Table 1 Enrichment of schizophrenia de novo variants in neurodevelopmental disorder (NDD) associated genes.

From: Schizophrenia, autism spectrum disorders and developmental disorders share specific disruptive coding mutations

NDD gene set (N genes)

Schizophrenia de novo variant enrichment

 

Mutation class

Obs/exp

P

Rate ratio (95% CI)

PTV enriched genes (127)

PTVs

20/3.41

2.14 × 10−8

4.89 (2.95, 7.67)

 

Missense (MPC > 2)

6/4.57

0.47

1.32 (0.48, 2.95)

 

PTV vs. missense (MPC > 2)

—

0.006

3.70 (1.46, 9.41)

Missense enriched genes (103)

PTVs

4/2.94

0.79

1.09 (0.29, 2.80)

 

Missense (MPC > 2)

14/7.85

0.04

1.86 (0.99, 3.23)

 

Missense (MPC > 2) vs. PTV

—

0.35

1.72 (0.56, 5.31)

PTV + missense enriched genes (53)

PTVs

7/1.64

0.0051

3.45 (1.38, 7.19)

 

Missense (MPC > 2)

9/3.77

0.014

2.47 (1.11, 4.83)

 

PTV vs. missense (MPC > 2)

—

0.52

1.40 (0.51, 3.82)

  1. Genes enriched for PTV or missense de novo variants in NDDs (significance threshold set at P < 2.5 × 10−6) were evaluated for enrichment of de novo variants in 3444 schizophrenia trios using a two-sample Poisson rate ratio test. P-values are uncorrected and two-tailed. NDD gene sets are defined as genes only associated with the given mutation class (i.e., excluding genes significant for the alternative mutation class) in the Deciphering Developmental Disorders study14. A Poisson regression model was used to evaluate differences between the rate of schizophrenia de novo PTVs and missense variants in NDD associated genes.
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