Table 2.
List of pathogenic CNVs
| Patients | Gender | Alteration (Hg19) | Type | Size (Mb) | Genes | Key gene(s) involved | Associated syndrome | Phenotype overlap | Inheritance | Confirmation | Array platform | Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| R1 | Male | arr 1p36.23-p36.21(8,593,674-15,396,672)x1dn | del | 6.7 | 86 | ANGPTL7, CASZ1, MAD2L2, RERE | – | – | de novo | NP | 1 | – |
| R2 | Male | arr 2p13.1-p13.3(70,894,906-74,986,518)x1dnc | del | 4 | 62 | CYP26B1, EXOC6B | – | – | de novo | NP | 1 | Wen J, 2013 |
| R3 | Male | arr 3q22.1-q23(131,415,639-141,618,552)x1dn | del | 1.020 | 65 | FOXL2 | BPES | Yes (eye features) | de novo | NP | 1 | – |
| C1 | Male | arr 5p15.33-p15.32(204,849-5,014,883)x1 | del | 4.81 | 30 | TERT [CTNND2 not involved] | – | – | ND | NP | 2 | – |
| R4 | Male | arr 6q25.3(156,012,754-158,804,494)x1dnc | del | 2.6 | 14 | ARID1B | Coffin-Siris syndrome | Yes | de novo | NP | 1 | Santen GW, 2013 |
| C2 | Male | arr 7q11.23(72,721,760-74,140,846)x1 | del | 1.419 | 28 | BAZ1B, STX1A, WBSCR22, ELN | Williams-Beuren syndrome | Partially | ND | NP | 2 | – |
| R5 | Female | arr 8p23.1(7,039,276-12,485,558)x1dn | del | 5.5 | 70 | SOX7, GATA4 | 8p23.1 deletion syndrome | Yes (cardiac) | de novo | NP | 1 | – |
| C3 | Male | arr 11q24.2-q25(125,232,584-134,446,160)x1dn | del | 9.214 | 54 | KIRREL3, ETS1, FLI1, KCNJ1, KCNJ5, RICS | – | Partially | de novo | qPCR | 2 | – |
| R6 | Female | arr 12q24.21-q24.22(115,505,500-117,441,683)x1dnc | del | 0.2 | 10 | MED13L | – | Yes | de novo | qPCR | 1 | Adegbola A, 2015 |
| C4 | Male | arr 16p11.2(29,674,336-30,198,123)x1dn | del | 0.524 | 29 | KCTD13 | 16p11.2 deletion syndrome | – | de novo | NP | 2 | – |
| C5 | Male | arr 17q21.31(43,710,371-44,215,352)x1 | del | 0.505 | 8 | CRHR1, MAPT, STH, and part of the KIAA1267 (KANSL1) | 17q21.31 deletion syndrome (Koolen-De Vries syndrome) | – | ND | NP | 3 | – |
| C6 | Male | arr 22q11.21(18,894,835-21,505,417)x1 | del | 2.611 | 59 | TBX1 | 22q11 deletion syndrome | – | ND | NP | 2 | – |
| C7 | Male | arr 22q13.3(49,513,903-51,178,264)x1 | del | 1.664 | 39 | SHANK3 | 22q13.3 deletion syndrome (Phelan-McDermid syndrome) | Partially | ND | NP | 2 | – |
| C8 | Male | arr 1q21.1q21.2(146,106,723-147,830,830)x3dn | dup | 1.7 | 17 | HYDIN2, PRKAB2 | 1q21.1 duplication syndrome e | Partially | de novo | qPCR | 4 | – |
| R7 | Male | arr 1q21.1(145,883,119-148,828,690)x3pat | dup | 2.5 | 23 | HYDIN2, PRKAB2, GJA5 | 1q21.1 duplication syndrome e | Yes | paternal | NP | 1 | – |
| R8 | Male | arr 12q24.21(116,408,736-116,704,303)x3dnc | dup | 0.3 | 2 | MED13L | – | Yes | de novo | qPCR | 1 | Adegbola A, 2015 |
| C9 | Male | arr 13q12.12-q34(23,749,431-115,083,342)x2.15a | dup | 91.33 | ## | – | Trisomy 13 (mosaicism) | Yes | ND | Karyotyped | 2 | – |
| C10 | Female | arr 15q11.2-q13.1(22880274–29,331,964)x3mat | dup | 6.45 | 111 | CYF1P1, NIPA2, NIPA1, MKRN3, NDN, MAGEL2, SNURF/SNRPN, UBE3A GABRB3 | 15q11-q13 duplication syndromeb | Yes | maternal | NP | 2 | – |
| C11 | Female | arr 16p13.11(15,034,010-16,199,882)x3 | dup | 1.166 | 11 | NDE1 | 16p13.11 duplication syndrome e | – | ND | NP | 5 | – |
| R9 | Male | arr 16p13.11(15,421,671-16,443,968)x3mat | dup | 1 | 19 | NDE1 | 16p13.11 duplication syndrome e | Yes | maternal | NP | 1 | – |
| R10 | Male | arr 16p13.11(15,484,180-16,308,344)x3mat | dup | 0.8 | 9 | NDE1 | 16p13.11 duplication syndrome e | Yes | maternal | NP | 1 | – |
| C12 | Male | arr 21q11.2-q22.11(14,417,523-34,894,625)x3 | dup | 20.47 | 110 | DSCR1, DSCR2, DSCR3, DSCR4, APP | – | No | ND | NP | 2 | – |
| R11 | Male | arr Xp11.22(53,569,653-53,769,748)x2mat | dup | 0.2 | 3 | HUWE1 | – | Yes | maternal | qPCR | 1 | – |
| R12 | Male | arr Xq28(152,348,378-155,228,013)x2dn | dup | 2.8 | 78 | MECP2 | MECP2 duplication syndrome | Yes | de novo | NP | 1 | – |
| R13 | Male | arr Xq28(153,130,545-153,602,293)x2mat | dup | 0.5 | 16 | MECP2 | MECP2 duplication syndrome | Yes | maternal | NP | 1 | – |
| R14 | Male | arr 9q34.13-q34.3(135,767,911-141,153,431)x3dn | dup | 5.516 | 135 | EHMT1, RXRA, GRIN1, UAP1L1 | 9q34 duplication syndrome | Partially | de novo | NP | 1 | – |
| arr 14q32.31-q32.33(102,959,110-104,578,612)x3dn | dup | 1.620 | 22 | MARK3, KLC1, EIF5 | – | – | de novo | NP | 1 | – | ||
| arr 14q32.33(105,104,831-106,531,339)x3dn | dup | 1.427 | 24 | – | – | de novo | NP | 1 | – |
Patients R1 to R14: from research cohort; Patients C1 to C12: from clinical cohort; NP Not performed, ND Not determined; (a): mosaicism; (b) methylation status for SNRPN is normal (studied by MLPA); (c): Published in detail elsewhere; (d): karyotype revealed a balanced translocation between chromosomes 13 and 14, resulting in mosaic trisomy 13; (e): Other causes of disease were not excluded therefore the variant might not explain the total phenotypic presentation. Array platform 1: Agilent 180 K; 2: KaryoArray®v3.0 (Agilent 8x60k); 3: Affymetrix CytoScan HD array; 4: Affymetrix CytoScan 750 K; 5: Agilent Whole Genome 244 K