Table 2 Pathogenic or likely pathogenic CNVs in 24 patients with syndromic CHD

5

M

7 m

Dup 8q24.21-q24.3 (17.7 Mb)

Chr8:128,538,700–146,262,124

Pathogenic: 0.862

Pathogenic

Pathogenic

AGO2, CYP11B2^a, FOXH1^a, KCNK9, PTK2^a, SLURP1, CYP11B1^a, NDRG1^a, SLC39A4^a

/

ASD

Mental retardation, cryptorchidism

Del 13q33.1-q34 (11.9 Mb)

Chr13:103,226,118–115,091,802

Pathogenic: 0.840

Pathogenic

Pathogenic

COL4A1^a, EFNB2^a, F10^a, IRS2^a, COL4A2^a, GAS6^a

/

11

M

1y2m

Del 1p36.33 (1.3 Mb)

Chr1:849,466–2,174,235

Pathogenic: 0.840

Pathogenic

Pathogenic

DVL1, GNB1, AGRN^a, SKI^a

1p36 microdeletion syndrome

VSD

Mental retardation

12

M

7 m

Del 2p16.3 (0.03 Mb)

Chr2:50,203,462–50,232,894

Benign: 0.123

NM

Pathogenic

NRXN1

/

TOF, RAA, abnormal origin of right coronary artery

Skewed mouth, left ear deformity, hydrocele

17

M

4y2m

Del 3q25.33-q26.1 (0.2 Mb)

Chr3:160,526,260–160,738,728

Likely pathogenic: 0.527

Likely benign

NM

/

/

DORV, TGA, VSD, PS, PDA, abnormal right coronary artery branch

Hydrocele, genu valgum

32

M

6 m

Del 22q11.21 (2.5 Mb)

Chr22:18,921,359–21,460,595

Pathogenic: 0.840

Pathogenic

Pathogenic

COMT^a, CRKL^a, SLC25A1, SNAP29, TBX1^a, TXNRD2^a, LZTR1^a

22q11.2 deletion syndrome (DiGeorge syndrome)

TOF, RAA

Athymism, immunodeficiency

33

M

3y9m

Del 2q13 (1.7 Mb)

Chr2:111,398,336–113,101,220

Likely pathogenic: 0.527

Uncertain

Pathogenic

MERTK^a, BCL2L11^a

/

ASD

Funnel chest

34

M

4y7m

Dup Xp22.31 (0.5 Mb)

ChrX:6,836,073–7,347,549

Likely benign: 0.154

Likely pathogenic

NM

STS

/

VSD

Cerebral dysplasia, mental retardation, multiple deformities of vertebrae

38

F

3 m

Del 17q25.3 (0.8 Mb)

Chr17:79,344,285–80,192,099

Likely pathogenic: 0.527

NM

Pathogenic

ARHGDIA^a, PYCR1^a

/

VSD, ASD, left aortic arch with right subclavian artery voyage

hydrocephalus, arachnoid cyst, congenital hip dysplasia

43

F

4 m

Del 5q35.3 (0.6 Mb)

Chr5:180,069,797–180,686,444

Likely pathogenic: 0.527

NM

Pathogenic

FLT4^a

/

VSD, abnormal right ventricular muscle bundle

Transverse facial cleft

44

M

6 m

Del 1q43-q44 (5.5 Mb)

Chr1:243,545,786–249,208,146

Likely pathogenic: 0.527

Pathogenic

Pathogenic

AKT3, HNRNPU^a, NLRP3, SDCCAG8

/

ASD

Cerebral dysplasia

53

M

2 m

Del 6q14.1-q16.1 (11.0 Mb)

Chr6:83,849,802–95,155,354

Likely pathogenic: 0.544

Pathogenic

Pathogenic

MAP3K7^a, NT5E^a

/

VSD, ASD

Cryptorchidism, mental retardation

60

M

2 m

Dup 15q11.2 (1.0 Mb)

Chr15:24,050,216–25,107,421

Uncertain: 0.187

Uncertain

Likely pathogenic

/

/

Solitary dextrocardia, bilateral right atrium heterogeneity, ventricular reversal, complete AVSD, anatomical DORV with TGA, PVS

Heterotaxy, cleft lip, cleft palate

66

M

2 m

Del 22q11.21 (2.5 MB)

Chr22:18,919,528–21,460,595

Pathogenic: 0.840

Pathogenic

Pathogenic

COMT^a, CRKL^a, SLC25A1, SNAP29, TBX1^a, TXNRD2^a, LZTR1^a

22q11.2 deletion syndrome (DiGeorge syndrome)

VSD

Abnormal facial features, narrow glottis

75

F

4 m

Del 11q23.3-q25 (13.5 Mb)

Chr11:121,057,903–134,928,850

Pathogenic: 0.840

Pathogenic

Pathogenic

CDON^a, CHEK1, ETS1, HYLS1^a, KCNJ5^a, SC5D^a, SCN3B^a, JAM3^a

/

DORV, CoA

Familial exudative vitreoretinopathy, horseshoe kidney, foot deformity, skull deformity

76

M

1y1m

Del 17p13.3 (0.2 Mb)

Chr17:226,043–438,909

Likely pathogenic: 0.544

NM

Pathogenic

/

Miller–Dieker syndrome

VSD

Mental retardation

Dup 18p11.31-p11.23 (0.5 Mb)

Chr18:7,086,919–7,605,032

Uncertain: 0.282

NM

Pathogenic

/

77

F

1y1m

Dup 7q34-q36.3 (19.1 Mb)

Chr7:139,520,175–159,123,167

Pathogenic: 0.862

Pathogenic

Pathogenic

BRAF^a, CNTNAP2, DNAJB6, DPP6, EZH2^a, KCNH2^a, MNX1, PRKAG2^a, RHEB^a, SHH^a, PRSS1^a

/

VSD

Hydrocephaly

96

F

5y10m

Dup Xq26.2 (0.1 Mb)

ChrX:133,025,264–133,159,421

Likely benign: 0.141

NM

Pathogenic

GPC3^a

/

ASD

Single transverse palmar crease, mental retardation

99

F

11 m

Del 5p15.33-p15.31 (7.8 Mb)

Chr5:113,576–8,101,272

Pathogenic: 0.840

Pathogenic

Pathogenic

/

Cri du Chat Syndrome (5p deletion)

VSD

mental retardation, motor retardation

Dup 5p15.31-p14.1 (19.1 Mb)

Chr5:8,115,306–27,645,325

Pathogenic: 0.862

Pathogenic

Pathogenic

DNAH5^a, MTRR

/

102

M

3y

Dup 3p26.3-p24.2 (25.7 Mb)

Chr3:105,511–25,830,553

Pathogenic: 0.862

Pathogenic

Pathogenic

CAV3^a, COLQ^a, CRELD1^a, RAB5A^a, RAF1^a, RARB^a, RPL15, SLC6A6^a, SUMF1^a, THRB^a, TMEM43, VHL^a, XPC, CRBN^a, ITPR1, PPARG^a, WNT7A^a

/

VSD, ASD

Hypothyroidism, developmental delay

103

F

1y11m

Del 9p24.3-p22.3 (14.5 Mb)

Chr9:204,149–14,724,068

Pathogenic: 0.840

Pathogenic

Pathogenic

GLDC^a, JAK2^a, KANK1, MPDZ^a, VLDLR^a

/

ASD

Cleft palate, mental retardation

Dup 9p22.3 (1.6 MB)

Chr9:14,762,293–16,349,620

Likely benign: 0.141

Likely pathogenic

Pathogenic

/

/

Dup 10p15.1-p14(1 MB)

Chr10:6,547,235–7,565,244

Likely benign: 0.141

Uncertain

NM

/

/

104

M

1y

Del 16q21-q22.1 (1.4 Mb)

Chr16:66,280,192–67,654,588

Likely pathogenic: 0.527

NM

Likely pathogenic

CTCF, HSD11B2^a, HSF4, CBFB^a, NOL3^a

/

VSD, ASD, PDA

Cryptorchidism, oblique inguinal hernia, hemangioma

107

M

11 m

Del 17p11.2 (3.7 Mb)

Chr17:16,603,146–20,274,157

Pathogenic: 0.840

Pathogenic

Pathogenic

B9D1^a, FLCN^a, TNFRSF13B, MAPK7^a

Smith–Magenis syndrome

VSD

Developmental disorder of speech and language, motor retardation

108

F

6y

Del 3p22.2 (0.6 Mb)

Chr3:38,455,532–39,035,153

Pathogenic: 0.854

Pathogenic

Pathogenic

ACVR2B^a, SCN5A^a

/

ASD, PVS

Genital tract malformation

109

F

6y

Dup 6p25.3-p22.2 (24.7 Mb)

Chr6:390,212–25,638,706

Pathogenic: 0.862

Likely pathogenic

Pathogenic

CAP2^a, EDN1^a, FOXC1^a, SOX4^a, TFAP2A^a

/

PDA

Rhinostenosis

Del 15q26.3 (1.0 Mb)

Chr15:101,341,696–102,391,143

Pathogenic: 0.840

Uncertain

Likely pathogenic

CHSY1

/