Table 3. All variants identified in second intracellular loop (L_II-III) of SCN9A.

ESP and 1000 Genome frequencies are only for “European American” and “European” population respectively. Case: Number of ASD case samples with variant/ Number of ASD case samples without variant. Control: Number of control samples with variant/ Number of control samples without variant. dbSNP: database of Short Genetic Variation. NA indicates that the variant is not present. SIFT, Polyphen-2 and GERP are described in Table 1.

Position	Nucleotide change	AA change	ESP6500 EU	1000Genome EUR	dbSNP132	Case	Control	SIFT	Polyphen2	GERP
chr2:167099083	c.T3523A	p.Y1175N	0	0	NA	1/1003	0/1127	0	0.969	5.01
chr2:167099157	c.G3449A	p.W1150X	0	0	NA	1/1003	0/1126	0	0	1.74
chr2:167108345	c.G3369T	p.L1123F	0.000364	0.0013	NA	3/1001	0/1126	0.05	0.13	−2.18
chr2:167108386	c.C3328T	p.R1110W	0.000854	0.0026	NA	1/901	0/1091	0.01	0.6	3.92
chr2:167129091	c.G3136A	p.D1046N	0.000121	0	NA	1/1003	0/1126	1	0.003	5.42
chr2:167129135	c.C3092T	p.T1031I	0	0	NA	1/1001	0/1110	0.23	0.054	5.42
chr2:167129256	c.G2971T	p.V991L	0.004177	0	rs4369876	21/976	2/1119	0.08	0.004	−0.949
#chr2:167133540	c.A2794C	p.M932L	0.004070	0	rs12478318	21/976	2/1119	0.53	0.043	5.65

^#This variant was initially filtered out due to poor quality of reads for that position. Capillary sequencing confirmed the presence of M932L in all subjects with the V991L variant.