Table 3. All variants identified in second intracellular loop (LII–III) of SCN9A.
| Position | Nucleotide change | AA change | ESP6500 EU | 1000Genome EUR | dbSNP132 | Case | Control | SIFT | Polyphen-2 | 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 |
| chr2:167133540a | c.A2794C | p.M932L | 0.004070 | 0 | rs12478318 | 21/976 | 2/1119 | 0.53 | 0.043 | 5.65 |
Abbreviations: AA, amino acid; ASD, autism spectrum disorder; dbSNP, database of short genetic variation; ESP, Exome Sequencing Project; GERP, genomic evolutionary rate profiling; NA, variant is not present; PolyPhen-2, polymorphism phenotyping v2; SIFT, sorting intolerant from tolerant.
ESP and 1000Genome 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. SIFT, Polyphen-2 and GERP are described in Table 1.
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.