Table 4 The phenotypes of each pathogenic or likely pathogenic CNV in DECIPHER database

1

Dup

8q24.21-q24.3

5.2%

(7/134)

Intellectual disability (4), Preauricular skin tag (2), Micrognathia (2), Low-set ears (2), High palate (2)

Ventricular septal defect (3), Tetralogy of Fallot (1), Pulmonic stenosis (1), Abnormal heart morphology (1), Atrial septal defect (1)

0

/

/

2

Del

13q33.1-q34

15.7%

(27/172)

Intellectual disability (14), Microcephaly (11), Micrognathia (11), Small for gestational age (11), Low-set ears (9)

Ventricular septal defect (12), Atrial septal defect (8), Abnormality of cardiovascular system morphology (6), Tetralogy of Fallot (3), Pulmonic stenosis (2)

0.6%

(1/172)

Tetralogy of Fallot (1)

SLC10A2

3

Del

1p36.33

12.8%

(25/195)

Intellectual disability (12), EEG abnormality (8), Microcephaly (7), Frontal bossing (6), Hypotonia (6)

Ventricular septal defect (9), Patent ductus arteriosus (8), Atrial septal defect (6), Tetralogy of Fallot (2), Abnormal heart morphology (1)

0

/

/

4

Del

2p16.3

0

(0/12)

/

/

0

/

/

5

Del

3q25.33-q26.1

11.1%

(1/9)

Abnormal esophagus morphology (1), Anosmia (1), Blepharophimosis (1), Choanal atresia (1), Hydrocephalus (1), Hypertelorism (1), Micrognathia (1), Renal hypoplasia (1), Talipes equinovarus (1), Tracheoesophageal fistula (1)

Ventricular septal defect (1)

0

/

/

6

Del

22q11.21

22.8%

(170/745)

Intellectual disability (53), Hypocalcemia (46), Aplasia/Hypoplasia of the thymus (44), Micrognathia (44), Abnormal pinna morphology (38)

Ventricular septal defect (85), Abnormality of cardiovascular system morphology (33), Tetralogy of Fallot (30), Atrial septal defect (23), Truncus arteriosus (22)

3.0%

(22/745)

Tetralogy of Fallot (7), Abnormality of cardiovascular system morphology (5), Ventricular septal defect (4), Pulmonic stenosis (3), Abnormal ventricular septum morphology (2)

ADA2, ATP6V1E1, IL17RA, PEX26, PRODH, TUBA8, USP18, BCR, CHCHD10, CRYBB2, CRYBB3, GGT1, IGLL1, MAPK1, MIF, SMARCB1, SPECC1L, UPB1

7

Del

2q13

3.4%

(2/58)

Feeding difficulties in infancy (1), Hypotonia (1), Microcephaly (1), Proportionate short stature (1), Talipes (1)

Atrioventricular canal defect (1),Ventricular septal defect (1), Tetralogy of Fallot (1)

0

/

/

8

Dup

Xp22.31

3.0%

(8/269)

Conductive hearing impairment (8), Intellectual disability (8), Protruding ear (8)

Ventricular septal defect (8)

1.1%

(3/269)

Atrial septal defect (2), Abnormal heart morphology (1)

STS

9

Del

17q25.3

18.2%

(2/11)

Camptodactyly of finger (2), Downslanted palpebral fissures (2), Generalized hirsutism (2), High palate (2), Micrognathia (2)

Abnormality of cardiovascular system morphology (2), Hypoplastic left heart (1), Mitral stenosis (1)

0

/

/

10

Del

5q35.3

29.6%

(8/27)

Feeding difficulties in infancy (4), Abnormal pinna morphology (3), Anteverted nares (3), Depressed nasal bridge (3), Intellectual disability (3)

Patent ductus arteriosus (4), Atrial septal defect (2), Aortic regurgitation (1), Atrioventricular canal defect (1), Pulmonic stenosis (1)

0

/

/

11

Del

1q43-q44

12.6%

(25/199)

Intellectual disability (14), Micrognathia (13), Hypertelorism (8), Low-set ears (8), Depressed nasal bridge (7)

Ventricular septal defect (13), Abnormality of cardiovascular system morphology (3), Pulmonic stenosis (3), Abnormal heart morphology (2), Atrial septal defect (2)

0

/

/

12

Del

6q14.1-q16.1

14.3%

(12/84)

Hypotonia (6), Intellectual disability (6), Abnormality of vision (5), Autistic behavior (5), Constipation (5)

Atrial septal defect (4), Patent ductus arteriosus (4), Sinus venosus atrial septal defect (1), Abnormality of the cardiovascular system (1), Ventricular septal defect(1)

0

/

/

13

Dup

15q11.2

2.3%

(6/257)

Intellectual disability (3), Delayed speech and language development (2), Hypotonia (2), Overlapping toe (2), Protruding ear (2)

Ventricular septal defect (3), Pulmonic stenosis (2), Tetralogy of Fallot (2), Abnormality of cardiovascular system morphology (1), Atrial septal defect (1)

0

/

/

14

Del

11q23.3-q25

26.7%

(66/247)

Intellectual disability (33), Low-set ears (33), Micrognathia (29), Hypertelorism (28), Small for gestational age (23)

Ventricular septal defect (31), Atrial septal defect (16), Patent ductus arteriosus (12), Abnormality of cardiovascular system morphology (11), Hypoplastic left heart (7)

0.4%

(1/247)

Hypoplastic left heart (1), Interrupted aortic arch (1)

SC5D, TECTA

15

Del

17p13.3

31.9%

(29/91)

Low-set ears (15), Intellectual disability (14), Micrognathia (14), Hypotonia (12), Small for gestational age (12)

Atrial septal defect (12), Patent ductus arteriosus (12), Ventricular septal defect (10), Abnormality of cardiovascular system morphology (7), Tetralogy of Fallot (3)

0

/

/

16

Dup

18p11.31-p11.23

15.1%

(21/139)

Intellectual disability (11), Low-set ears (8), Micrognathia (8), Epicanthus (7), High palate (7)

Ventricular septal defect (9), Abnormality of cardiovascular system morphology (5), Atrial septal defect (5), Atrioventricular canal defect (2), Patent ductus arteriosus (2)

0.7%

(1/139)

Abnormal heart morphology (1)

LAMA1

17

Dup

7q34-q36.3

9.0%

(9/100)

Low-set ears (3), Small for gestational age (3), Delayed speech and language development (2), Downslanted palpebral fissures (2), Global developmental delay (2)

Ventricular septal defect (4), Atrial septal defect (3), Patent ductus arteriosus (2), Abnormal heart morphology (1), Pulmonary artery stenosis (1)

2.0%

(2/100)

Abnormal cardiac septum morphology (1), Abnormal aortic valve morphology (1), Tetralogy of Fallot (1)

AGK, BRAF, CLCN1, KEL, PRSS1, PRSS2, SSBP1, TAS2R38, TBXAS1, TRPV6, WEE2, ASB10, CDK5, CNTNAP2, EZH2, GIMAP5, KCNH2, NOBOX, NOS3, TPK1, DNAJB6, DPP6, DYNC2I1, KMT2C, LMBR1, MNX1, NCAPG2, SHH, XRCC2

18

Dup

Xq26.2

5.7%

(2/35)

Delayed speech and language development (1), Microcephaly (1), Cupped ear (1), Long palpebral fissure (1), Short stature (1)

Tetralogy of Fallot (1), Supravalvular aortic stenosis (1)

0

/

/

19

Del

5p15.33-p15.31

17.3%

(31/179)

Micrognathia (17), Intellectual disability (15), Low-set ears (15), Hypertelorism (13), Hypotonia (12)

Ventricular septal defect (12), Atrial septal defect (8), Patent ductus arteriosus (8), Abnormality of cardiovascular system morphology (4), Abnormal heart morphology (3)

0.6%

(1/179)

Atrioventricular canal defect (1)

AGXT2, AMACR, ANKH, CCT5, CTNND2, DNAH5, DNAJC21, IL7R, LMBRD2, MARCHF6, NADK2, NPR3, OTULIN, PRLR, RETREG1, SLC1A3, SLC45A2, SPEF2, TARS1, TRIO

20

Dup

5p15.31-p14.1

8.8%

(11/125)

Intellectual disability (4), Single transverse palmar crease (3), Iris coloboma (2), Low-set ears (2), Proportionate short stature (2)

Ventricular septal defect (4), Atrial septal defect (3), Patent ductus arteriosus (3), Abnormality of cardiovascular system morphology (1), Mitral regurgitation (1)

0.8%

(1/125)

Abnormal heart morphology (1)

CCT5, CTNND2, MARCHF6, ANKH, DNAH5, OTULIN, RETREG1, TRIO

21

Dup

3p26.3-p24.2

6.3%

(19/302)

Intellectual disability (6), Micrognathia (5), Delayed speech and language development (4), Downslanted palpebral fissures (4), Low-set ears (4)

Atrial septal defect (8), Ventricular septal defect (6), Abnormal heart morphology (2), Patent ductus arteriosus (2), Abnormal atrioventricular valve morphology (1)

1.0%

(3/302)

/

ABHD5, ACOX2, ACVR2B, ACY1, ADAMTS9, AMT, ANO10, APPL1, ARL13B, ARL6, ARPC4, ATG7, ATP2B2, ATXN7, BAP1, BRPF1, BTD, CACNA1D, CACNA2D2, CAV3, CCDC174, CCR2, CCR5, CHMP2B, CIDEC, CISH, CLEC3B, COL7A1, COLQ, CPOX, CRBN, CRELD1, CRTAP, CTNNB1, CX3CR1, DAG1, DALRD3, DAZL, DHX30, DNAH1, DNASE1L3, DOCK3, EOGT, FANCD2, FLNB, FOXP1, FYCO1, GBE1, GHRL, GLB1, GLYCTK, GMPPB, GNAI2, GNAT1, GPD1L, GPX1, GRM7, HESX1, HYAL1, HYAL2, IL17RC, IL17RD, IMPDH2, IQSEC1, ITPR1, JAGN1, KIF15, KLHDC8B, KLHL40, LAMB2, LARS2, LMOD3, LZTFL1, MAPKAPK3, MITF, MLH1, MRPS25, MST1, MST1R, MTMR14, MYD88, MYL3, NBEAL2, NDUFAF3, NEK10, NGLY1, NPRL2, NSUN3, OGG1, P4HTM, PBRM1, PDHB, PLCD1, POC1A, POMGNT2, POU1F1, PPARG, PRKCD, PROK2, PROS1, PTH1R, PTPN23, QARS1, QRICH1, RAF1, RARB, RFT1, RHOA, ROBO2, RPL15, RPSA, SATB1, SCN10A, SCN11A, SCN5A, SETD2, SETD5, SGO1, SHQ1, SLC25A20, SLC25A26, SLC25A38, SLC38A3, SLC6A1, SLC6A20, SLC6A6, STT3B, SUMF1, SYN2, TDGF1, TGFBR2, THRB, TKT, TMEM43, TMIE, TNNC1, TOP2B, TRAIP, TRAK1, TREX1, TRIM71, TRNT1, TSEN2, TTC21A, UQCRC1, VHL, WNT5A, WNT7A, XPC, ZMYND10, ATG7, ATP2B2, BTD, CCDC174, COLQ, DAZL, FANCD2, GHRL, IQSEC1, MRPS25, NGLY1, PPARG, RAF1, RARB, RPL15, SATB1, SGO1, SLC6A1, SLC6A6, SYN2, THRB, TMEM43, TOP2B, TSEN2, VHL, WNT7A, XPC

22

Del

9p24.3-p22.3

17.7%

(53/300)

Micrognathia (29), Low-set ears (25), Intellectual disability (22), Abnormal pinna morphology (17), Trigonocephaly (17)

Atrial septal defect (19), Ventricular septal defect (19), Patent ductus arteriosus (14), Abnormality of cardiovascular system morphology (12), Pulmonic stenosis (5)

0.3%

(1/300)

Transposition of the great arteries (1)

DOCK8, KANK1, SMARCA2

23

Dup

9p22.3

11.6%

(5/43)

Micrognathia (3), Brachydactyly (2), Downslanted palpebral fissures (2), Finger clinodactyly (2), Intellectual disability (2)

Abnormal heart morphology (1), Abnormality of the cardiovascular system (1), Mitral regurgitation (1), Patent ductus arteriosus (1), Tricuspid regurgitation (1)

0

/

/

24

Del

16q21-q22.1

17.9%

(5/28)

Intellectual disability (4), Micrognathia (4), Hypotonia (3), Low-set ears (3), Microcephaly (3)

Aortic valve stenosis (2), Atrioventricular canal defect (2), Patent ductus arteriosus (2), Abnormality of cardiovascular system morphology (1), Pulmonic stenosis (1)

0

/

/

25

Del

17p11.2

13.4%

(13/97)

Global developmental delay (6), Intellectual disability (5), Abnormal facial shape (3), Downturned corners of mouth (3), Myopia (3)

Tetralogy of Fallot (6), Patent ductus arteriosus (3), Abnormal heart morphology (2), Abnormal ventricular septum morphology (1), Abnormality of cardiovascular system morphology (1)

0

/

/

26

Del

3p22.2

50.0%

(1/2)

Abnormal mandible morphology (1), Abnormal pinna morphology (1), Abnormality of the outer ear (1), Absent nipple (1), Craniosynostosis (1)

Transposition of the great arteries (1)

0

/

/

27

Dup

6p25.3-p22.2

10.2%

(12/118)

Intellectual disability (4), Narrow mouth (4), Abnormal pinna morphology (3), Anteverted nares (3), Brachydactyly (3)

Abnormality of cardiovascular system morphology (3), Ventricular septal defect (3), Atrioventricular canal defect (2), Pulmonic stenosis (2), Atrial septal defect (1)

0

/

/

28

Del

15q26.3

17.1%

(20/117)

Low-set ears (10), Intellectual disability (9), Small for gestational age (7), Abnormal pinna morphology (6), Hypertelorism (6)

Ventricular septal defect (10), Atrial septal defect (6), Patent ductus arteriosus (6), Abnormality of cardiovascular system morphology (2), Pulmonic stenosis (2)

0

/

/