Table 3.

Enrichment of neurodevelopmental disorder variants in schizophrenia.

NDD variant set (N variants)	Schizophrenia de novo variant enrichment
	Observed / expected	P	Rate ratio (95% CI)
Primary variant set (5863)	9 / 1.20	5.0 × 10−6	7.48 (3.42, 14.20)
Comparator variant set (40,909)	8 / 9.86	0.75	0.81 (0.35, 1.60)

The number of observed and expected de novo variants from the neurodevelopmental variant sets in 3444 schizophrenia trios is shown. The NDD primary variant set includes neurodevelopmental variants annotated as PTVs in genes with “probability of loss of function intolerance” (pLi) scores ≥ 0.9 or missense variants with MPC scores ≥2. The comparator variant set includes neurodevelopmental variants annotated as PTVs in genes with pLi scores < 0.9, missense variants with MPC scores <2 and all synonymous variants. Enrichment statistics were generated using a Poisson rate ratio test. P-values are uncorrected and two-tailed. PTVs protein-truncating variants, NDD neurodevelopmental disorders, CI confidence interval.