Table 2. Basic burden tests associating disruptive variants in SETD1A to schizophrenia and developmental disorders.

Phenotype	Data set	Case	Control	Test	P value
Schizophrenia	All schizophrenia case-control samples (ignoring de novo status)	10 of 7,776	0 of 13,028
	Non-schizophrenia ExAC exomes		2 of 45,376
	All samples	10 of 7,776	2 of 58,404	Fisher’s exact	2.6 × 10−8
Neurodevelopmental disorders	DDD study	4 of 4,281	See notea	Fisher’s exact	2.9 × 10−4
	ASD trios	0 of 2,297
	ID trios	0 of 151
Combined	All samples	14 of 14,505	2 of 58,404	Fisher’s exact	1.2 × 10−8

De novo status of variants was ignored was non-schizopherenia exomes from the ExAC database were incorporated as controls. The number of SETD1A LoF variants and the sample size of each data set were indicated in each cell.

^aThe full control data set (n = 58,404) was used to calculated the P value.