Table 3 Significant CNVRs identified in the GLGS-UGLI cohort

1

17,361,781

17,371,377

9598

Gain

4.70e-02

2.89e-01

SDHB

1.71

0.458

1

25,599,085

25,655,563

56,480

Gain

8.90e-06

1.60e-04

RHD

11.1

20.5

1

25,599,085

25,655,563

56,480

Loss

1.87e-05

3.19e-04

RHD

15.8

7.94

1

115,400,087

115,545,917

145,832

Gain

8.35e-03

7.30e-02

SYCP1

0

1.22

2

39,250,139

39,294,016

43,879

Gain

4.60e-07

1.05e-05

SOS1

0.685

5.5

2

47,672,361

47,698,203

25,844

Gain

7.06e-15

6.02e-13

MSH2

1.37

11.9

2

166,850,678

166,866,353

15,677

Gain

2.05e-14

1.40e-12

SCN1A

2.23

13.6

2

166,850,678

166,866,353

15,677

Loss

4.91e-02

2.89e-01

SCN1A

0.685

0

2

189,850,694

189,871,691

20,999

Gain

1.74e-03

1.97e-02

COL3A1

0.856

3.51

4

107,133,338

107,181,616

48,280

Gain

2.78e-06

5.57e-05

TBCK

0

3.05

4

128,811,117

129,098,453

287,338

Gain

7.39e-05

1.14e-03

PLK4, MFSD8, LARP1B

1.54

5.8

5

700,560

850,514

149,956

Loss

7.00e-03

6.69e-02

ZDHHC11

5.99

2.75

5

36,995,722

37,046,626

50,906

Gain

1.75e-10

6.62e-09

NIPBL

2.4

11.5

5

112,082,255

112,116,602

34,349

Gain

3.03e-05

4.93e-04

APC

1.2

5.5

5

131,915,022

131,953,804

38,784

Gain

1.06e-03

1.29e-02

RAD50

0.856

3.66

5

140,230,509

140,237,998

7491

Loss

9.50e-05

1.35e-03

PCDHA1, PCDHA2, PCDHA3, PCDHA4, PCDHA5, PCDHA6, PCDHA7, PCDHA8, PCDHA9, PCDHA10

4.11

0.763

5

180,385,378

180,425,019

39,643

Gain

1.11e-03

1.31e-02

BTNL3

1.54

0

5

180,385,378

180,425,019

39,643

Loss

1.60e-16

1.82e-14

BTNL3

8.05

0

6

29,856,571

29,911,837

55,268

Loss

3.08e-02

2.14e-01

HLA-H, HLA-A, HLA-G, HLA-J

4.79

2.44

6

30,105,743

30,111,610

5869

Gain

8.35e-03

7.30e-02

TRIM40

0

1.22

6

32,450,297

32,572,251

121,956

Gain

2.24e-06

4.77e-05

HLA-DRB1,HLA-DRB5, HLA-DRB6

10.4

20.2

6

32,450,297

32,572,251

121,956

Loss

4.56e-12

2.22e-10

HLA-DRB1,HLA-DRB5, HLA-DRB6

19.3

6.41

7

75,362,387

75,371,553

9168

Gain

1.10e-04

1.54e-03

HIP1

2.05

0

7

117,246,728

117,251,848

5122

Gain

3.24e-02

2.17e-01

CFTR

0

0.916

7

141,760,798

141,798,014

37,218

Gain

5.62e-03

5.63e-02

MGAM

3.42

1.07

7

141,760,798

141,798,014

37,218

Loss

1.88e-02

1.46e-01

MGAM

13.5

9.16

10

83,945,607

83,955,217

9612

Loss

4.91e-02

2.89e-01

NRG3

0.685

0

10

89,653,781

89,699,055

45,276

Gain

4.26e-11

1.82e-09

PTEN

0.856

8.4

10

91,468,829

91,521,366

52,539

Gain

2.81e-03

3.09e-02

KIF20B

0.342

2.29

11

524,055

545,087

21,034

Gain

9.39e-08

2.46e-06

HRAS

0.514

5.5

11

32,749,279

32,774,462

25,185

Loss

1.08e-02

8.58e-02

CCDC73

1.03

0

11

72,723,762

72,814,435

90,675

Gain

3.24e-02

2.17e-01

FCHSD2

0

0.916

11

108,098,352

108,115,754

17,404

Gain

8.21e-08

2.33e-06

ATM

1.2

7.18

11

108,150,237

108,190,766

40,531

Gain

1.49e-09

5.10e-08

ATM

2.4

10.8

12

10,568,395

10,588,422

20,029

Loss

4.25e-03

4.40e-02

KLRC32, KLRC3

0

1.37

12

11,226,421

11,257,845

31,426

Gain

2.30e-02

1.74e-01

PRB4, TAS2R43

0.171

1.37

12

11,495,064

11,567,700

72,638

Loss

3.30e-04

4.32e-03

PRB1

5.14

1.53

12

88,221,580

88,632,786

411,208

Gain

3.84e-06

7.27e-05

CEP290, TMTC3

1.54

6.72

13

32,912,277

32,921,033

8758

Gain

9.57e-13

5.44e-11

BRCA2

4.79

17.4

13

32,912,277

32,921,033

8758

Loss

9.27e-03

7.79e-02

BRCA2

1.88

0.305

14

29,225,492

29,237,924

12,434

Gain

1.08e-02

8.58e-02

FOXG1

1.03

0

14

73,993,018

74,051,067

58,051

Gain

2.92e-07

7.11e-06

HEATR4, ACOT1, ACOT2

8.22

1.98

14

73,993,018

74,051,067

58,051

Loss

5.71e-55

1.95e-52

HEATR4, ACOT1, ACOT2

30.3

1.07

15

30,579,250

31,092,983

513,735

Loss

4.91e-02

2.89e-01

CHRFAM7A, ARHGAP11B

0.685

0

15

91,331,546

91,346,951

15,407

Gain

8.35e-03

7.30e-02

BLM

0

1.22

16

5,105,306

5,123,005

17,701

Loss

4.91e-02

2.89e-01

ALG1

0.685

0

17

2,568,663

2,576,056

7395

Gain

7.67e-05

1.14e-03

PAFAH1B1

0

2.29

17

34,436,532

34,534,847

98,317

Gain

4.03e-02

2.64e-01

TBC1D3B, CCL3L1

5.82

3.36

17

42,858,950

42,896,377

37,429

Loss

2.38e-09

7.37e-08

ADAM11, GJC1

4.45

0

19

483,488

517,315

33,829

Gain

2.45e-02

1.78e-01

MADCAM1,TPGS1

0.342

1.68

19

1,219,342

1,247,118

27,778

Gain

4.25e-03

4.40e-02

STK11, ATP5D

0

1.37

19

1,618,982

1,627,422

8442

Gain

7.06e-03

6.69e-02

TCF3

0.171

1.68

19

43,279,237

43,858,478

579,243

Gain

9.37e-03

7.79e-02

PSG1, PSG6, PSG7, PSG11, PSG2, PSG4, PSG5, PSG9, PSG3, CD177

2.23

0.458

19

43,279,237

43,858,478

579,243

Loss

2.50e-02

1.78e-01

PSG1, PSG6, PSG7, PSG11, PSG2, PSG4, PSG5, PSG9, PSG3, CD177

5.65

3.05

19

52,272,131

52,356,648

84,519

Gain

4.91e-02

2.89e-01

FPR2, FPR3

0.685

0

19

53,518,590

53,547,846

29,258

Gain

7.70e-04

9.70e-03

ERVV-1

4.11

1.07

20

58,426,497

58,476,841

50,346

Gain

5.18e-18

8.84e-16

SYCP2

1.88

15.1

20

58,426,497

58,476,841

50,346

Loss

2.47e-02

1.78e-01

SYCP2

2.23

0.611