Frequency of pathogenic CNVs identified in this study
| Cytogenetic location of CNVs | De novo loss | De novo gain | Inherited loss | Inherited gain | Total |
| 16p11.2 | 12 | 2 | 18 | 17 | 49 |
| 1q21.1q21.2 | 5 | 1 | 13 | 21 | 40 |
| 22q11.21 | 30 | 2 | 3 | 0 | 35 |
| 15q13.2q13.3 | 0 | 0 | 27 | 1 | 28 |
| 15q11.2q13.1 | 11 | 2 | 1 | 6 | 20 |
| 16p13.11 | 3 | 0 | 8 | 7 | 18 |
| 17q12 | 4 | 2 | 1 | 8 | 15 |
| 7q11.23 | 7 | 4 | 1 | 1 | 13 |
| 16p12.2 | 1 | 0 | 12 | 0 | 13 |
| 17p12 | 1 | 0 | 6 | 4 | 11 |
| 15q13.3 | 0 | 0 | 8 | 1 | 9 |
| 17p11.2 | 5 | 3 | 0 | 1 | 9 |
| 3q29 | 3 | 0 | 0 | 5 | 8 |
| 2p16.3 | 3 | 0 | 4 | 0 | 7 |
| 17p13.3 | 2 | 3 | 1 | 0 | 6 |
| 22q13.33 | 5 | 0 | 1 | 0 | 6 |
| 21q11.2q22.3 | 0 | 4 | 0 | 0 | 4 |
| 4p16.3 | 1 | 0 | 2 | 0 | 3 |
| 6q27 | 2 | 0 | 1 | 0 | 3 |
| 9p24.3p23 | 3 | 0 | 0 | 0 | 3 |
| 16p13.11p12.3 | 1 | 0 | 2 | 0 | 3 |
| 20p13 | 1 | 0 | 1 | 1 | 3 |
| 22q11.21q11.22 | 3 | 0 | 0 | 0 | 3 |
| 22q11.23q13.33 | 0 | 3 | 0 | 0 | 3 |
| 2q37.1q37.3 | 1 | 1 | 0 | 0 | 2 |
| 5q14.3 | 2 | 0 | 0 | 0 | 2 |
| 6p25.3p25.2 | 1 | 0 | 1 | 0 | 2 |
| 7p22.1 | 2 | 0 | 0 | 0 | 2 |
| 8p23.1 | 1 | 0 | 0 | 1 | 2 |
| 9p24.2p23 | 1 | 0 | 1 | 0 | 2 |
| 9p24.3p13.1 | 0 | 2 | 0 | 0 | 2 |
| 10q26.2q26.3 | 2 | 0 | 0 | 0 | 2 |
| 10q26.3 | 1 | 0 | 1 | 0 | 2 |
| 11q24.2q25 | 2 | 0 | 0 | 0 | 2 |
| 13q12.3q13.1 | 2 | 0 | 0 | 0 | 2 |
| 15q11.1q13.1 | 1 | 1 | 0 | 0 | 2 |
| 16p13.3 | 1 | 0 | 1 | 0 | 2 |
| 17q21.31 | 2 | 0 | 0 | 0 | 2 |
| 18p11.32p11.21 | 0 | 2 | 0 | 0 | 2 |
| 18p11.32p11.31 | 0 | 0 | 1 | 1 | 2 |
| 22q11.1q11.21 | 0 | 2 | 0 | 0 | 2 |
| Other CNVs with single instance only | 71 | 28 | 23 | 5 | 127 |
Pathogenic CNVs identified in this study are listed in the descending order of their total frequencies in our cohort. Note that the individual CNVs grouped to generate frequencies have been grouped according to their chromosomal location and may include overlapping CNVs with different breakpoints. Only chromosomal locations with at least two CNVs in the study have been individually listed here. Full details of all the CNVs and their specific locations are provided in online supplementary table S1.