Table 1.

Partitioning FMRP targets genetic association by overrepresented functional annotation.

Gene set	N	Common SNPs		Rare variants		De novo variants
		β	P	β	P	Rate ratio	P
Genes exclusive to functional terms	1195	0.066	0.13	LoF: 0.010 NS: 0.015	LoF: 1.0 NS: 1.0	LoF: 0.89 NS: 0.98	LoF: 1.0 NS: 1.0
Overlapping genes	401	0.29	3.7 × 10−6	LoF: 0.43 NS: 0.052	LoF: 3.5 × 10−5 NS: 0.14	LoF: 1.50 NS: 1.24	LoF: 0.085 NS: 0.014
Genes exclusive to FMRP targets	438	0.17	0.0063	LoF: 0.34 NS: 0.025	LoF: 0.0023 NS: 0.92	LoF: 1.64 NS: 1.35	LoF: 0.024 NS: 1.2 × 10−4

GO and MP functional terms independently overrepresented among FMRP targets were merged, then divided by FMRP targets membership. Genes were either exclusively in the functional terms gene set, exclusively in the FMRP targets gene set, or common to both sets (Overlapping genes). Genes not brain-expressed were removed. Background association originating from brain expression was controlled for within gene set association analyses. Shown are the resulting effect sizes (β or rate ratio) and P values (P). For each variant type, P values were Bonferroni adjusted for three tests.

SNPs single nucleotide polymorphisms, LoF loss-of-function, NS nonsynonymous.