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Table 1 Top de novo genes associated with ND risk

From: Molecular subtyping and improved treatment of neurodevelopmental disease

Gene

ASDb

ID/DDc

EPd

SZe

Total cases

Control countsf

p value

OR (95 % CI)

Pathwayg

SYNGAP1 a

7

9

0

0

16

1

1.45E-12

88.0 (13.7–3613.0)

S

SCN2A a

6

7

0

1

14

1

1.34E-11

86.7 (13.2–3587.4)

S

ARID1B a

5

11

0

0

16

5

9.29E-10

17.6 (6.2–61.5)

C, T, W

ANKRD11 a

2

8

0

0

10

1

2.63E-08

61.9 (8.8–2644.0)

D

CHD8 a

12

0

0

1

13

4

3.52E-08

17.9 (5.5–75.2)

C, T, W

ADNP a

5

4

0

0

9

2

1.99E-06

24.7 (5.1–234.2)

T

DYRK1A a

5

3

0

0

8

1

2.46E-06

44.0 (5.9–1929.7)

K, D

CTNNB1 a

1

6

0

0

7

1

1.42E-05

38.5 (4.9–1716.8)

T, W

CHD2 a

5

2

1

0

8

3

3.36E-05

14.7 (3.5–85.7)

C, T

STXBP1

0

5

1

0

6

1

8.12E-05

32.9 (4.0–1503.0)

S

POGZ

3

2

0

1

6

2

1.58E-04

18.5 (3.3–187.6)

R

MED13L

2

4

0

0

6

2

2.82E-04

16.5 (2.9–166.8)

T, W

TRIP12

2

2

0

0

4

0

5.63E-04

∞ (3.6–∞)

U

KMT2A

2

4

0

0

6

4

9.24E-04

9.3 (2.2–44.7)

C

EP300

1

4

0

0

5

3

2.03E-03

10.3 (2.0–66.5)

C, T, W

GRIN2B

3

1

0

0

4

1

2.47E-03

22.0 (2.2-1075.1)

S

DDX3X a

1

2

0

0

3

0

2.70E-03

∞ (2.6–∞)

T, W

SUV420H1

3

0

0

0

3

0

2.70E-03

∞ (2.6–∞)

C, T

WDR45

0

2

1

0

3

0

2.70E-03

∞ (2.6–∞)

A

CHAMP1 a

0

3

0

0

3

0

3.66E-03

∞ (2.3–∞)

R

SCN1A a

0

0

4

0

4

2

6.50E-03

11.0 (1.6–121.5)

S

WAC a

2

2

0

0

4

2

6.50E-03

11.0 (1.6–121.5)

C, T

AHDC1 a

1

2

0

0

3

1

9.68E-03

18.5 (1.5–967.5)

Db

SATB2

0

3

0

0

3

1

9.68E-03

18.5 (1.5–967.5)

C, T

  1. All counts represent de novo mutations that are likely to be gene-disruptive, including frameshift, splice and nonsense mutations aGene also identified through genotype-first approaches. b5001–5922 individuals with ASD were screened depending on the gene. ASD data have been previously published [19, 23–28]. c1284 individuals with ID/DD were screened. ID/DD data have been previously published [29–31]. d274 individuals with EP were screened. EP data have been previously published [32, 33]. e785 individuals with SZ were screened. SZ data have been previously published [34–36]. fData from 45,376 control individuals were obtained from the ExAC database. The disruptive mutations counted here represent unaffected population control individuals and individuals with diseases other than neuropsychiatric disorders [37]. These data were used to calculate the Fisher’s exact test p value. Only disruptive (frameshift, splice, nonsense) variants were scored in cases and controls. gPathway annotations determined using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 [57, 58]. A Autophagy, ASD Autism spectrum disorders, C Chromatin remodeling, CI Confidence interval, D Broad development, Db DNA binding, DD Developmental delay, EP Epilepsy, ID Intellectual disability, K Kinase, OR Odds ratio, R Replication, S Synapse function, SZ Schizophrenia, T Gene transcription, U E3 ubiquitin-protein ligase, W Wnt/β-catenin signaling