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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 *
     Dup 1p36.33
p36.32
2225679-2694799 469120    --
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 *
     Dup 2q37.1
q37.2
235090417-236802930 1712513    --
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 *
     Dup 2q37.1 233867403-234794816 927413    UTG1A1 *
P14 5y F BMI 24.0 (99.7th) Del 2q37.3 240880562-242948060 2067498 Unk Unbalanced translocation GPC1 , * CAPN10 , * GPR35 , * KIF1A , PASK , STK25 *
     Dup 17q25.3 78709250-81036261 2327011    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
     Dup 12p13.33
p13.31
204618-8309473 8104855    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
     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 *
     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
     Dup 11q22.3
q25
106251478-134668665 28417187    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
     Dup 3q11.2
q13.31
93558505-115890384 22331879    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
     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
     Dup 6q27 169505179-170694486 1189307    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
     Dup 13q11
q12.3
19440913-31031907 11590994 Not mat   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 *
     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
     Dup Xq21.31
q21.32
88489522-92357353 3867831    TGIF2 LX , PABPC5-AS1 , PABPC5 , PCDH11X
  1. Abbreviations: M male, F female, Del deletion, Dup duplication, y years, m months, BMI body mass index, SD standard deviation, unk unknown, mat maternally inherited, pat paternally inherited, not mat not maternally inherited; Genes in bold were listed in the CNV morbidity map of IDDs [34]. Underlined genes were retrieved from the Text-mined Hypertension, Obesity and Diabetes candidate gene database (T-HOD), the Human Genome Epidemiology (HUGE) Phenopedia, and from a list of obesity candidate genes curated from the literature [33]. Genes found at the intersection of at least two gene sets are highlighted (asterisks). Patients 6-12, 14, 15, 18, 23, 28, 30-33, 35, 40-43, 46-48, 51, 52, 55, 56, 58-60) have been published previously as separate studies [36-38]