Table 4.
Details of likely pathogenic CNVs in FISH negative∗ suspected 22q11.2 microdeletion cases.
| DBN | Locus/loci | CNV | Start | End | Size | Genes | Gene details/disease |
|---|---|---|---|---|---|---|---|
| 18 | 22q11.22 | 3 | 22901370 | 23307965 | 0.4 | 7 | PRAME, LOC648691, POM121L1P, GGTLC2, MIR650, IGLL5; hsa-mir-650 |
| 7q11.21 | 1 | 64651296 | 65148399 | 0.49 | 3 | INTS4L1, ZNF92, INTS4L2 (cutis marmorata, epicanthus, everted lower lip vermilion, intellectual disability, microcephaly, retinoblastoma, short nasal septum, and thick lower lip vermilion) | |
|
| |||||||
| 20 | 1q21.2 | 3 | 147828939 | 149723885 | 1.9 | 18 | 2-3-toe syndactyly, abnormality of the helix, aplasia cutis congenita over the scalp vertex, attention deficit hyperactivity disorder, clinodactyly of the 5th finger, facial asymmetry, flat occiput, gait ataxia, global developmental delay, hyperpigmentation of the skin, hypoplastic areola, long eyelashes, microcephaly, muscular hypotonia, pointed chin, short 3rd toe, short neck, short stature, skull asymmetry, and walking on tiptoes FLJ39739; PPIAL4B; PPIAL4A; NBPF14; PPIAL4F; NBPF15; NBPF15; NBPF16; PPIAL4E; NBPF16; PPIAL4F; LOC645166; LOC645166; LOC388692; FCGR1C; HIST2H2BF; PPIAL4B; LOC728855 |
|
| |||||||
| 46 | 19p13.11 p12 p11 |
3 | 19863014 | 24556461 | 4.6 | 35 | LOC284440; ZNF506; ZNF253; ZNF93; ZNF682; ZNF90; ZNF486; LOC284441; ZNF826; ZNF737; ZNF626; ZNF626; ZNF85; ZNF430; ZNF714; ZNF431; ZNF708; ZNF738; ZNF493; ZNF429; ZNF100; LOC641367; ZNF43; ZNF208; ZNF257; ZNF676; ZNF98; ZNF492; ZNF99; ZNF91; ZNF675; ZNF681; RPSAP58; ZNF254; LOC100101266 |
| 11p11.2 p11.12 |
3 | 48359268 | 51530241 | 3.1 | 10 | OR4C45; OR4A47; FOLH1; LOC440040; OR4C13; OR4C12; LOC441601; LOC646813; OR4A5; OR4C46 | |
|
| |||||||
| 49 | 1q31.3 | 4 | 193973521 | 197781198 | 3.8 | 13 | KCNT2; CFH; CFHR3; CFHR1; CFHR4; CFHR2; CFHR5; F13B; ASPM; ZBTB41; CRB1; DENND1B; DENND1B |
| Xq21.1-q22.1 | 2 | 80368850 | 99441815 | 19 | 27 | HMGN5; SH3BGRL; POU3F4; CYLC1; RPS6KA6; HDX; UBE2DNL; APOOL; SATL1; ZNF711; POF1B; CHM; CHM; DACH2; DACH2; KLHL4; CPXCR1; TGIF2LX; PABPC5; PCDH11X; PCDH11X; PCDH11X; NAP1L3; FAM133A; LOC643486; DIAPH2; RPA4; LOC442459 | |
| Xq23 q24 | 2 | 112244679 | 117105172 | 4.8 | 18 | HTR2C; SNORA35; MIR764; MIR1912; MIR1264; MIR1298; MIR1911; MIR448; IL13RA2; LRCH2; RBMXL3; LUZP4; PLS3; PLS3; AGTR2; SLC6A14; CXorf61; KLHL13 | |
| Xq27.2-q28 | 2 | 141247401 | 148041505 | 6.7 | 36 | MAGEC2; SPANXN4; SPANXN3; SLITRK4; SPANXN2; UBE2NL; SPANXN1; SLITRK2; SLITRK2; CXorf1; MIR890; MIR888; MIR892A; MIR892B; MIR891B; MIR891A; CXorf51; CXorf51; MIR506; MIR507; MIR508; MIR509-2; MIR509-3; MIR509-3; MIR509-1; MIR509-2; MIR509-3; MIR510; MIR514-1; MIR514-3; MIR514-3; ASFMR1; FMR1; FMR1NB; AFF2; AFF2 | |
|
| |||||||
| 51 | 1q21.1 | 3 | 144007842 | 145384225 | 1.3 | 12 | LOC728855; LOC728875; PPIAL4B; PPIAL4A; LOC728875; COAS3; NBPF20; PDE4DIP; PDE4DIP; PDE4DIP; SEC22B; NOTCH2NL; NBPF10 |
| Xp22.33 | 2 | 449065 | 1705775 | 1.2 | 10 | SHOX; CRLF2; CRLF2; CSF2RA; CSF2RA; IL3RA; SLC25A6; PP1164; ASMTL; P2RY8 | |
|
| |||||||
| 71 | 15q11.2 | 1 | 20482360 | 22754322 | 2.2 | 19 | CYFIP1; CYFIP1; p; WHAMML1; GOLGA9P; HERC2P2; GOLGA8E; MKRN3; MAGEL2; NDN; PWRN2; PWRN1; C15orf2; SNRPN; SNRPN; SNURF; SNURF |
| 10q11.22 | 3 | 46167847 | 48338944 | 2.1 | 23 | BMS1P1; FAM35B; SYT15; SYT15; GPRIN2; PPYR1; LOC728643; ANXA8; ANXA8L1; FAM25C; LOC642826; FAM35B2; ANTXRL; ANXA8L2; FAM21B; LOC642826; FAM25G; ANXA8; ANXA8L1; ZNF488; RBP3; GDF2; GDF10 | |
|
| |||||||
| 197 | 1q21.1 | 3 | 144943150 | 146916824 | 1.9 | 24 | PDZK1; GPR89A; GPR89C; PDZK1; LOC200030; NBPF11; LOC728989; PRKAB2; PDIA3P; FMO5; FMO5; CHD1L; BCL9; ACP6; GJA5; GJA8; GPR89B; GPR89C; PDZK1; LOC200030; NBPF11; FLJ39739; PPIAL4B; PPIAL4A; NBPF14; PPIAL4F; NBPF15; NBPF15; NBPF16; PPIAL4E; NBPF16; PPIAL4F; LOC645166; LOC645166 |
|
| |||||||
| 204 | 22q11.23 | 3 | 23980648 | 24240879 | 0.26 | 2 | IGLL3; LRP5L (downslanted palpebral fissures, long palpebral fissure, moderate global developmental delay, short upturned nose, and wide nasal bridge) |
FISH negative∗ means normal FISH results or FISH that failed or FISH not carried out due to cell lysis (frozen sample) or clotted sample.
DBN: database number (CNV 1 = deletion; CNV 3 = duplication).