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Table 2 Gene-specific significance in the ACGC cohort and in the ACGC+SSC+ASC combined samples based on two statistical models

From: Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Gene

ACGC (n = 2145)

ACGC+SSC+ASC (n = 6107)

Phase-I

Phase-II

All

CH model

denovolyzeR

LGD

MIS

All

CH model

denovolyzeR

LGD

MIS

LGD

MIS

LGD

MIS

LGD_q

prot_q

LGD_q

prot_q

LGD_q

prot_q

LGD_q

prot_q

SCN2A

6

4

5

9

11

13

3.68E−25

1.23E−40

4.21E−18

1.05E−29

15

21

36

7.77E−28

2.23E−49

3.52E-22

3.35E-42

CHD8

3

1

2

1

5

2

3.18E−09

7.56E−08

5.40E−07

1.68E−04

14

4

18

7.49E−25

7.45E−18

3.52E−22

1.19E−13

MECP2

1

3

2

1

3

4

1.00E−06

1.12E−11

1.78E−05

4.12E−08

3

5

8

6.26E−04

1.33E−08

1.78E−03

1.42E−06

DYRK1A

1

1

2

0

3

1

1.51E−05

2.78E−04

5.92E−05

2.75E−03

8

1

9

3.78E−13

2.51E−07

1.31E−13

4.23E−07

ASXL3

0

1

3

1

3

2

7.28E−04

5.62E−03

1.82E−04

4.29E−03

5

2

7

6.33E−04

0.894

6.03E−06

0.0200

WAC

0

0

2

0

2

0

9.05E−04

0.0311

5.14E−03

0.2322

4

0

4

2.12E−05

0.0532

6.57E−05

0.1384

FOXP1

0

0

2

1

2

1

1.04E−03

3.46E−03

0.0103

0.0285

4

1

5

3.36E−05

0.014

3.81E−04

0.0235

CTTNBP2

0

1

2

0

2

1

4.69E−03

0.0189

0.0226

0.2162

3

1

4

0.0331

1

0.1072

1

TNRC6B

0

0

2

0

2

0

7.00E−03

0.2549

0.0158

0.5818

4

0

4

1.97E−03

1

1.17E−03

1

MED13L

1

0

1

0

2

0

7.00E−03

0.2549

0.0386

0.9485

4

1

5

1.97E−03

0.9197

9.40E−03

1

CDKL5

1

0

1

0

2

0

8.26E−03

0.2732

7.14E−03

0.3409

2

1

3

1

1

0.5527

1

DSCAM

2

0

0

1

2

1

0.0130

0.0770

0.0226

0.3035

6

2

8

1.03E−05

0.0272

1.55E−06

0.0135

ZNF292

1

0

1

0

2

0

0.0139

0.6051

0.0158

0.8299

3

2

5

0.2763

1

0.0508

1

POGZ

1

1

0

0

1

1

0.0507

0.0153

0.3864

0.5818

4

4

8

2.40E−06

1.84E−09

3.48E−03

7.13E−04

WDFY3

1

1

0

2

1

3

0.2966

0.0153

0.7292

0.2736

3

7

10

0.2778

7.21E−04

1

5.44E−03

NAA15

0

0

1

1

1

1

0.0851

0.0228

0.3452

0.3025

2

2

4

0.1747

0.0287

1

0.4185

CUL3

1

0

0

1

1

1

0.1056

0.0446

0.3825

0.3035

2

1

3

0.2778

1

1

1

STXBP1

1

0

0

0

1

0

0.1056

0.6051

0.3267

1

1

1

2

1

1

1

1

ADNP

1

0

0

0

1

0

0.1314

0.9222

0.2294

1

5

0

5

2.40E−06

0.0764

4.55E−07

0.0669

DDX3X

0

1

1

0

1

1

0.1335

0.0871

0.2367

0.2989

2

1

3

0.7186

1

0.4989

1

RALGAPB

0

0

1

1

1

1

0.1335

0.0815

0.3267

0.5816

2

1

3

0.6237

1

1

1

GIGYF2

1

1

0

0

1

1

0.1335

0.0770

0.6428

0.5818

2

3

5

0.7186

0.0363

1

0.5211

NCKAP1

1

0

0

0

1

0

0.1335

0.9135

0.5383

1

3

0

3

0.0206

1

0.4100

1

GRIN2B

1

0

0

0

1

0

0.1359

1

0.2367

1

4

0

4

4.61E−04

1

1.17E−04

1

MYT1L

1

0

0

0

1

0

0.1717

1

0.2294

1

2

2

4

1

1

0.4100

1

SHANK2

0

0

1

0

1

0

0.2017

1

0.3267

1

2

1

3

1

1

1

1

SYNGAP1

1

0

0

0

1

0

0.2966

1

0.3154

1

6

3

9

1.84E−05

0.0168

8.04E−08

8.79E−05

PHIP

1

0

0

0

1

0

0.2966

1

0.5095

1

1

1

2

1

1

1

1

CHD2

0

0

1

1

1

1

0.3536

0.9217

0.5095

0.7736

4

4

8

0.0331

0.5391

0.0125

3.31E−03

SHANK1

1

0

0

0

1

0

0.3536

1

0.3267

1

1

1

2

1

1

1

1

DOCK8

1

0

0

0

1

0

0.4837

1

0.3267

1

2

0

2

1

1

1

1

ANK2

0

1

1

0

1

1

0.7356

1

0.6639

1

5

4

9

0.0587

1

2.54E−03

0.0396

ASH1L

0

1

0

1

0

2

1

0.2732

1

1

3

2

5

0.0825

1

0.5350

1

RIMS1

0

0

0

1

0

1

1

1

1

1

2

1

3

0.7186

1

1

1

TSC2

0

1

0

0

0

1

1

1

1

1

0

4

4

1

1

1

1

KMT2C

0

1

0

1

0

2

1

1

1

1

1

4

5

1

1

1

1

ITPR1

0

1

0

0

0

1

1

1

1

1

0

3

3

1

1

1

1

WHSC1

0

0

0

1

0

1

1

0.9499

1

1

1

1

2

1

1

1

1

  1. Significant q values (< 0.05) are italicized
  2. LGD likely gene-disrupting variants, MIS missense variants, LGD_q q values of truncated DNMs (FDR corrected), prot_q q values of LGD and missense DNMs (FDR corrected)
  3. Previously well-defined genes in neurodevelopmental disorders