Table 3 Clinically relevant CNVs found in the patients with intellectual disability and developmental delay.
Region name | No. of subjects | Cytoband | CNV type | Size (kb) | Parent of origin | Pathogenicity |
|---|---|---|---|---|---|---|
Genetic syndromes | ||||||
1p36 deletion syndrome | 2 | 1p36.33p36.23; 1p36.33p36.32 | Deletion | 4515–7908 | De novo (2) | Pathogenic |
1q21.1 microduplication syndrome | 1 | 1q21.1q21.2 | Duplication | 1626 | Maternal | Pathogenic |
2q37 microdeletion syndrome | 2 | 2q37.3 | Deletion | 3656–3973 | De novo (2) | Pathogenic |
Wolf-Hirschhorn syndrome | 1 | 4p16.3p16.2 | Deletion | 5868 | De novo | Pathogenic |
Cri-du-chat syndrome | 2 | 5p15.33p15.1; 5p15.31p15.1 | Deletion | 7595–16,576 | De novo (2) | Pathogenic |
5q trisomy syndrome | 1 | 5q34q35.3 | Duplication | 15,248 | De novo | Pathogenic |
Sotos syndrome | 1 | 5q35.2q35.3 | Deletion | 1911 | De novo | Pathogenic |
Silver–Russell syndrome | 1 | 7p13q34 | UPD | 95,119 | maternal | Pathogenic |
Williams–Beuren syndrome | 11 | 7q11.23 | Deletion | 1424–1570 | De novo (11) | Pathogenic |
Waardenburg syndrome | 3 | 8p23.3p23.1 | Deletion | 6841–9905 | De novo (1), unknown (2) | Pathogenic |
Branchio–Otorenal syndrome | 1 | 8q12.3q13.3 | Deletion | 10,009 | De novo | Pathogenic |
9 partial monosomy syndrome | 1 | 9p24.3p23 | Deletion | 10,487 | De novo | Pathogenic |
9p partial trisomy | 5 | 9p24.3p13.1; 9p24.3p21.1; 9p24.3q21.11; 9p24.3p21.13 | Duplication (4), duplication x3 + duplication x4 (1)a | 29,995–74,596 | De novo (5) | Pathogenic |
10p partial deletion | 1 | 10p15.3p14 | Deletion | 11,049 | De novo | Pathogenic |
10p15.3 deletion syndrome | 1 | 10p15.3p15.2 | Deletion | 3472 | De novo | Pathogenic |
Distal trisomy 10q syndrome | 1 | 10q24.2q26.3 | Duplication | 35,938 | De novo | Pathogenic |
10qter deletion syndrome | 1 | 10q26.2q26.3 | Deletion | 5640 | De novo | Pathogenic |
Prader–Willi syndrome (deletion) | 2 | 15q11.2q13.1 | Deletion | 5259–6261 | Paternal (2) | Pathogenic |
Prader–Willi syndrome (UPD) | 2 | 15q11.2q26.3 | UPD (2) | 79,659–79,677 | Maternal | Pathogenic |
Angelman syndrome (deletion) | 1 | 15q11.2q13.1 | Deletion | 5239 | Maternal | Pathogenic |
Angelman syndrome (UPD) | 1 | 15q11.2q21.1 | UPD | 25,942 | Paternal | Pathogenic |
15q11-q13 duplication syndrome | 4 | 15q11.2q13.1; 15q11.2q13.2; 15q13.2q13.3 | Duplication (1), duplication x3 (1), duplication x4 (1), duplication x3 + duplication x4 (1)b | 4929–9674 | De novo (3), unknown (1) | Pathogenic |
15q26 deletion syndrome | 1 | 15q26.3 | Deletion | 3134 | Unknown | Pathogenic |
16p13.11 microduplication syndrome | 1 | 16p13.11 | Duplication | 1429 | maternal | VUS |
16p11.2 microduplication syndrome (BP4-BP5) | 2 | 16p11.2 | Duplication | 586–826 | De novo (1), unknown (1) | Pathogenic |
16 partial trisomy syndrome | 1 | 16q22.1q24.3 | Duplication | 19,668 | De novo | Pathogenic |
17 partial trisomy syndrome | 1 | 17q25.3 | Duplication | 5701 | De novo (1) | Pathogenic |
18q deletion syndrome | 4 | 18q21.2q21.31; 18q21.31q23; 18q21.33q23; 18q22.3q23 | Deletion (3), deletion x1–2 (1) | 3042–77,943 | De novo (3), unknown (1) | Pathogenic |
18q duplication syndrome | 1 | 18q21.32q23 | Duplication | 77,943 | De novo | Pathogenic |
22q11.2 duplication syndrome | 1 | 22q11.1q11.21; 22q11.21 | Duplication x4 + duplication x3c | 2893; 1682 | De novo | Pathogenic |
22q11.2 deletion syndrome | 3 | 22q11.21 | Deletion | 2549–2884 | De novo (3) | Pathogenic |
MECP2 microduplication syndrome | 2 | Xq28 | Duplication | 377–424 | Maternal (1), paternal (1) | Pathogenic |
Other clinically relevant CNVs | ||||||
1q25.1q31.1 deletion | 1 | 1q25.1q31.1 | Deletion | 12,292 | De novo | Pathogenic |
2p16.1p12 deletion | 1 | 2p16.1p12 | Deletion | 16,664 | Unknown | Pathogenic |
2p21p13.2 duplication | 1 | 2p21p13.2 | Duplication | 28,560 | De novo | Pathogenic |
2p25.3p25.2 duplication | 1 | 2p25.3p25.2 | Duplication | 6544 | Unknown | Pathogenic |
2q13 deletion | 1 | 2q13 | Deletion | 1734 | De novo | Likely pathogenic |
3p14.1p11.1 duplication | 1 | 3p14.1p11.1 | Duplication | 21,577 | De novo | Pathogenic |
4p16.3p16.1 duplication | 1 | 4p16.3p16.1 | Duplication | 9452 | Unknown | Pathogenic |
4p16.3 deletion | 1 | 4p16.3 | Deletion | 1195 | Unknown | Pathogenic |
4p16.2p16.1 duplication | 1 | 4p16.2p16.1 | Duplication | 493 | De novo | VUS |
4q31.3q35.2 duplication | 1 | 4q31.3q35.2 | Duplication | 38,587 | Unknown | Pathogenic |
4q34.14q35.2 duplication | 1 | 4q34.14q35.2 | Duplication | 18,897 | De novo | Pathogenic |
6q23.3q24.2 deletion | 1 | 6q23.3q24.2 | Deletion | 7405 | Unknown | Pathogenic |
7q11.22q21.11 deletion | 1 | 7q11.22q21.11 | Deletion | 17,988 | De novo | Likely pathogenic |
8p23.3p22 deletion | 1 | 8p23.3p22 | Deletion | 17,300 | De novo | Pathogenic |
13q21.1q32.2 deletion | 1 | 13q21.1q32.2 | Deletion | 39,073 | De novo | Pathogenic |
14q11.2q21.2 duplication | 1 | 14q11.2q21.2 | Duplication | 23,595 | Unknown | Pathogenic |
14q11.2q32.33 UPD | 1 | 14q11.2q32.33 | UPD | 86,774 | maternal | Pathogenic |
14q32.12p32.33 duplication | 1 | 14q32.12p32.33 | Duplication | 11,616 | Unknown | Pathogenic |
15q26.2q26.3 deletion | 1 | 15q26.2q26.3 | Deletion | 3006 | De novo | Pathogenic |
16q24.2q24.3 duplication | 1 | 16q24.2q24.3 | Duplication | 2671 | Unknown | Pathogenic |
18p11.32p11.31 deletion | 1 | 18p11.32p11.31 | Deletion | 5987 | De novo | Pathogenic |
18p11.32p11.21 deletion | 1 | 18p11.32p11.21 | Deletion | 13,649 | De novo | Pathogenic |
18q21.32q23 duplication | 1 | 18q21.32q23 | Duplication | 19,416 | De novo | Pathogenic |
19p13.2 deletion | 1 | 19p13.2 | Deletion | 2260 | De novo | Likely pathogenic |
19p13.3p13.2 duplication | 1 | 19p13.3p13.2 | Duplication | 7327 | De novo | Pathogenic |
20p13 deletion | 1 | 20p13 | Deletion | 978 | De novo | Pathogenic |
20p13p12.3 deletion | 1 | 20p13p12.3 | Deletion | 9844 | Unknown | Pathogenic |
21q22.11q22.3 deletion | 1 | 21q22.11q22.3 | Deletion | 13,055 | De novo | Pathogenic |
21q22.3 duplication | 1 | 21q22.3 | Duplication | 2858 | De novo | VUS |
22q13.31q13.33 duplication | 2 | 22q13.31q13.33 | Duplication | 5648 | Unknown (2) | Pathogenic |
Xq22.3q27.1 duplication | 1 | Xq22.3q27.1 | Duplication | 32,324 | Unknown | Pathogenic |
