Table 1.
Allele and genotype frequencies of common SNPs of the DLGAP2 gene in ASD patients and control subjects (MAF >5%)
| SNP | Location | Diagnosis | n | Genotype | P value | Q value | Allele | P value | Q value | Odds ratio (95 % CI) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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%) | ||||||||
ASD, autistic spectrum disorders; MAF, minor allele frequency; SNPs, single nucleotide polymorphisms.