Table 1 Allele and genotype frequencies of common SNPs of the DLGAP2 gene in ASD patients and control subjects (MAF > 5%)

rs6996621

intron 1

C/C

C/A

A/A

C

A

C versus A

c.-68-61C > A

total

autism

454

387 (85.2%)

62 (13.7%)

5 (1.1%)

0.619

0.312

836 (92.1%)

72 (7.9%)

0.401

0.204

1.11 (0.83 to 1.57)

control

557

467 (83.8%)

80 (14.4%)

10 (1.8%)

1014 (91.0%)

100 (9.0%)

male

autism

394

336 (85.3%)

55 (14.0%)

3 (0.7%)

0.593

0.203

727 (92.3%)

61 (7.7%)

0.611

0.611

control

246

208 (84.6%)

34 (13.8%)

4 (1.6%)

450 (91.5%)

42 (8.5%)

female

autism

60

51 (85%)

7 (11.7%)

2 (3.3%)

0.663

0.266

109 (90.8%)

11 (9.2%)

0.956

0.956

control

311

259 (83.3%)

46 (14.8%)

6 (1.9%)

564 (90.7%)

58 (9.3%)

rs2906568

intron 1

C/C

C/G

G/G

C

G

C versus G

c.-68-25C > G

total

autism

456

188 (41.2%)

169 (37.1%)

99 (21.7%)

0.142

0.112

545 (59.8%)

367 (40.2%)

0.125

0.105

1.15 (0.96 to 1.37)

control

557

197 (35.4%)

234 (42.0%)

126 (22.6%)

628 (56.4%)

486 (43.6%)

male

autism

396

171 (43.2%)

138 (34.8%)

87 (22.0%)

0.072

0.107

480 (60.6%)

312 (39.4%)

0.146

0.299

control

246

86 (35.0%)

106 (43.0%)

54(22.0%)

278 (56.5%)

214 (43.5%)

female

autism

60

17 (28.3%)

31 (51.7%)

12 (20%)

0.316

0.266

65 (54.2%)

55 (45.8%)

0.671

0.897

control

311

111 (35.7%)

128 (41.1%)

72 (23.2%)

350 (56.3%)

272 (43.7%)

rs2906569

intron 1

A/A

A/G

G/G

A

G

A versus G

c.-68-4A > G

total

autism

458

219 (47.8%)

138 (30.1%)

101 (22.1%)

0.0006

0.095

576 (62.9%)

340 (37.1%)

0.112

0.105

1.16 (0.97 to 1.38)

control

557

215 (38.6%)

232 (41.7%)

110 (19.7%)

662 (59.4%)

452 (40.6%)

male

autism

398

199 (50.0%)

109 (27.4%)

90 (22.6%)

0.0001

0.107

507 (63.7%)

289 (36.3%)

0.075

0.299

control

246

91 (37.0%)

107 (43.5%)

48 (19.5%)

289 (58.7%)

203 (41.3%)

female

autism

60

20 (33.3%)

29 (48.3%)

11 (18.4%)

0.491

0.266

69 (57.5%)

51 (42.5%)

0.614

0.897

control

311

124 (39.9%)

125 (40.2%)

62 (19.9%)

373 (60.0%)

249 (40.0%)

rs60089073

exon 2

C/C

C/T

T/T

C

T

C versus T

His73

total

autism

466

401 (86.1%)

54 (11.6%)

11 (2.3%)

0.989

0.388

856 (91.8%)

76 (8.2%)

0.891

0.363

0.98 (0.71 to 1.35)

control

557

481 (86.4%)

63 (11.3%)

13 (2.3%)

1025 (92.0%)

89 (8.0%)

male

autism

404

346 (85.6%)

48 (11.9%)

10 (2.5%)

0.236

0.133

740 (91.6%)

68 (8.4%)

0.093

0.299

control

246

219 (89.0%)

25 (10.2%)

2 (0.8%)

463 (94.1%)

29 (5.9%)

female

autism

62

55 (88.7%)

6 (9.7%)

1 (1.6%)

0.607

0.266

116 (93.5%)

8 (6.5%)

0.259

0.897

control

311

262 (84.3%)

38 (12.2%)

11 (3.5%)

562 (90.4%)

60 (9.6%)

rs2301963

exon 3

C/C

C/A

A/A

C

A

C versus A

Pro384Gln

total

autism

513

171 (33.3%)

231 (45.1%)

111 (21.6%)

0.0005

0.095

573 (55.8%)

453 (44.2%)

0.026

0.105

1.21 (1.02 to 1.43)

control

593

139 (23.4%)

328 (55.%)

126 (21.2%)

606 (51.1%)

580 (48.9%)

male

autism

448

150 (33.5%)

202 (45.1%)

96 (21.4%)

0.068

0.107

502 (56.0%)

394 (44.0%)

0.102

0.299

control

260

66 (25.4%)

136 (52.3%)

58 (22.3%)

268 (51.5%)

252 (48.5%)

female

autism

65

21 (32.3%)

29 (44.6%)

15 (23.1%)

0.124

0.266

71 (54.6%)

59 (45.4%)

0.420

0.897

control

333

73 (21.9%)

192 (57.7%)

68 (20.4%)

338 (50.8%)

328 (49.2%)

rs6995760

intron 5

A/A

A/G

G/G

A

G

A versus G

c.1570 + 14A > G

total

autism

500

346 (69.2%)

141 (28.2%)

13 (2.6%)

0.913

0.388

833 (83.3%)

167 (16.7%)

0.925

0.363

1.01 (0.80 to 1.27)

control

531

368 (69.3%)

147 (27.7%)

16 (3.0%)

883 (83.1%)

179 (16.9%)

male

autism

432

305 (70.6%)

115 (26.6%)

12 (2.8%)

0.502

0.193

725 (83.9%)

139 (16.1%)

0.245

0.299

control

234

155 (66.3%)

71 (30.3%)

8 (3.4%)

381 (81.4%)

87 (18.6%)

female

autism

68

41 (60.3%)

26 (38.2%)

1 (1.5%)

0.103

0.266

108 (79.4%)

28 (20.6%)

0.148

0.897

control

297

213 (71.7%)

76 (25.6%)

8 (2.7%)

502 (84.5%)

92 (15.5%)

rs2235112

exon 6

A/A

A/G

G/G

A

G

A versus G

Glu598

total

autism

509

95 (18.8%)

233 (45.7%)

181 (35.5%)

0.028

0.095

424 (41.6%)

595 (58.4%)

0.012

0.105

1.29 (1.05 to 1.50)

control

513

66 (12.9%)

239 (46.6%)

208 (40.5%)

371 (36.2%)

655 (63.8%)

male

autism

444

85 (19.1%)

205 (46.2%)

154 (34.7%)

0.049

0.107

375 (42.2%)

513 (57.8%)

0.014

0.299

control

224

28 (12.5%)

102 (45.5%)

94 (42.0%)

158 (35.3%)

290 (64.7%)

female

autism

66

11 (16.7%)

28 (42.4%)

27 (40.9%)

0.671

0.266

50 (37.9%)

82 (62.1%)

0.825

0.928

control

289

38 (13.2%)

137 (47.4%)

114 (39.4%)

213 (36.9%)

365 (63.1%)

rs2235113

intron 6

C/C

C/G

G/G

C

G

C versus G

c.1920 + 19C > G

total

autism

510

156 (30.6%)

233 (45.7%)

121 (23.7%)

0.050

0.095

545 (53.4%)

475 (46.6%)

0.030

0.105

1.21 (1.02 to 1.44)

control

509

121 (23.8%)

253 (49.7%)

135 (26.5%)

495 (48.6%)

523 (51.4%)

male

autism

443

137 (30.9%)

205 (46.3%)

101 (22.8%)

0.303

0.139

479 (54.1%)

407 (45.9%)

0.243

0.299

control

222

56 (25.2%)

113 (50.9%)

53 (23.9%)

225 (50.7%)

219 (49.3%)

female

autism

67

19 (28.3%)

28 (41.8%)

20 (29.9%)

0.513

0.266

66 (49.3%)

68 (50.7%)

0.644

0.897

control

287

65 (22.6%)

140 (48.8%)

82 (28.6%)

270 (47.0%)

304 (53.0%)

rs2293909

intron 11

T/T

T/C

C/C

T

C

T versus C

c.2709 + 71T > C

total

autism

460

255 (55.4%)

166 (36.1%)

39 (8.5%)

0.012

0.095

676 (73.5%)

244 (26.5%)

0.012

0.105

1.28 (1.06 to 1.55)

control

573

265 (46.2%)

254 (44.3%)

54 (9.4%)

784 (68.4%)

362 (31.6%)

male

autism

403

230 (57.1%)

138 (34.2%)

35 (8.7%)

0.117

0.107

598 (74.2%)

208 (25.8%)

0.165

0.299

control

256

127 (49.6%)

108 (42.2%)

21 (8.2%)

362 (70.7%)

150 (29.3%)

female

autism

57

25 (43.9%)

28 (49.1%)

4 (7.0%)

0.719

0.266

78 (68.4%)

36 (31.6%)

0.698

0.897

control

317

138 (43.5%)

146 (46.1%)

33 (10.4%)

422 (66.6%)

212 (33.4%)