Table 3 All variants identified in second intracellular loop (LII–III) of SCN9A

From: Association of rare missense variants in the second intracellular loop of NaV1.7 sodium channels with familial autism

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

  1. 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.
  2. 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.
  3. aThis 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.
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