Table 3 Pathogenic copy number variations (PCNVs) detected in 279 patients with syndromic obesity
From: Chromosomal microarray analysis in the genetic evaluation of 279 patients with syndromic obesity
Case number | Age | Gender | Weight Status | CNV Type | Cytoband | Genome Coordinate | Size | Origin | Clinical significance | RefSeq genes |
|---|---|---|---|---|---|---|---|---|---|---|
Genomic imbalance disorders | ||||||||||
 P1 | 5y | F | Referred as obese | Del | 1p36.33 | 734595-1970865 | 1236270 | Unk | 1p36 terminal deletion | KLHL17 , AGRN , TAS1R3 , * DVL1 , VWA1 , MMP23B , GABRD |
 P2 | 34y | F | BMI 59.1 | Del | 1p36.33 | 734595-2223317 | 1488722 | Unk | 1p36 terminal deletion, complex | KLHL17 , AGRN , TAS1R3 , * DVL1 , VWA1 , MMP23B, GABRD, PRKCZ , SKI * |
| Â | Â | Â | Â | Dup | 1p36.33 p36.32 | 2225679-2694799 | 469120 | Â | Â | -- |
 P3 | 14y | F | BMI 26.8 (93.3th) | Del | 1p36.33 p36.32 | 794592-2377269 | 1582677 | De novo | 1p36 terminal deletion | KLHL17 , AGRN , TAS1R3 , * DVL1 , VWA1 , MMP23B , GABRD, PRKCZ , SKI * |
 P4 | 6y | F | BMI 19.7 (96.8th) | Del | 1p36.33 p36.32 | 734595-3531040 | 2796445 | Unk | 1p36 terminal deletion | KLHL17 , AGRN , TAS1R3 , * DVL1 , VWA1 , MMP23B , GABRD, PRKCZ , SKI ,* TNFRSF14 , PRDM16 * |
 P5 | 11y | M | BMI 30.8 (99th) | Del | 1p36.31 p36.22 | 6204969-9433118 | 3228149 | Unk | 1p36 interstitial deletion | CAMTA1 , PER3 , UTS2 , RERE, H6PD * |
 P6 | 15y | F | BMI 37.1 (99.1th) | Del | 1p22.1 p21.2 | 93919217-99846176 | 5926959 | De novo | 1p21.3 deletion | F3 , PTBP2 , * DPYD , MIR137 |
 P7 | 8y | F | BMI 33.2 (99.7th) | Del | 1p21.3 p13.3 | 95696444-107755879 | 12059435 | Unk | 1p21.3 deletion | PTBP2 , * DPYD , MIR137 , VCAM1 , * COL11A1 , AMY2B , AMY2A , AMY1A * |
 P8 | 6y | M | BMI 28.8 (99.9th) | Dup | 1q21.1 | 146074084-147828029 | 1753945 | Unk | 1q21.1 distal duplication | PRKAB2 , CHD1L , GJA5 , GJA8 |
 P9 | 7y | F | BMI 22.6 (98.2th) | Del | 2p25.3 | 63452-3215593 | 3152141 | De novo | 2p25.3 terminal deletion | ACP1 , * TMEM18 , * SNTG2 , TPO , * MYT1L |
 P10 | 8y | F | BMI 29.1 (99.5th) | Del | 2q37.2 q37.3 | 237220842-242995835 | 5774993 | De novo | 2q37 terminal deletion | PRLH , LRRFIP1 , PER2 , HDAC4 , GPC1 , * CAPN10 , * GPR35 , * KIF1A , PASK , STK25 * |
 P11 | 21y | M | Referred as obese | Del | 2q37.2 q37.3 | 236854160-242995835 | 6141675 | Unk | 2q37 terminal deletion | AGAP1 , PRLH , LRRFIP1 , PER2 , HDAC4 , GPC1 , * CAPN10 , * GPR35 , * KIF1A , PASK , STK25 * |
 P12 | 10y | M | BMI 29.8 (99th) | Del | 2q37.2 q37.3 | 236944801-243014630 | 6069829 | De novo | 2q37 terminal deletion, complex | AGAP1 , PRLH , LRRFIP1 , PER2 , HDAC4 , GPC1 , * CAPN10 , * GPR35 , * KIF1A , PASK , STK25 * |
| Â | Â | Â | Â | Dup | 2q37.1 q37.2 | 235090417-236802930 | 1712513 | Â | Â | -- |
 P13 | 9y | F | BMI 24.7 (98.2th) | Del | 2q37.1 q37.3 | 234850276-243028335 | 8178059 | Unk | 2q37 terminal deletion, complex | TRPM8 , AGAP1 , PRLH , LRRFIP1 , PER2 , HDAC4 , GPC1 , * CAPN10 , * GPR35 , * KIF1A , PASK , STK25 * |
| Â | Â | Â | Â | Dup | 2q37.1 | 233867403-234794816 | 927413 | Â | Â | UTG1A1 * |
 P14 | 5y | F | BMI 24.0 (99.7th) | Del | 2q37.3 | 240880562-242948060 | 2067498 | Unk | Unbalanced translocation | GPC1 , * CAPN10 , * GPR35 , * KIF1A , PASK , STK25 * |
| Â | Â | Â | Â | Dup | 17q25.3 | 78709250-81036261 | 2327011 | Â | Â | RPTOR , ACTG1 , GCGR , * PCYT2 , FASN , * CSNK1D , UTS2R |
 P15 | 10y | M | BMI 31.0 (99.3th) | Del | 6q16.1 q21 | 95836632-108010940 | 12174308 | De novo | 6q16 deletion | KLHL32 , POU3F2, MCHR2 , * SIM1 , * GRIK2 , LIN28B , * ATG5 |
 P16 | 15y | F | BMI 40.5 (99.4th) | Del | 7q11.23 | 72420782-74985644 | 2564862 | Unk | 7q11.23 deletion | FKBP6 , FZD9 , BCL7B , TBL2 , MLXIPL , STX1A , * CLDN3 , ELN , LIMK1 , RFC2 , * CLIP2 , GTF2IRD1 , GTF2I , NCF1 |
 P17 | 6y | M | BMI 30.6 (99.9th) | Del | 7q11.23 | 72437606-75053787 | 2616181 | Unk | 7q11.23 deletion | FKBP6 , FZD9 , BCL7B , TBL2 , MLXIPL , STX1A , * CLDN3 , ELN , LIMK1 , RFC2 , * CLIP2 , GTF2IRD1 , GTF2I , NCF1 |
 P18 | 6y | M | BMI 33.4 (99.9th) | Del | 8p23.3 p23.1 | 176464-7786759 | 7610295 | De novo | Unbalanced translocation | CLN8 , CSMD1 , DEFA1 , * DEFB103A , DEFB103B , DEFB104A , DEFB106A , DEFB105A , DEFB107A , DEFB4A |
| Â | Â | Â | Â | Dup | 12p13.33 p13.31 | 204618-8309473 | 8104855 | Â | Â | SLC6A13 , WNT5B , * ADIPOR2, * CACNA2D4 , CACNA1C , FOXM1 , TEAD4 , PARP11 , KCNA1 , NTF3 , VWF , TNFRSF1A , * SCNN1A , GAPDH , CD4 , GNB3 , * CD163 , APOBEC1 , GDF3 , SLC2A14 , C3AR1 |
 P19 | 6y | M | BMI 25.8 (99.8th) | Dup | 8p23.1 | 8054556-11985356 | 3930800 | Not mat | 8p23.1 duplication | CLDN23 , MFHAS1 , PPP1R3B , LOC157273 , TNKS , * MSRA , * SOX7 , MTMR9 , * BLK , GATA4 , * NEIL2 , FDFT1 , * CTSB |
|  |  |  |  | Dup | 13q12.12 | 23706634-24910765 | 1204131 | Not mat | Uncertain | SGCG, ¶ SACS, MIPEP |
 P20 | 11y | F | BMI 26.7 (97.6th) | Del | 9p24.3 p22.3 | 40910-14304973 | 14264063 | De novo | 9p terminal deletion | KANK1 , DMRT1 , SMARCA2 , VLDLR , * GLIS3 , JAK2 , RLN1 , IL33 , * KDM4C , PTPRD * |
 P21 | 12m | F | Weight-for Height +1sd | Del | 9p24.3 p22.3 | 204149-15260439 | 15056290 | De novo | 9p terminal deletion | KANK1 , DMRT1 , SMARCA2 , VLDLR , * GLIS3 , JAK2 , RLN1 , IL33 , * KDM4C , PTPRD, * TTC39B |
 P22 | 17y | M | BMI 28.7 (95.7th) | Del | 9p24.3 p22.3 | 201149-8807593 | 8606444 | Unk | 9p terminal deletion | KANK1 , DMRT1 , SMARCA2 , VLDLR , * GLIS3 , JAK2 , RLN1 , IL33 , * KDM4C , PTPRD * |
 P23 | 9y | F | BMI 31.1 (99.5th) | Del | 9q34.3 | 140665414-141018984 | 353570 | De novo | 9q34.3 deletion | EHMT1 , * CACNA1B |
 P24 | 14y | M | BMI 28.7 (97.6th) | Del | 13q12.3 q13.1 | 29081250-33529310 | 4448060 | De novo | 13q12.3 deletion | POMP , SLC46A3 , MTUS2 , SLC7A1 , UBL3, KATNAL1 , LINC00426, HMGB1, ALOX5AP , * RXFP2, BRCA2* |
 P25 | 8y | M | BMI 25.4 (99.2th) | Del | 15q11.2 | 22729423-23086969 | 357546 | Unk | 15q11.2 microdeletion | NIPA1 , NIPA2 , CYFIP1 |
 P26 | 10y | F | BMI 22.1 (93.4th) | Del | 16p13.12 p13.11 | 14780302-16400774 | 1620472 | Pat | 16p13.1 deletion | NDE1 , MYH11 , * ABCC1 , ABCC6 |
 P27 | 4y | F | Hyperphagia | Dup | 16p13.12 p13.11 | 14796004-16586941 | 1790937 | Pat | 16p13.1 duplication | NDE1 , MYH11 , * ABCC1 , ABCC6 |
 P28 | 7y | F | BMI 20.5 (96.6th) | Del | 16p11.2 | 28843754-29044850 | 201096 | De novo | 16p11.2 (BP 2-3) deletion | ATXN2L , * TUFM , * MIR4721 , SH2B1 , * ATP2A1 ,* SPNS1 |
 P29 | 12y | M | BMI 30.4 (98.8th) | Del | 16p11.2 | 29592751-30197466 | 604715 | Not mat | 16p11.2 (BP 4-5) deletion | QPRT , PRRT2 , SEZ6L2 , DOC2A , ALDOA , TBX6 , MAPK3 |
 P30 | 8y | M | Referred as obese | Dup | 16p11.2 | 29592751-30197466 | 604715 | Pat | 16p11.2 (BP 4-5) duplication | QPRT , PRRT2 , SEZ6L2 , DOC2A , ALDOA , TBX6 , MAPK3 |
 P31 | 11y | M | BMI 42.2 (99.7th) | Del | 17p11.2 | 17006987-20171357 | 3164370 | De novo | 17p11.2 deletion | COPS3 , NT5M , MED9 , PEMT , * RAI1 , SREBF1 , * ATPAF2 , DRG2 , SMCR8 , MFAP4 , SLC47A1 , ALDH3A2, SPECC1 |
 P32 | 6y | M | BMI 31.2 (99.9th) | Del | 17p11.2 | 16757563-20395535 | 3637972 | Not mat | 17p11.2 deletion | TNFRSF13B , COPS3 , NT5M , MED9 , PEMT , * RAI1 , SREBF1 , * ATPAF2 ,, DRG2 , SMCR8 , MFAP4 , SLC47A1 , ALDH3A2, SPECC1 |
 P33 | 7y | F | BMI 21.9 (97.9th) | Del | 17p11.2 | 16603145-20395535 | 3792390 | De novo | 17p11.2 deletion | TNFRSF13B , COPS3 , NT5M , MED9 , PEMT , * RAI1 , SREBF1 , * ATPAF2 , DRG2 , SMCR8 , MFAP4 , SLC47A1 , ALDH3A2, SPECC1 |
 P34 | 8y | F | BMI 25.9 (98.9th) | Del | 17p11.2 | 16603145-20395535 | 3792390 | Unk | 17p11.2 deletion | TNFRSF13B , COPS3 , NT5M , MED9 , PEMT , * RAI1 , SREBF1 , * ATPAF2 , DRG2 , SMCR8 , MFAP4 , SLC47A1 , ALDH3A2, SPECC1 |
 P35 | 10y | M | BMI 28.1 (99th) | Del | 17p11.2 | 16603145-20463399 | 3860254 | De novo | 17p11.2 deletion | TNFRSF13B , COPS3 , NT5M , MED9 , PEMT , * RAI1 , SREBF1 , * ATPAF2 , DRG2 , SMCR8 , MFAP4 , SLC47A1 , ALDH3A2, SPECC1 |
 P36 | 9y | M | BMI 22.2 (96.8th) | Dup | 17q21.31 q21.32 | 40993738-45166786 | 4173048 | De novo | 17q21.3 duplication | AOC3 , G6PC , * BRCA1 , * SOST , * PPY , * PYY , * TMEM101 , HDAC5 , ITGA2B , EFTUD2 , PLCD3 , CRHR1 , * MAPT , KANSL1 |
 P37 | 8y | F | BMI 22.3 (97.4th) | Dup | 19p13.2 | 12640509-13231703 | 591194 | Unk | 19p13.2 duplication | MAST1, CALR, NFIX |
| Â | Â | Â | Â | Dup | 9p22.1 | 19066513-19497724 | 431211 | Unk | Uncertain | PLIN2 * |
 P38 | 18y | F | BMI 41.5 (99th) | Del | 19p13.12 | 14384925-16034584 | 1649659 | De novo | 19p13.12 deletion | CD97, DDX39A , PKN1 , PTGER1, GIPC1, CASP14, NOTCH3, CYP4F11 |
 P39 | 8y | F | Referred as obese | Del | 22q11.21 | 18890162-20311554 | 1421392 | De novo | 22q11.2 deletion | PRODH , DGCR2 , DGCR14 , CDC45 , TBX1 , * GNB1L , TXNRD2 , COMT , * DGCR8 , ZDHHC8 |
 P40 | 3y | M | BMI 34.7 (99.9th) | Del | 22q11.21 | 18661758-21684798 | 3023040 | De novo | 22q11.2 deletion | PRODH , DGCR2 , DGCR14 , CDC45 , TBX1 , * GNB1L , TXNRD2 , COMT , * DGCR8 , ZDHHC8 , PI4KA, SLC74A |
 P41 | 9y | M | BMI 32.5 (99.6th) | Del | 22q11.21 | 18661758-21684798 | 3023040 | De novo | 22q11.2 deletion | PRODH , DGCR2 , DGCR14 , CDC45 , TBX1 , * GNB1L , TXNRD2 , COMT , * DGCR8 , ZDHHC8 , PI4KA, SLC74A |
 P42 | 13m | M | Weight-for Height +1sd | Del | 22q11.21 | 18818429-21661436 | 2843007 | Pat | 22q11.2 deletion | PRODH , DGCR2 , DGCR14 , CDC45 , TBX1 , * GNB1L , TXNRD2 , COMT , * DGCR8 , ZDHHC8 , PI4KA, SLC74A |
 P43 | 18y | M | Referred as obese | Dup | 22q11.21 | 18890162-21464056 | 2573894 | Pat | 22q11.2 duplication | PRODH , DGCR2 , DGCR14 , CDC45 , TBX1 , * GNB1L , TXNRD2 , COMT , * DGCR8 , ZDHHC8 , PI4KA, SLC74A |
 P44 | 5y | M | BMI 27.9 (99.9th) | Del | 22q11.21 q11.23 | 21759572-23822925 | 2063353 | Unk | 22q11.2 deletion, distal | HIC2, MAPK1, * GNAZ , BCR |
 P45 | 7y | F | BMI 24.8 (98.9th) | Del | 22q11.21 q11.22 | 21468437-22959609 | 1491172 | Not mat | 22q11.2 deletion, distal | HIC2 , MAPK1 * |
| Â | Â | Â | Â | Dup | 3p26.3 | 857110-1414719 | 557609 | Not mat | Uncertain | -- |
 P46 | 2y | F | BMI 17.7 (85th) | Del | 22q11.22 q11.23 | 23012069-23648827 | 636758 | Mat | 22q11.2 deletion, distal | GNAZ , BCR |
 P47 | 15y | M | BMI 39.5 (99.6th) | Del | 22q11.22 q11.23 | 23063178-23696464 | 633286 | Unk | 22q11.2 deletion, distal | GNAZ , BCR |
Other pathogenic imbalances | ||||||||||
 P48 | 2y | M | BMI 24.4 (99.9th) | Del | 3p26.3 | 73603-1273300 | 1199697 | De novo | Unbalanced translocation | CHL1 |
| Â | Â | Â | Â | Dup | 11q22.3 q25 | 106251478-134668665 | 28417187 | Â | Â | ACAT1 , ATM , POU2AF1 , IL18 , * ANKK1 , DRD2 , * HTR3B, HTR3A , NNMT , BUD13 , APOA5 , * APOA4 , * APOC3 , * APOA1 , * BACE1 , IL10RA , CD3E , HYOU1 , H2AFX , CBL , * USP2 , THY1 , ARHGEF12 , BSX , * HSPA8 , CLMP , NRGN , SLC37A2 , TIRAP , KCNJ1 , KCNJ5 , * OPCML |
 P49 | 14y | F | Referred as obese | Del | 3p24.1 | 28719852-30169971 | 1450119 | Unk | Complex rearrangement | LINC00693, RBMS3-AS3, RBMS3 , RBMS3-AS1 |
| Â | Â | Â | Â | Dup | 3q11.2 q13.31 | 93558505-115890384 | 22331879 | Â | Â | EPHA6 , ARL6 , * STG3GAL6 , COL8A1 , CCDC80 , BOC , ZDHHC23 , ZBTB20 , GAP43, LSAMP, DRD3 |
 P50 | 10y | M | BMI 30.4 (99.3th) | Del | 3q25.33 | 159252702-160555217 | 1302515 | De novo | Uncertain | IL12A |
| Â | Â | Â | Â | Del | 13q31.2 q32.1 | 89522636-95065310 | 5542674 | De novo | Feingold syndrome | MIR17HG , GPC5 , * GPC6 |
 P51 | 14y | F | BMI 27.9 (95.8th) | Del | 7q22.1 q22.3 | 102358320-105487655 | 3129335 | De novo | Clinically relevant | NAPEPLD , RELN , LHFPL3 |
 P52 | 2y | F | BMI 27.0 (99.9th) | Del | 10p15.3 p14 | 269695-11579546 | 11309851 | De novo | Unbalanced translocation | ZMYND11 , DIP2C , * IDI1 , ADRAB2 , PFKP , * KLF6 , ARK1C1 , AKR1C2 , ARK1C3 , AKR1C4 , UCN3 , IL15RA , IL2RA , * PFKFB3 , PRKCQ , GATA3 |
| Â | Â | Â | Â | Dup | 6q27 | 169505179-170694486 | 1189307 | Â | Â | WDR27 |
 P53 | 5m | F | Referred as obese | Dup | 10p15.3 p12.31 | 119794-19509585 | 19389791 | Not mat | Complex rearrangement | ZMYND11 , DIP2C , * IDI1 , ADRAB2 , PFKP , * KLF6 , ARK1C1 , AKR1C2 , ARK1C3 , AKR1C4 , UCN3 , IL15RA , IL2RA , * PFKFB3 , PRKCQ , GATA3, CDC123 , CAMK1D , CCDC3 , PTER , * CUBN , MRC1 , CACNB2 |
| Â | Â | Â | Â | Dup | 13q11 q12.3 | 19440913-31031907 | 11590994 | Not mat | Â | TUBA3C , GJB2 , CRYL1 , SGCG, SACS, MIPEP, GPR12 , GTF3A , MTIF3 , * POLR1D , PDX1 , * CDX2 , POMP , SLC46A3 , MTUS2 , SLC7A1 , UBL3, KATNAL1, LINC00426 |
 P54 | 9y | F | BMI 34.3 (99.7th) | Dup | 10q26.11 q26.3 | 120306959-135434409 | 15127450 | De novo | 10qter duplication | PRLHR , * PRDX3 , BAG3 , WDR11 , FGFR2 , * ACADSB , BUB3 , OAT , TCERG1L , PRAP1 , CYP2E1 * |
 P55 | 7y | F | BMI 23.6 (98.8th) | Del | 12q15 q21.1 | 70555659-73153191 | 2597532 | De novo | Clinically relevant | PTPRB , TSPAN8 , * LGR5TPH2 |
 P56 | 13y | F | BMI 36.8 (99.4th) | Dup | 12q21.32 q23.1 | 88684581-101464859 | 12780278 | De novo | Insertional translocation | KITLG , ATP2B1 , SOCS2 , LTA4H , RMST , NR1H4 * |
 P57 | 15y | M | BMI 43.1 (99.7th) | Del | 13q33.2 q34 | 106648660-115105655 | 8456995 | Not mat | 13qter deletion | EFNB2 , MYO16 , IRS2 , * COL4A1 , ARHGEF7 , F7 , GAS6 , CHAMP1 |
 P58 | 4y | M | BMI 22.0 (99.9th) | Dup | 14q11.2 | 21244696-22250879 | 1006183 | De novo | 14q11.2 microduplication | SUPT16H , CHD8 |
 P59 | 16y | F | BMI 38.5 (99th) | Del | 14q12 | 29781404-30552936 | 771532 | De novo | 14q12 deletion, non-critical | PRKD1 * |
| Â | Â | Â | Â | Dup | 4p16.1 | 10068064-10529023 | 460959 | Mat | Likely benign | WDR1 |
 P60 | 7y | F | BMI 24.8 (99.3th) | Del | Xp22.12 p22.13 | 18214020-19833634 | 1619614 | Unk | Rett syndrome-like | CDKL5 , RS1 , PHKA2 , PDHA1 , * SH3KBP1 |
 P61 | 14y | M | BMI 37.0 (99.5th) | Dup | Xp22.3 | 75943-2685605 | 2609662 | De novo | Complex rearrangement | SHOX , ASMTL , ASMT |
| Â | Â | Â | Â | Dup | Xq21.31 q21.32 | 88489522-92357353 | 3867831 | Â | Â | TGIF2 LX , PABPC5-AS1 , PABPC5 , PCDH11X |