Table 3.
List of likely pathogenic CNVs
| Patients | Gender | Alteration (Hg19) | Type | Size (Kb) | Genes | Relevant genes involved | Confirmation | Inheritance | DGV controls | DECIPHER | Array platform | Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C13 | Male | arr 1q43-q44(240,043,427-249,233,096)x1dn f | del | 3.7 | 18 | AKT3 | qPCR | de novod | No | 250,152, 250,915 (smaller) | 1 | Lopes F, et al., 2019 |
| R15 | Female | arr 1q43-q44(243,552,007-243,738,675)x1dn f | del | 0.19 | 2 | AKT3 | qPCR | de novod | No | 252,432 (smaller) | 2 | Lopes F, et al., 2019 |
| C14 | Male | arr 1q43q44(243,592,147-243,749,968)x1pat f | del | 0.16 | 2 | AKT3 | qPCR | paternal | No | 252,432 (smaller) | 1 | Lopes F, et al., 2019 |
| R16 | Female | arr 2q11.2-q12.2(101,756,265-106,265,018)x1dn | del | 4500 | 24 | MAP4K4, FHL2, POU3F3, CNOT11 | qPCR | de novo | No | 251,756 | 2 | – |
| R17, R18e | Male, Female | arr 7q33(133,176,651-135,252,871)x1mat f | del | 2076 | 23 | AGBL3, CNOT4, CALD1, EXOC4 | qPCR | maternala | No | 256,036 | 2 | Lopes F, et al., 2018 |
| R19 | Female | arr 10q26.3(131,374,701-132,030,468)x1dn | del | 600 | 3 | EBF3 | qPCR | de novo | 3/6564b | No | 2 | Lopes F et al., 2017 |
| C15 | Male | arr 17p11.2(16,757,564-17,178,161)x1mat | del | 420 | 5 | COPS3 | NP | maternala | No | No | 3 | – |
| arr 17p11.2(18,478,816-21,255,056)x1mat | del | 2770 | 36 | EPN2, RNF112, ULK2, ALDH3A2, AKAP10, B9D1 | NP | maternala | No | 340,692 (smaller) | – | |||
| R20 | Female | arr 20q13.12-q13.13(43,283,820-48,850,844)x1dn | del | 5500 | 88 | KCNB1, PIGT, CTSA, SLC2A10, ARFGEF2 | NP | de novo | No | 309 | 2 | – |
| C16 | Female | arr 1p22.1p21.3(92,227,986-98,689,243)x3mat | dup | 6461 | 44 | FAM69A, TGFBR3, GLMN, EVI5, RPL5, MTF2, DR1, ABCA4, ABCD3, CNN3, PTBP2, DPYD | qPCR | maternala | No | 318,358 | 1 | – |
| C17,C18e | Male, Male | arr 7q33(134,598,205-134,815,177)x3mat f | dup | 216 | 2 | CALD1, AGBL3 | qPCR | maternala | No | No | 1 | Lopes F, et al., 2018 |
| R21 | Female | arr 9q33.2-q33.3(123,525,064-127,187,619)x4dn | tri | 3600 | 52 | CRB2, LHX2, LHX6, DENND1A, STRBP, RAB14, GSN, PSMB7, ZBTB26 | qPCR | de novo | No | No | 2 | – |
| C19 | Female | arr 9q34.3(140540819–140,659,057)×3mat | dup | 0.118 | 2 | EHMT1 | NP | maternal | 1/2504 (smaller) | No | 1 | – |
| R22, R23e | Male, Male | arr Xq24(119,592,606-119,904,981)x2mat | dupc | 300 | 4 | CUL4B, LAMP2, C1GALT1C1, MCTS1 | qPCR | maternal | No | No | 2 | – |
| C20 | Male | arr Xq26.3(135,293,144-135,863,290)x2mat | dup | 570 | 9 | ARHGEF6, CD40LG, BRS3, MAP7D3 | qPCR | maternal | No | No | 3 | – |
Patients R15 to R23: from research cohort; Patients C13 to C20: from clinical cohort; NP Not performed; (a): inherited from an affected parent; (b): doubt regarding the quality of the call in these controls; (c) duplication may disrupt gene if located in tandem; (d) paternity and maternity confirmed; (e): siblings; (f): family described elsewhere. Array platform 1: Affymetrix Cystoscan 750 K; 2: Agilent 180 K; 3: KaryoArray®v3.0 (Agilent 8x60k)