List of 54 CNVs analysed in this study
| CNV locus | Location (hg19) | Genes (n) | Carriers, n (%) | N sign. FDR=0.1 |
| TAR_del | chr1:145,39–145,81 | 17 | 75 (0.018) | 0 |
| TAR_dup | chr1:145,39–145,81 | 17 | 436 (0.1) | 1 |
| 1q21.1del | chr1:146,53–147,39 | 9 | 113 (0.027) | 2 |
| 1q21.1dup | chr1:146,53–147,39 | 9 | 177 (0.042) | 1 |
| NRXN1_del | chr2:50,14–51,26 | 1 | 163 (0.039) | 1 |
| 2q11.2del | chr2:96,74–97,68 | 22 | 31 (0.007) | 0 |
| 2q11.2dup | chr2:96,74–97,68 | 22 | 29 (0.007) | 0 |
| 2q13del(NPHP1) | chr2:110,86–110,98 | 3 | 2448 (0.58) | 0 |
| 2q13dup(NPHP1) | chr2:110,86–110,98 | 3 | 1976 (0.47) | 0 |
| 2q13del | chr2:111,39–112,01 | 3 | 53 (0.013) | 0 |
| 2q13dup | chr2:111,39–112,01 | 3 | 71 (0.017) | 1 |
| 2q21.1del | chr2:131,48–131,93 | 5 | 41 (0.01) | 0 |
| 2q21.1dup | chr2:131,48–131,93 | 5 | 59 (0.014) | 0 |
| 3q29del | chr3:195,72–197,35 | 28 | 9 (0.002) | 0 |
| 3q29dup | chr3:195,72–197,35 | 28 | 5 (0.001) | 6 |
| WBS_dup | chr7:72,74–74,14 | 26 | 14 (0.003) | 0 |
| 7q11.23dup_distal | chr7:75,14–76,06 | 16 | 24 (0.006) | 0 |
| 8p23.1dup | chr8:8,10–11,87 | 35 | 6 (0.001) | 0 |
| 10q11.21q11.23del | chr10:49,39–51,06 | 19 | 57 (0.014) | 0 |
| 10q11.21q11.23dup | chr10:49,39–51,06 | 19 | 43 (0.01) | 0 |
| 10q23dup | chr10:82,05–88,93 | 29 | 7 (0.002) | 0 |
| 13q12del(CRYL1) | chr13:20,98–21,10 | 2 | 379 (0.09) | 0 |
| 13q12dup(CRYL1) | chr13:20,98–21,10 | 2 | 10 (0.002) | 0 |
| 13q12.12del | chr13:23,56–24,88 | 10 | 85 (0.02) | 0 |
| 13q12.12dup | chr13:23,56–24,88 | 10 | 236 (0.056) | 0 |
| 15q11.2del | chr15:22,81–23,09 | 5 | 1664 (0.39) | 0 |
| 15q11.2dup | chr15:22,81–23,09 | 5 | 2041 (0.48) | 0 |
| PWS_dup | chr15:23,68–28,39 | 116 | 19 (0.005) | 0 |
| 15q11q13del_BP3-BP4(APBA2, TJP) | chr15:29,16–30,38 | 4 | 16 (0.004) | 1 |
| 15q11q13dup_BP3-BP4(APBA2, TJP) | chr15:29,16–30,38 | 4 | 53 (0.013) | 0 |
| 15q11q13dup_BP3-BP5 | chr15:29,16–32,46 | 17 | 9 (0.002) | 0 |
| 15q13.3del | chr15:31,08–32,46 | 8 | 42 (0.01) | 2 |
| 15q13.3dup | chr15:31,08–32,46 | 8 | 240 (0.057) | 0 |
| 15q13.3del(CHRNA7) | chr15:32,02–32,46 | 1 | 10 (0.002) | 0 |
| 15q13.3dup(CHRNA7) | chr15:32,02–32,46 | 1 | 3031 (0.72) | 0 |
| 15q24dup | chr15:72,90–78,15 | 77 | 9 (0.002) | 0 |
| 16p13.11del | chr16:15,51–16,29 | 7 | 131 (0.031) | 1 |
| 16p13.11dup | chr16:15,51–16,29 | 7 | 828 (0.2) | 2 |
| 16p12.1del | chr16:21,95–22,43 | 8 | 246 (0.058) | 7 |
| 16p12.1dup | chr16:21,95–22,43 | 8 | 202 (0.048) | 0 |
| 16p11.2distal_del | chr16:28,82–29,05 | 11 | 58 (0.014) | 3 |
| 16p11.2distal_dup | chr16:28,82–29,05 | 11 | 137 (0.033) | 0 |
| 16p11.2del | chr16:29,65–30,20 | 30 | 110 (0.026) | 7 |
| 16p11.2dup | chr16:29,65–30,20 | 30 | 138 (0.033) | 2 |
| 17p12del(HNPP) | chr17:14,14–15,43 | 8 | 237 (0.056) | 1 |
| 17p12dup(CMT1A) | chr17:14,14–15,43 | 8 | 124 (0.029) | 3 |
| Potocki-Lupski syndrome | chr17:16,81–20,21 | 59 | 5 (0.001) | 0 |
| 17q11.2del(NF1) | chr17:29,12–30,27 | 19 | 9 (0.002) | 0 |
| 17q12del | chr17:34,81–36,22 | 17 | 9 (0.002) | 2 |
| 17q12dup | chr17:34,81–36,22 | 17 | 101 (0.024) | 1 |
| 22q11.2del | chr22:19,04–21,47 | 61 | 10 (0.0024) | 0 |
| 22q11.2dup | chr22:19,04–21,47 | 61 | 280 (0.066) | 2 |
| 22q11.2distal_del | chr22:21,92–23,65 | 26 | 5 (0.001) | 1 |
| 22q11.2distal_dup | chr22:21,92–23,65 | 26 | 13 (0.003) | 0 |
The column ‘N sign. FDR=0.1’ shows the number of significant associations between the CNV and medical phenotypes at a threshold of FDR=0.1. Further details are given in online supplementary table 1. First-degree relatives are included in the numbers of carriers.
FDR, false discovery rate.