 0.0843 | 0.0044 |
|
| |||||
| 1q21.1 | 0.4533 | 0.6966 | 0.3205 | 0.1832 | |
| 2p16.3 | 0.4775 | 0.3580 | 0.4703 | 0.2750 | |
| 3q29 | 0.1054 | 0.0068 | 0.0123 | 0.0006 | |
| 7q36.3 | 0.8642 | 0.5750 | 0.6411 | 0.2688 | |
| 7q11.23 | 0.7199 | 0.6800 | 0.3329 | 0.2207 | |
| 15q11.2 | 0.3208 | 0.1616 | 0.5138 | 0.1362 | |
| 15q13.3 | 0.0883 | 0.3976 | 0.3672 | 0.2746 | |
| 16p13.11 | 0.4194 | 0.3775 | 0.8346 | 0.4124 | |
| 16p11.2 | 0.1613 | 0.1240 | 0.0655 | 0.0974 | |
| 17q12 | 0.7377 | 0.5205 | 0.4313 | 0.1385 | |
| 22q11.21 | 0.9386 | 0.9977 | 0.5456 | 0.8754 | |
|
| |||
|---|---|---|---|
| Gene | A/U | Gene name | |
| 3q29 genes | DLG1 | 5/0 | discs, large homolog 1 (Drosophila) |
| RNF168 | 5/1 | ring finger protein 168, E3 ubiquitin protein ligase | |
| CEP19 | 2/0 | centrosomal protein 19kDa | |
| LRRC33 | 2/0 | leucine rich repeat containing 33 | |
| PAK2 | 2/0 | p21 protein (Cdc42/Rac)-activated kinase 2 | |
| PCYT1A | 5/2 | phosphate cytidylyltransferase 1, choline, alpha | |
| PIGX | 6/3 | phosphatidylinositol glycan anchor biosynthesis, class X | |
| FBXO45 | 1/0 | F-box protein 45 | |
| NCBP2 | 1/0 | nuclear cap binding protein subunit 2, 20kDa | |
| PIGZ | 1/0 | phosphatidylinositol glycan anchor biosynthesis, class Z | |
| TFRC | 1/0 | transferrin receptor (p90, CD71) | |
| ZDHHC19 | 1/0 | zinc finger, DHHC-type containing 19 | |
| C3orf43 | 4/2 | chromosome 3 open reading frame 43 | |
| MFI2 | 15/12 | antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5 | |
| SLC51A | 1/1 | solute carrier family 51, alpha subunit | |
| BDH1 | 0/1 | 3-hydroxybutyrate dehydrogenase, type 1 | |
| TCTEX1D2 | 0/1 | Tctex1 domain containing 2 | |
| WDR53 | 0/1 | WD repeat domain 53 | |