Table 2. Ratios of functional classes of de novo mutations across various samples.

Classes of de novo mutation in the present study, previous studies of schizophrenia (Gulsuner¹⁴ and Xu¹³), and in all studies of schizophrenia combined (SZ (ALL)), which includes this study and an additional small study¹². ASD = Autism Spectrum Disorder, ID = Intellectual Disability. Controls are unaffected individuals or unaffected siblings of probands with ASD or SZ. To control for factors that influence estimates of absolute rates (sequencing depth, calling, parental age, etc.), we tested for differences between the ratios of classes of de novo mutations (nonsynonymous to silent, loss-of-function to missense) in the disorder groups and the controls, using Fisher’s exact test. Nominally significant p-values (<0.05) are bold. NS = nonsynonymous, S = synonymous (silent), LoF = loss-of-function.

	Controls7-10,13-14	Current study	Schizophrenia (ref.14)	Schizophrenia (ref.13)	Schizophrenia all (refs 12-14)	Autism spectrum disorder6-9	Intellectual disability10,11
Nonsynonymous	434	482	68	137	702	789	141
Synonymous	155	155	29	27	211	255	25
Ratio	2.8	3.1	2.3	5.1	3.3	3.1	5.6
P vs. Controls	-	0.43	0.46	0.0097	0.18	0.41	0.0027
Loss-of-function	49	64	12	20	100	134	34
Missense	376	408	56	113	588	638	104
Ratio	0.13	0.16	0.21	0.18	0.17	0.21	0.33
P vs. Controls	-	0.37	0.17	0.29	0.17	0.0072	0.0003