Table 2.
Common CNV disorders including the candidate genes involved in the clinical phenotype (where applicable), and genes contained within with reported epigenetic machinery roles.
| Syndrome | Chromosome Region | Candidate Gene | Genes in Region with Epigenetic Function |
|---|---|---|---|
| 1p36 Deletion/Duplication | 1p36 | - | ICMT, CHD5, TP73, PMRD16, SKI, NOC2L |
| 1q21.1 Deletion/Duplication | 1q21.1 | - | CHD1L |
| 1q43q44 Deletion | 1q43q44 | - | HNRNPU, DESI2, ZBTB18, AKT3 |
| 2q11.2 Deletion/Duplication | 2q11.2 | - | KANSL3, ARID5A |
| 2q13 Deletion/Duplication | 2q13 | - | MIR4435-2HG |
| 2q37 Deletion | 2q37 | - | HDAC4, D2HGDH, ING5, HDLBP, PASK |
| 3q29 Deletion/Duplication | 3q29 | - | PAK2, RNF168 |
| 4p16.3 Deletion (Wolf–Hirschhorn)/4p16.3 Duplication | 4p16.3 | NSD2 | NSD2, CTBP1, SLBP, CTBP1, PCGF3 |
| 5p15 Deletion (Cri du Chat)/5p15 Duplication | 5p15 | - | ATPSCKMT, MTRR, NSUN2, LPCAT1, BRD9 |
| 5q35 Deletion (Sotos)/5q35 Duplication (Hunter–McAlpine) | 5q35 | NSD1 | NSD1, UIMC1 |
| 7q11.23 Deletion (Williams–Beuren)/7q11.23 Duplication | 7q11.23 | - | METTL27, BUD23, BCL7B, BAZ1B |
| 8p23.1 Deletion/Duplication | 8p23.1 | - | TNKS |
| 9q34 Deletion (Kleefstra)/9q34 Duplication | 9q34 | EHMT1 | EHMT1 |
| 10q22.3q23.2 Deletion/Duplication | 10q22.3q23.2 | - | WAPL, DYDC1, MAT1A |
| 11p11.2 Deletion (Potocki–Shaffer)/11p11.2 Duplication | 11p11.2 | - | PHF21A, CD82, ALKBH3 |
| 11q13.2q13.4 Deletion | 11q13.2q13.4 | - | KMT5B |
| 15q11.2 Deletion (non-imprinting region) | 15q11.2 | - | - |
| 15q11q13 Deletion (Prader–Willi/Angelman)/15q11q13 Duplication | 15q11q13 | - | HERC2 |
| 15q13.3 Deletion/Duplication | 15q13.3 | - | OTUD7A, KLF13 |
| 15q24 (BP0-BP1) Deletion/Duplication | 15q24 | - | - |
| 15q24 (BP2-BP3) Deletion | 15q24 | - | SIN3A, COMMD4 |
| 15q25.2 Deletion | 15q25.2 | - | HDGFL3, BNC1 |
| 16p13.3 Deletion (Rubinstein–Taybi)/16p13.3 Duplication | 16p13.3 | CREBBP | CREBBP |
| 16p13.11 Deletion/16p13.11 Duplication | 16p13.11 | - | NDE1 |
| 16p11.2 Distal Deletion/Duplication | 16p11.2 | - | SH2B1 |
| 16p11.2 Deletion/Duplication | 16p11.2 | - | PPP4C, HIRIP3, PAGR1, INO80E |
| 17p13.3 Deletion (Miller–Dieker)/17p13.3 Duplication | 17p13.3 | - | HIC1, SMYD4, MYO1C |
| 17p11.2 Deletion (Smith–Magenis)/17p11.2 Duplication (Potocki–Lupski) | 17p11.2 | RAI1 | ALKBH5, RAI1, PEMT |
| 17q11.2 Deletion/Duplication | 17q11.2 | - | SUZ12 |
| 17q12 Deletion/Duplication | 17q12 | - | HNF1B, TADA2A, AATF, PIGW |
| 17q21.31 Deletion (Koolen–de Vries)/17q21.31 Duplication | 17q21.31 | KANSL1 | KANSL1 |
| 22q11.2 Tetrasomy/Triplication (Cat eye syndrome) | 22q11.2 | - | CECR2, ADA2 |
| 22q11.2 Deletion (DiGeorge/Velocardiofacial)/22q11.2 Duplication | 22q11.2 | - | THAP7, TRMT2A, COMT, HIRA |
| 22q11.2 recurrent region distal type I (D-E/F) Deletion/Duplication | 22q11.2 | - | TOP3B, PPM1F |
| 22q13.3 Deletion (Phelan–McDermid) | 22q13.3 | SHANK3 | BRD1 |
| Xp11.22 Duplication (MRX17) | Xp11.22 | - | HUWE1, HSD17B10, SMC1A |