Gene families | DNMs expected | DNMs observed | P value | 5264 DD patients | 3982 ASD patients | 822 EPI patients | 2087 controls |
---|---|---|---|---|---|---|---|
ARID1B (40), ARID1A (5) | 0.96 | 45 | 4.28E−58 | 39 | 6 | 0 | 0 |
SCN2A (38), SCN1A (18), SCN8A (11), SCN3A (4), SCN11A (2), SCN9A (1), SCN5A, SCN7A, SCN4A, SCN10A | 6.16 | 74 | 1.77E−52 | 36 | 16 | 22 | 0 |
DDX3X (35), DDX3Y | 0.49 | 35 | 8.94E−52 | 34 | 1 | 0 | 0 |
DYRK1A (26), DYRK1B (1) | 0.37 | 27 | 1.89E−40 | 21 | 5 | 1 | 0 |
EP300 (20), CREBBP (16) | 1.39 | 36 | 8.81E−38 | 30 | 5 | 1 | 1 |
KCNQ2 (23), KCNQ3 (7), KCNQ5 (3) | 1.14 | 33 | 3.09E−36 | 27 | 2 | 4 | 0 |
SYNGAP1 (24), DAB2IP, RASAL2 | 1.33 | 24 | 4.35E−22 | 17 | 6 | 1 | 0 |
STXBP1 (20), STXBP3 (1), STXBP2 | 0.88 | 21 | 5.93E−22 | 14 | 2 | 5 | 0 |
GRIN2B (16), GRIN2A (6), GRIN2C (1), GRIN2D | 1.89 | 23 | 1.46E−17 | 17 | 3 | 3 | 0 |
CTNNB1 (16), JUP (1) | 0.79 | 17 | 2.27E−17 | 15 | 2 | 0 | 0 |
CHD2 (16), CHD1 (3) | 1.15 | 19 | 4.00E−17 | 10 | 8 | 1 | 0 |
PURA (13), PURB | 0.41 | 13 | 1.13E−15 | 12 | 0 | 1 | 0 |
CHD3 (10), CHD4 (6), CHD5 (5) | 1.94 | 21 | 3.45E−15 | 19 | 2 | 0 | 0 |
TCF4 (11), TCF12 (3), TCF3 (2) | 0.93 | 16 | 5.76E−15 | 14 | 2 | 0 | 1 |
CDK13 (14), CDK12 | 0.66 | 14 | 1.71E−14 | 13 | 1 | 0 | 0 |
PPP2R5D (16), PPP2R5A (1), PPP2R5B, PPP2R5C, PPP2R5E | 1.25 | 17 | 3.62E−14 | 16 | 1 | 0 | 1 |
WDR45 (11), WDR45B | 0.32 | 11 | 7.60E−14 | 9 | 0 | 2 | 0 |
MEF2C (11), MEF2D (2), MEF2A | 0.58 | 13 | 7.77E−14 | 9 | 2 | 2 | 0 |
EHMT1 (13), EHMT2 | 0.66 | 13 | 3.93E−13 | 13 | 0 | 0 | 0 |
FOXP1 (10), FOXP2 (4), FOXP4 | 0.86 | 14 | 6.02E−13 | 12 | 2 | 0 | 0 |
FOXG1 (11), FOXQ1, FOXN3, FOXN2 | 0.39 | 11 | 6.36E−13 | 7 | 1 | 3 | 0 |
CHD8 (12), CHD7 (7), CHD9 (1) | 2.30 | 20 | 7.73E−13 | 11 | 9 | 0 | 0 |
CSNK2A1 (12), CSNK2A3, CSNK2A2 | 0.63 | 12 | 5.00E−12 | 10 | 1 | 1 | 0 |
CACNA1E (10), CACNA1A (9), CACNA1B (1) | 2.72 | 20 | 1.53E−11 | 13 | 1 | 6 | 0 |
HDAC8 (9), HDAC3 (2), HDAC1 (1), HDAC2 | 0.83 | 12 | 1.06E−10 | 11 | 0 | 1 | 0 |
GNAO1 (7), GNAI1 (7), GNAZ (1), GNA11 (1), GNA14, GNAI3, GNAT2, GNAT3, GNAT1, GNAI2, GNA15, GNAQ | 1.82 | 16 | 1.31E−10 | 13 | 2 | 1 | 0 |
CASK (8), DLG4 (6), DLG2 (1), DLG1, DLG3 | 1.58 | 15 | 1.67E−10 | 12 | 1 | 2 | 0 |
GATAD2B (10), GATAD2A | 0.65 | 10 | 2.10E−09 | 10 | 0 | 0 | 0 |
MED13L (12), MED13 (2) | 1.68 | 14 | 3.47E−09 | 10 | 4 | 0 | 0 |
TBL1XR1 (9), TBL1Y, TBL1X | 0.52 | 9 | 5.01E−09 | 7 | 2 | 0 | 0 |
PHIP (10), BRWD3 (2) | 1.46 | 13 | 5.64E−09 | 10 | 2 | 1 | 0 |
CTCF (9), CTCFL | 0.56 | 9 | 9.00E−09 | 7 | 2 | 0 | 0 |
RAB11A (3), RAB2A (2), RAB11B (2), RAB14 (2), RAB19 (1), RAB43 (1), RAB39A, RAB25, RAB4B, RAB39B, RAB4A, RAB30, RAB2B | 1.01 | 11 | 1.14E−08 | 9 | 2 | 0 | 0 |
GABRB3 (8), GABRB2 (3), GLRA2 (1), GABRB1 (2), GLRB (1), GLRA1, GABRR1, GABRD, GABRR3, GABRP, GLRA4, GABRQ, GABRR2, GLRA3 | 2.35 | 15 | 3.15E−08 | 7 | 4 | 4 | 0 |
TCF20 (9), RAI1 (3) | 1.40 | 12 | 3.33E−08 | 11 | 1 | 0 | 1 |
NFIX (6), NFIA (2), NFIB (2), NFIC | 0.90 | 10 | 4.31E−08 | 8 | 2 | 0 | 1 |
USP9X (10), USP24 (1), USP9Y | 1.18 | 11 | 5.29E−08 | 9 | 2 | 0 | 0 |
SATB2 (9), SATB1 | 0.75 | 9 | 1.04E−07 | 9 | 0 | 0 | 0 |
HECW2 (9), HECW1 (1) | 1.04 | 10 | 1.61E−07 | 8 | 1 | 1 | 0 |
SOX11 (4), SOX4 (3), SOX9 (1), SOX10 (1), SOX17, SOX1, SOX8, SOX7 | 0.82 | 9 | 2.21E−07 | 9 | 0 | 0 | 0 |
ZBTB18 (6), ZBTB3 | 0.28 | 6 | 5.43E−07 | 6 | 0 | 0 | 0 |
TCF7L2 (6), TCF7L1 (1) | 0.53 | 7 | 1.48E−06 | 4 | 3 | 0 | 0 |
TBR1 (6), EOMES | 0.35 | 6 | 2.01E−06 | 1 | 5 | 0 | 0 |