Table 4 Top NDD Genes (adjusted by mutation rate, one-tailed binomial test p < 0.05) with de novo PT or D-mis variants from the two CHD cohorts.
From: De novo damaging variants associated with congenital heart diseases contribute to the connectome
Gene | Chromatin Modifiers | Connectome | Mutation Rate | Size | DDD-Plus | PCGC | Observed | Expected | P-value |
|---|---|---|---|---|---|---|---|---|---|
PTPN11 | − | + | 2.58E-05 | 1801 | 7 | 9 | 16 | 0.80 | 1.54E-34 |
CHD7 | + | + | 1.19E-04 | 8909 | 3 | 14 | 17 | 3.96 | 7.56E-26 |
CHD4 | + | + | 8.01E-05 | 5678 | 3 | 3 | 6 | 2.52 | 2.29E-08 |
KMT2A | + | + | 1.48E-04 | 11810 | 5 | 2 | 7 | 5.25 | 3.49E-08 |
NOTCH1 | − | + | 1.59E-04 | 7699 | 1 | 5 | 6 | 3.42 | 1.21E-06 |
ADNP | − | + | 3.92E-05 | 3299 | 4 | 0 | 4 | 1.47 | 1.59E-06 |
SMAD2 | − | + | 1.71E-05 | 1410 | 0 | 3 | 3 | 0.63 | 6.84E-06 |
KDM5B | + | + | 6.13E-05 | 4662 | 1 | 3 | 4 | 2.07 | 9.19E-06 |
NSD2 | + | + | 2.56E-05 | 4192 | 1 | 2 | 3 | 1.86 | 2.27E-05 |
FOXP1 | − | + | 3.02E-05 | 2216 | 3 | 0 | 3 | 0.99 | 3.69E-05 |
MED13L | − | + | 8.79E-05 | 6615 | 3 | 1 | 4 | 2.94 | 3.72E-05 |
DYRK1A | − | + | 3.12E-05 | 2387 | 3 | 0 | 3 | 1.06 | 4.08E-05 |
POGZ | − | + | 5.66E-05 | 4179 | 0 | 3 | 3 | 1.86 | 2.35E-04 |
PTEN | − | + | 1.40E-05 | 1326 | 0 | 2 | 2 | 0.59 | 3.97E-04 |
KAT6A | + | + | 8.14E-05 | 5995 | 2 | 1 | 3 | 2.66 | 6.73E-04 |
ARID1B | + | + | 9.02E-05 | 6412 | 2 | 1 | 3 | 2.85 | 9.03E-04 |
SMAD4 | − | + | 2.14E-05 | 1670 | 1 | 1 | 2 | 0.74 | 9.28E-04 |
EP300 | + | + | 9.32E-05 | 7214 | 2 | 1 | 3 | 3.21 | 9.92E-04 |
WAC | + | − | 2.42E-05 | 1958 | 1 | 1 | 2 | 0.87 | 1.18E-03 |
FRYL | − | − | 1.07E-04 | 9100 | 1 | 2 | 3 | 4.04 | 1.45E-03 |
NAA15 | − | + | 2.84E-05 | 2621 | 0 | 2 | 2 | 1.17 | 1.61E-03 |
DDX3X | − | + | 2.90E-05 | 2006 | 1 | 1 | 2 | 0.89 | 1.68E-03 |
CUL3 | − | − | 2.98E-05 | 2323 | 1 | 1 | 2 | 1.03 | 1.77E-03 |
CTNNB1 | − | + | 2.99E-05 | 2332 | 0 | 2 | 2 | 1.04 | 1.78E-03 |
ANKRD11 | + | + | 1.59E-04 | 7964 | 3 | 0 | 3 | 3.54 | 4.44E-03 |
LZTR1 | + | − | 4.81E-05 | 2544 | 0 | 2 | 2 | 1.13 | 4.50E-03 |
SETD5 | + | − | 5.43E-05 | 4329 | 1 | 1 | 2 | 1.92 | 5.69E-03 |
ASH1L | + | + | 1.07E-04 | 8868 | 1 | 1 | 2 | 3.94 | 2.05E-02 |
NAT8L | − | + | 1.06E-05 | 912 | 0 | 1 | 1 | 0.41 | 2.13E-02 |
TECTA | − | − | 1.10E-04 | 6255 | 1 | 1 | 2 | 2.78 | 2.18E-02 |
ITPR1 | − | − | 1.18E-04 | 8337 | 2 | 0 | 2 | 3.71 | 2.45E-02 |
NTM | − | + | 1.77E-05 | 1176 | 0 | 1 | 1 | 0.52 | 3.55E-02 |
PSMD12 | − | − | 1.82E-05 | 1382 | 0 | 1 | 1 | 0.61 | 3.64E-02 |
PCOLCE | − | − | 2.19E-05 | 1359 | 0 | 1 | 1 | 0.60 | 4.37E-02 |
EP400 | + | − | 1.63E-04 | 9360 | 1 | 1 | 2 | 4.16 | 4.45E-02 |
ANK3 | − | + | 1.67E-04 | 13243 | 0 | 2 | 2 | 5.89 | 4.63E-02 |
CCSER1 | − | − | 2.35E-05 | 2705 | 0 | 1 | 1 | 1.20 | 4.68E-02 |
KMT2C | + | + | 1.74E-04 | 14569 | 0 | 2 | 2 | 6.48 | 4.97E-02 |
