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Table 2 Gene-specific significance in the ACGC cohort and in the ACGC+SSC+ASC combined samples based on two statistical models

From: Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Gene ACGC (n = 2145) ACGC+SSC+ASC (n = 6107)
Phase-I Phase-II All CH model denovolyzeR LGD MIS All CH model denovolyzeR
LGD MIS LGD MIS LGD MIS LGD_q prot_q LGD_q prot_q LGD_q prot_q LGD_q prot_q
SCN2A 6 4 5 9 11 13 3.68E−25 1.23E−40 4.21E−18 1.05E−29 15 21 36 7.77E−28 2.23E−49 3.52E-22 3.35E-42
CHD8 3 1 2 1 5 2 3.18E−09 7.56E−08 5.40E−07 1.68E−04 14 4 18 7.49E−25 7.45E−18 3.52E−22 1.19E−13
MECP2 1 3 2 1 3 4 1.00E−06 1.12E−11 1.78E−05 4.12E−08 3 5 8 6.26E−04 1.33E−08 1.78E−03 1.42E−06
DYRK1A 1 1 2 0 3 1 1.51E−05 2.78E−04 5.92E−05 2.75E−03 8 1 9 3.78E−13 2.51E−07 1.31E−13 4.23E−07
ASXL3 0 1 3 1 3 2 7.28E−04 5.62E−03 1.82E−04 4.29E−03 5 2 7 6.33E−04 0.894 6.03E−06 0.0200
WAC 0 0 2 0 2 0 9.05E−04 0.0311 5.14E−03 0.2322 4 0 4 2.12E−05 0.0532 6.57E−05 0.1384
FOXP1 0 0 2 1 2 1 1.04E−03 3.46E−03 0.0103 0.0285 4 1 5 3.36E−05 0.014 3.81E−04 0.0235
CTTNBP2 0 1 2 0 2 1 4.69E−03 0.0189 0.0226 0.2162 3 1 4 0.0331 1 0.1072 1
TNRC6B 0 0 2 0 2 0 7.00E−03 0.2549 0.0158 0.5818 4 0 4 1.97E−03 1 1.17E−03 1
MED13L 1 0 1 0 2 0 7.00E−03 0.2549 0.0386 0.9485 4 1 5 1.97E−03 0.9197 9.40E−03 1
CDKL5 1 0 1 0 2 0 8.26E−03 0.2732 7.14E−03 0.3409 2 1 3 1 1 0.5527 1
DSCAM 2 0 0 1 2 1 0.0130 0.0770 0.0226 0.3035 6 2 8 1.03E−05 0.0272 1.55E−06 0.0135
ZNF292 1 0 1 0 2 0 0.0139 0.6051 0.0158 0.8299 3 2 5 0.2763 1 0.0508 1
POGZ 1 1 0 0 1 1 0.0507 0.0153 0.3864 0.5818 4 4 8 2.40E−06 1.84E−09 3.48E−03 7.13E−04
WDFY3 1 1 0 2 1 3 0.2966 0.0153 0.7292 0.2736 3 7 10 0.2778 7.21E−04 1 5.44E−03
NAA15 0 0 1 1 1 1 0.0851 0.0228 0.3452 0.3025 2 2 4 0.1747 0.0287 1 0.4185
CUL3 1 0 0 1 1 1 0.1056 0.0446 0.3825 0.3035 2 1 3 0.2778 1 1 1
STXBP1 1 0 0 0 1 0 0.1056 0.6051 0.3267 1 1 1 2 1 1 1 1
ADNP 1 0 0 0 1 0 0.1314 0.9222 0.2294 1 5 0 5 2.40E−06 0.0764 4.55E−07 0.0669
DDX3X 0 1 1 0 1 1 0.1335 0.0871 0.2367 0.2989 2 1 3 0.7186 1 0.4989 1
RALGAPB 0 0 1 1 1 1 0.1335 0.0815 0.3267 0.5816 2 1 3 0.6237 1 1 1
GIGYF2 1 1 0 0 1 1 0.1335 0.0770 0.6428 0.5818 2 3 5 0.7186 0.0363 1 0.5211
NCKAP1 1 0 0 0 1 0 0.1335 0.9135 0.5383 1 3 0 3 0.0206 1 0.4100 1
GRIN2B 1 0 0 0 1 0 0.1359 1 0.2367 1 4 0 4 4.61E−04 1 1.17E−04 1
MYT1L 1 0 0 0 1 0 0.1717 1 0.2294 1 2 2 4 1 1 0.4100 1
SHANK2 0 0 1 0 1 0 0.2017 1 0.3267 1 2 1 3 1 1 1 1
SYNGAP1 1 0 0 0 1 0 0.2966 1 0.3154 1 6 3 9 1.84E−05 0.0168 8.04E−08 8.79E−05
PHIP 1 0 0 0 1 0 0.2966 1 0.5095 1 1 1 2 1 1 1 1
CHD2 0 0 1 1 1 1 0.3536 0.9217 0.5095 0.7736 4 4 8 0.0331 0.5391 0.0125 3.31E−03
SHANK1 1 0 0 0 1 0 0.3536 1 0.3267 1 1 1 2 1 1 1 1
DOCK8 1 0 0 0 1 0 0.4837 1 0.3267 1 2 0 2 1 1 1 1
ANK2 0 1 1 0 1 1 0.7356 1 0.6639 1 5 4 9 0.0587 1 2.54E−03 0.0396
ASH1L 0 1 0 1 0 2 1 0.2732 1 1 3 2 5 0.0825 1 0.5350 1
RIMS1 0 0 0 1 0 1 1 1 1 1 2 1 3 0.7186 1 1 1
TSC2 0 1 0 0 0 1 1 1 1 1 0 4 4 1 1 1 1
KMT2C 0 1 0 1 0 2 1 1 1 1 1 4 5 1 1 1 1
ITPR1 0 1 0 0 0 1 1 1 1 1 0 3 3 1 1 1 1
WHSC1 0 0 0 1 0 1 1 0.9499 1 1 1 1 2 1 1 1 1
  1. Significant q values (< 0.05) are italicized
  2. LGD likely gene-disrupting variants, MIS missense variants, LGD_q q values of truncated DNMs (FDR corrected), prot_q q values of LGD and missense DNMs (FDR corrected)
  3. Previously well-defined genes in neurodevelopmental disorders