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

From: Deep exon resequencing of DLGAP2 as a candidate gene of autism spectrum disorders

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%)    
  1. ASD, autistic spectrum disorders; MAF, minor allele frequency; SNPs, single nucleotide polymorphisms.