Table 5.

Overlaps with FMRP-Associated Genes

Gene List	Number	FMRP Targets	p Value
LGD in probands	59	14	0.006
CNV candidates	72	13	0.0004
LGD + CNV candidates	129	26	<10−13
LGD in siblings	28	2	0.8
Missense in probands	207	22	0.9
Missense in siblings	207	30	0.1

The overlap of six different gene lists with the set of FMRP-associated genes (Darnell et al., 2011) is shown. “LGD in probands” is the list of genes affected by de novo LGDs in affected children; “CNV candidates”are the best gene candidates for ASD derived from de novo CNVs analyzed in a previous study (Gilman et al., 2011); “LGD + CNV candidates”is the union of the previous two categories; “LGD in siblings” is the list of genes affected by de novo LGD in unaffected siblings; and “missense in probands” and “missense in siblings” are the lists of genes affected by de novo missense variants in probands and unaffected siblings, respectively. For each list, we show the total number of genes, the number of genes that are associated with FMRP, and the p value under the hypothesis that the overlap is random. See Experimental Procedures for details of the p value computation.