Research Article

Chromosomal Aberrations in Pediatric Patients with Developmental Delay/Intellectual Disability: A Single-Center Clinical Investigation

Table 2

Characteristics of pCNVs detected by CMA among the 127 patients.

No.Clinical featureAgeGenderCMA resultsSizes of CNVs (kb)Copy numberSyndromesOMIM geneInherited or de novo

1ID17 yFarr[GRCh37] 12p12.1(21369190_25634175)x13995LossLamb-Shaffer syndromeSOX5de novo
2DD3 yFarr[GRCh37] 4p16.3p16.1(68345_8066350)x17998LossWolf–Hirschhorn syndromede novo
3ID5 yMarr[GRCh37] 7q11.23(72723370_74136633)x11413LossWilliams-Beuren syndromeELNde novo
4DD4 yMarr[GRCh37] Xq28(153118233_153878720)x2760GainXq28 (MECP2) duplicationMECP2Inherited from normal mother
5ID5 yMarr[GRCh37] 15q11.2q26.3(22817870_102397317)hmz79,579LOH (paternal UPD15)Angelman syndromeUBE3Ade novo
6DD4 yMarr[GRCh37] 7q11.23(72718123_74136633)x11419LossWilliams-Beuren syndromeELNde novo
7DD19 mMarr[GRCh37] 15q11.2q13.1(23632677_28704050)x15071LossAngelman syndromeUBE3Ade novo
8ID16 yFarr[GRCh37] 7q11.23(72718123_74141494)x11423LossWilliams-Beuren syndromeELNde novo
9DD16 mMarr[GRCh37] 11p11.2(44506359_47897669)x13391LossPotocki–Shaffer syndromeMYBPC3de novo
10ID6 yMarr[GRCh37] 15q11.2q13.1(23290787_28526905)x15147LossAngelman syndromeUBE3Ade novo
11ID7 yMarr[GRCh37] Xq28(153030708_155233098)x22202GainXq28 (MECP2) duplicationMECP2Inherited from normal mother
12ID16 yFarr[GRCh37] 15q11.2q26.3(22817870_102397317)hmz79,579LOH (paternal UPD15)Angelman syndromeUBE3Ade novo
13ID6 yMarr[GRCh37] 7q11.23 (72611954_75147402)x11745LossWilliams-Beuren syndromeELNde novo
14ID5 yMarr[GRCh37] 16p13.3(85880_2045435)x11960LossATR-16 syndromede novo
15DD17 mFarr[GRCh37] 7q11.23(72692112_74184702)x11496LossWilliams-Beuren syndromeELNde novo
16ID16 yFarr[GRCh37] 22q13.33(50974299_51197766)x1223Loss22q13 deletion syndrome (Phelan–Mcdermid syndrome)SHANK3de novo
17ID9 yFarr[GRCh37] 17p11.2 (16761814_20304118)x33542GainPotocki–Lupski syndrome (17p11.2 duplication syndrome)de novo
18DD9 mFarr[GRCh37] 7q11.23(72723370_74136633)x11413LossWilliams-Beuren syndromeELNde novo
19ID6 yFarr[GRCh37] 22q13.31q13.33(48234841_51197766)x12963Loss22q13 deletion syndrome (Phelan–Mcdermid syndrome)SHANK3de novo
20DD13 mFarr[GRCh37] 22q11.21(18919477_21436003)x32516Gain22q11 duplication syndromede novo
21ID9 yMarr[GRCh37] 7q11.23(72723370_74136633)x11413LossWilliams-Beuren syndromeELNde novo
22ID12 yMarr[GRCh37] 16p13.11(14892975_16538596)x31646Gain16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)Inherited from normal mother
23ID5 yFarr[GRCh37] 15q11.2q13.1(22770421_28560664)x35790Gain15q11-q13 duplication syndromeInherited from normal mother
24ID17 yFarr[GRCh37] 15q11.2q13.1(22770421_28526905)x35756Gain15q11-q13 duplication syndromeInherited from normal mother
25DD13 mFarr[GRCh37] 5q23.3q31.2(129203365_139475046)x310,272Gainde novo
26ID16 yFarr[GRCh37] 8p23.3p23.1(158048_9781509)x19623Loss8p23.1 deletion syndromeCSMD1de novo
27ID9 yFarr[GRCh37] 7q36.1q36.3(151376795_159119707)x17743LossSHH; KMT2C; DPP6; MNX1de novo
28DD3 yMarr[GRCh37] 1q43q44(239750391_249224684)x19474Loss1q43-q44 deletion syndromeCHRM3; AKT3; HNRNPUde novo
29ID12 yMarr[GRCh37] 3q23q25.1(141486765_151354816)x19868LossZIC1; ZIC4de novo
30DD4 yFarr[GRCh37] 18p11.32p11.21(136227_12342194)x112,206LossTGIF1de novo
31ID16 yFarr[GRCh37] 11q24.2q25(124419306_134937416)x110,518Lossde novo
32ID17 yFarr[GRCh37] 3q27.3q29(187068732_194767726)x17699LossTP63; FGF12de novo
33DD8 mMarr[GRCh37] 10q26.13q26.3(123584147_135426386)x111,842LossEBF3de novo
34DD3 yMarr[GRCh37] 11q14.1(77492774_85312824)x17820LossDLG2de novo
35DD4 yMarr[GRCh37]Mosaic 15q14q24.1(35050247_75972909)x1.6340,923Loss (Mosaic)15q24 recurrent microdeletion syndromede novo
36DD4 yMarr[GRCh37] 1q42.13q44(228801122_249181598)x320,380Gainde novo
37ID6 yMarr[GRCh37] 1q42.13q44(229917977_249224684)x319,307Gainde novo
38DD3 yFarr[GRCh37] 12p13.33q12(173786_40931729)x340,758GainPartial chromosome 12
trisomy
de novo
39ID8 yMarr[GRCh37] Xp21.3p11.23(27954516_48270449)x120,316LossXp11.23 region (includes MAOA and MAOB)de novo
40ID10 yFarr[GRCh37] 18q21.32q23(58617060_78013728)x119,847Lossde novo
41ID16 yFarr[GRCh37] 11q14.2q22.3(87455736_109777755)x122,322Lossde novo
42DD4 yFarr[GRCh37] 4p16.3p15.31(290685_18118492)x317,828Gain4p16.3 terminal (Wolf–Hirschhorn syndrome) regionde novo
arr[GRCh37] 4q34.1q35.2(176152080_190957460)x114,805Loss
43DD3 yMarr[GRCh37] 8p23.3p23.1(158048_10915395)x310,757Gain8p23.1 duplication syndromeSOX7de novo
arr[GRCh37] 9p24.3p24.1(208454_6308953)x16100LossDMRT1
44ID8 yMarr[GRCh37] 4p16.3p16.1(68345_9514461)x39446Gain4p16.3 terminal (Wolf–Hirschhorn syndrome) regionPaternal balanced
translocation 46,XY,t(4; 8) (p16q23)
arr[GRCh37] 8p23.3p23.1(158048_7044046)x16886LossCSMD1
45ID17 yFarr[GRCh37] 9p24.3p24.1(208454_8748943)x38540Gainde novo
arr[GRCh37] 18q22.1q23(65906752_78013728)x112,107Loss
46ID3 yMarr[GRCh37] 6q27(169727875_170914297)x31186Gainde novo
arr[GRCh37] 13q33.3q34(107636085_115107733)x17472LossCHAMP1; BSVD2
47ID17 yMarr[GRCh37] 11q25(131001110_134937416)x13936LossMaternal balanced
translocation 46,XX,t(11; 18) (q25; q21.2)
arr[GRCh37] 18q21.2q23(50912872_78013728)x327,101Gain
48ID16 yFarr[GRCh37] 9p24.3p21.1(208454_30555044)x330,347GainPaternal balanced
translocation 46,XY,t(9; 18) (p21; p11.3)
arr[GRCh37] 18p11.32p11.31(136227_5485196)x15349LossTGIF1
49ID7 yMarr[GRCh37] 3p26.3p26.1(61891_5189701)x15128LossCNTN4; CNTN6; ITPR1de novo
arr[GRCh37] 7q33q36.3(134287922_159119707)x324,832GainSHH
50DD3 yFarr[GRCh37] 6q25.3q27(159131590_170914297)x311,783GainMaternal balanced
translocation 46,XX,t(6; 10) (q25.3; p15.3)
arr[GRCh37] 10p15.3(100047_1947393)x11847LossZMYND11
51ID16 yFarr[GRCh37] 9p24.3p13.3(208454_33702198)x333,494Gainde novo
arr[GRCh37] 19p13.3(260911_1247822)x1987Loss
52DD3 yMarr[GRCh37] 12q12(44719567_46210900)x11491LossARID2de novo
53ID7 yFarr[GRCh37] Xq27.3q28(145269560_149282242)x14013LossFMR1; AFF2; IDSde novo
54DD4 yMarr[GRCh37] 2q22.3(144457537_145255844)x1798LossZEB2de novo
55ID16 yMarr[GRCh37] Xq28(154476199_155233098)x1759LossRAB39BInherited from normal mother
56ID10 yMarr[GRCh37] 8p11.22(38344498_39172014)x38575Gainde novo
57ID10 yMarr[GRCh37] 1p36.33p36.32(1156338_2468052)x11302LossGNB1; GABRDde novo
58ID14 yFarr[GRCh37] 9q34.11(131231815_132005416)x1774LossSPTAN1de novo
59ID17 yFarr[GRCh37] 6q27(169471201_170914297)x11443LossERMARD; TBPde novo
60ID12 yFarr[GRCh37] 1p36.33p36.32(849466_2516031)x11667LossGNB1; GABRDde novo
61DD + MCA (short status)3 yMarr[GRCh37] Xp11.22(53359258_53647606)x2288GainXp11.22-linked intellectual disabilityHUWE1Inherited from normal mother
62DD + MCA (microtia, cleft palate, ventricular septal defect)8 mFarr[GRCh37] 4p16.3(68345_3488721)x13420LossWolf–Hirschhorn syndromede novo
63DD + MCA (facial dysmorphism, supravalvular aortic stenosis (SVAS) and supravalvular pulmonary stenosis)11 mMarr[GRCh37] 7q11.23(72718123_74136633)x11419LossWilliams-Beuren syndromeELNde novo
64ID + MCA (facial dysmorphism, short status)6 yMarr[GRCh37] 17p11.2(16657318_20287758)x13630LossSmith–Magenis syndromeRAI1; FLCNde novo
65DD + MCA (facial dysmorphism, short status)9 mMarr[GRCh37] 7q11.23(72697461_74136633)x11439LossWilliams-Beuren syndromeELNde novo
66ID + MCA (facial dysmorphism, short status)16 yFarr[GRCh37] 17p11.2(16736261_20417235)x13681LossSmith–Magenis syndromeRAI1; FLCNde novo
67ID + MCA (facial dysmorphism, cleft palate, short status)6 yFarr[GRCh37] 7q11.23(72713282_74154209)x11441LossWilliams-Beuren syndromeELNde novo
68DD + MCA (facial dysmorphism, muscular hypotonia)2 yFarr[GRCh37] 7p22.3p11.1(50943_58019983)hmz57,969LOH (maternal UPD7)Silver–Russell syndromede novo
69ID + MCA (ventricular septal defect)5 yFarr[GRCh37] 15q11.2q13.1(22770421_28704050)x15934LossPrader–Willi syndromeUBE3Ade novo
70DD + MCA (facial dysmorphism, short status)16 mMarr[GRCh37] 7q11.23(72697239_74136633)x11439LossWilliams-Beuren syndromeELNde novo
71DD + MCA (facial dysmorphism, hypoplasia of the corpus callosum, ventricular septal defect, short status)9 mMarr[GRCh37] 17p13.3(525_2780094)x12780LossMiller–Dieker syndromePAFAH1B1de novo
72DD + MCA (facial dysmorphism, supravalvular aortic stenosis (SVAS), ventricular septal defect)9 mMarr[GRCh37] 7q11.23(72713282_74136633)x11423LossWilliams-Beuren syndromeELNde novo
73DD + MCA (muscular hypotonia, dysphagia, cryptorchidism)3 mMarr[GRCh37] 15q11.2q13.1(23290787_28540345)x15250LossPrader–Willi syndromeUBE3Ade novo
74DD + MCA (triangular shaped face, short status, body asymmetry)13 mFarr[GRCh37] 7p22.3p11.1(50943_58019983)hmz57,969LOH (maternal UPD7)Silver–Russell syndromede novo
75DD + MCA (facial dysmorphism, cafe-au-lait spots, atrial septal defect)18 mMarr[GRCh37] 17q11.2(29025996_30369402)x11343LossNF1-microdeletion syndromeNF1de novo
76ID + MCA (facial dysmorphism, short status)13 yFarr[GRCh37] 5p15.33p15.31(113576_9756329)x19643LossCri du chat syndrome (5p deletion)de novo
77ID + MCA (facial dysmorphism, brachydactyly)9 yFarr[GRCh37] 2q37.3(239755969_242782258)x13026Loss2q37 monosomyHDAC4de novo
78DD + MCA (hypertelorism, overgrowth)5 mFarr[GRCh37] 15q24.3q26.3(78160033_102429040)x324,269Gain15q26 overgrowth syndromePaternal balanced
translocation 46,XY,t(3; 15) (p26; q24)
arr[GRCh37] 3p26.3(61891_1542088)x11480LossCNTN6
79DD + MCA (facial dysmorphism, esophageal atresia, external auditory canal atresia)7 mMarr[GRCh37] 22q13.31q13.33(48283717_51197766)x12914Loss22q13 deletion syndrome (Phelan–Mcdermid syndrome)SHANK3de novo
arr[GRCh37] 9q34.2q34.3(136244652_141018648)x34774GainEHMT1
80ID + MCA (atrial septal defect, cleft palate, hearing impairment)5 yMarr[GRCh37] 22q11.1q11.21(16888899_20716903)x33828GainCat eye syndromeMaternal balanced translocation 46,XX,t(11; 22) (q23.3; q11.2)
arr[GRCh37] 11q23.3q25(116683754_134937416)x318,254Gain
81DD + MCA (polysyndactyly)7 mMarr[GRCh37] 16p11.2(29351825_30176508)x1825Loss16p11.2 recurrent microdeletionde novo
82DD + MCA (triangular shaped face, short status, muscular hypotonia)14 mFarr[GRCh37] 7p22.3p11.1(50943_58019983)hmz57,969LOH (maternal UPD7)Silver–Russell syndromede novo
83ID + MCA (atrial septal defect, ventricular septal defect)9 yMarr[GRCh37] 22q11.21(18648855_21800471)x13152Loss22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)TBX1de novo
84DD + MCA (short status)3 yMarr[GRCh37] 15q11.2q13.1(23290787_28928730)x15638LossAngelman syndromeUBE3Ade novo
85ID + MCA (congenital heart disease, polysyndactyly)16 yFarr[GRCh37] 22q11.21(18648855_21800471)x13152Loss22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)TBX1de novo
86DD + MCA (facial dysmorphism)13 mMarr[GRCh37] 16p13.11(14913788_16282869)x31369Gain16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)Inherited from normal mother
87DD + MCA (muscular hypotonia, ventricular septal defect, cryptorchidism)3 mMarr[GRCh37] 15q11.2q13.1(23290787_28540345)x15250LossPrader–Willi syndromeUBE3Ade novo
88DD + MCA (cleft palate)3 yMarr[GRCh37] 16p11.2(29428531_30176508)x1748Loss16p11.2 recurrent microdeletionde novo
89ID + MCA (facial dysmorphism, cleft palate, polysyndactyly, short status)11 yMarr[GRCh37] 17q21.31q21.32(43170339_44988790)x11818Loss17q21.31 recurrent microdeletion syndrome (Koolen–de Vries syndrome)KANSL1de novo
90ID + MCA (short status)9 yFarr[GRCh37] 22q11.21(18648855_21800471)x13169Loss22q11 deletion syndrome (velocardiofacial/DiGeorge syndrome)TBX1de novo
91DD + MCA (cleft palate)3 yFarr[GRCh37] 16p13.11(15481747_16390970)x3909Gain16p13.11 recurrent microduplication (neurocognitive disorder susceptibility locus)de novo
92ID + MCA (cleft palate)13 yFarr[GRCh37] 15q11.2q13.1(23281885_28526905)x35245Gain15q11-q13 duplication syndromeInherited from normal mother
arr[GRCh37] 16p11.2(29428531_30176508)x1748Loss16p11.2 recurrent microdeletionInherited from normal father
93DD + MCA (facial dysmorphism, catlike cry, ventricular septal defect, short status)3 mFarr[GRCh37] 5p15.33p13.3(113576_32114177)x132,001LossCri du chat syndrome (5p deletion)TRIO; CTNND2de novo
94DD + MCA (short status)11 mFarr[GRCh37] Xp22.33p22.31(168551_8030262)x17862LossLeri–Weill dyschondrosteosis (LWD): SHOX deletionSHOX; ARSEde novo
95ID + MCA (cleft palate)6 yFarr[GRCh37] 7q11.23(72692112_74154209)x11462LossWilliams-Beuren syndromeELNde novo
96ID + MCA(micrognathia)16 yFarr[GRCh37] 8p23.3p23.1(158048_10029980)x19872Loss8p23.1 deletion syndromeCSMD1de novo
97ID + MCA (atrial septal defect, microtia, polysyndactyly)7 yMarr[GRCh37] 5q34q35.3(162638031_180329359)x317,691Gain5q35 recurrent (Sotos syndrome) region (includes NSD1)FBXW11Maternal balanced
translocation 46,XX,t(5; 12) (q34; p13.32)
arr[GRCh37] 12p13.33p13.32(173786_4264694)x14091Loss12p13.33 microdeletion syndrome
98DD + MCA (cryptorchidism, short status)19 mMarr[GRCh37] 4q34.1q35.2(174352834_190957460)x316605Gainde novo
arr[GRCh37] Xp22.33p22.31(168551_6455151)x06287LossLeri–Weill dyschondrosteosis (LWD): SHOX deletionSHOX; ARSE
99DD + MCA (gallbladder agenesis)3 yFarr[GRCh37] 8p23.3p23.1(158048_7044046)x16686LossCSMD1de novo
arr[GRCh37] 8p23.1p12(11936000_33616243)x321,860Gain
100ID + MCA (atrial septal defect, hypermyotonia)6 yMarr[GRCh37] 2p23.1p22.1(32046639_38823958)x16777LossSPASTde novo
101DD + MCA (hypoplasia of the corpus callosum)3 mFarr[GRCh37] 13q33.2q34(106348324_115107733)x18759LossCHAMP1; BSVD2de novo
102ID + MCA (micrognathia, polysyndactyly)14 yFarr[GRCh37] 18p11.32q11.2(136227_20989843)x320,854GainMaternal balanced
translocation 46,XX,t(18; 21) (q11.2; q21)
arr[GRCh37] 21q11.2q21.1(15016486_20371429)x15355Loss
103DD + MCA (hypermyotonia, blepharophimosis)3 mMarr[GRCh37] 3q22.1q23(132876177_139772196)x16896LossFOXL2de novo
104DD + MCA (facial dysmorphism)8 mFarr[GRCh37] 10p15.3p12.2(100047_23162330)x323,062GainPaternal inversion 46,XY,inv(10) (p12q26)
arr[GRCh37] 10q26.3(134248768_135426386)x11178Loss
105DD + MCA (ventricular septal defect, aortic stenosis)21 mMarr[GRCh37] 7p21.1p11.2(16641066_56373573)x339,733Gainde novo
arr[GRCh37] 4q13.1q13.2(65818383_68116457)x12298Loss
106DD + MCA (facial dysmorphism, cryptorchidism)3 yMarr[GRCh37] 3q13.33q25.1(121200603_151876470)x330,676Gainde novo
107ID + MCA (facial dysmorphism)3 yMarr[GRCh37] 14q12(28897081_31268243)x12371LossRett syndromeFOXG1de novo
108DD + MCA (atrial septal defect)14 mFarr[GRCh37] 20p13(61661_2150330)x12089LossCSNK2A1; PDYNde novo
109DD + MCA (facial dysmorphism, overgrowth, body asymmetry)2 yFarr[GRCh37] Xq21.31q27.3(86577241_145860589)x359,283GainPelizaeus–Merzbacher disease (carrier)PLP1de novo
110DD + MCA (cryptorchidism, hypospadias)3 mMarr[GRCh37] 5p14.3p12(19454082_45506818)x326,053Gainde novo
111DD + MCA (facial dysmorphism, bilateral single transverse palmar creases)3 mFarr[GRCh37] 9p24.3q13(208454_68216577)x310,188GainChromosome 9p trisomyde novo
112ID + MCA (facial dysmorphism, webbed neck, low-set ears)5 yFarr[GRCh37] Xp22.33p11.22(168551_52706689)x152,538Lossde novo
arr[GRCh37] Xp11.22q28(52833230_155233098)x3102,400Gain
113ID + ASD13 yFarr[GRCh37] 17p11.2(16657318_20463423)x13806LossSmith–Magenis syndromeRAI1; FLCNde novo
114DD + ASD3 yMarr[GRCh37] 17p11.2 (16745600_20417235)x33672GainPotocki–Lupski syndrome (17p11.2 duplication syndrome)de novo
115ID + ASD10 yMarr[GRCh37] 2q37.2q37.3(235790877_242782258)x16991Loss2q37 monosomyHDAC4Paternal inversion 46,XY,inv(2) (p24q37.2)
arr[GRCh37] 2p25.3p24.3(12770_12658812)x312,646Gain
116ID + epilepsy (ichthyosis)12 yMarr[GRCh37] Xp22.31(6455151_8141076)x01686LossSteroid sulphatase deficiency (STS)STSInherited from normal mother
117ID + epilepsy8 yMarr[GRCh37] 15q11.2q13.1(22770421_28704050)x15934LossAngelman syndromeUBE3Ade novo
118DD + epilepsy3 yFarr[GRCh37] 16p13.12p13.11(14777379_16533107)x11756Loss16p13.11 recurrent microdeletion (neurocognitive disorder susceptibility locus)de novo
119ID + epilepsy6 yMarr[GRCh37] 15q11.2q13.1(23620191_28526905)x14907LossAngelman syndromeUBE3Ade novo
120DD + epilepsy3 yFarr[GRCh37] 16p11.2(28557432_30176508)x11619Loss16p11.2 microduplication syndromeSH2B1de novo
121DD + epilepsy11 mFarr[GRCh37] 20q13.33(61485437_62790113)x11305LossCHRNA4; KCNQ2de novo
122ID + epilepsy5 yFarr[GRCh37] 13q33.3q34(108237906_115107733)x16870LossCHAMP1; BSVD2de novo
123DD + epilepsy4 yFarr[GRCh37] Xq23q24(111170674_117964845)x16794Lossde novo
124ID + epilepsy8 yMarr[GRCh37] Xp22.13p21.3(17125886_28993521)x211,868Gainde novo
125ID + epilepsy6 yMarr[GRCh37] 2p24.3p24.2(15850097_16790467)x1940LossMYCNde novo
126ID + epilepsy3 yMarr[GRCh37] 2q24.3(164444391_168745074)x14301LossSCN1A; SCN2A; SCN9Ade novo
127ID + epilepsy6 yMarr[GRCh37] 1p36.33(849466_2226509)x11377LossGNB1; GABRDde novo

LOH: loss of heterozygosity; UPD: uniparental disomy.