Table 2.
Information of genes prioritized for congenital heart disease (CHD).
| Gene | dn_MiD_DD | dn_LoF_DD | dn_MiD_CHD | dn_LoF_CHD | PP | dn_MiD_CHD2018 | dn_LoF_CHD2018 | pPoisson | Known_Gene | Top 25 genes from Jin et al., 2018 |
|---|---|---|---|---|---|---|---|---|---|---|
| KDM5B | 0 | 3 | 0 | 3 | 1 | 0 | 0 | 1.00E+00 | N | 2.90E-04 |
| MLL2 | 0 | 2 | 0 | 4 | 1 | 0 | 7 | 5.50E-15 | Y | 8.50E-19 |
| NAA15 | 0 | 2 | 0 | 2 | 1 | 0 | 0 | 1.00E+00 | N | – |
| CHD7 | 2 | 2 | 0 | 2 | 1 | 3 | 9 | 3.98E-24 | Y | 7.50E-19 |
| RBFOX2 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 1.00E+00 | N | 1.10E-06 |
| PTPN11 | 2 | 0 | 3 | 0 | 1 | 2 | 0 | 1.17E-04 | Y | 1.80E-15 |
| POGZ | 0 | 6 | 1 | 1 | 1 | 0 | 1 | 1.32E-02 | N | 2.90E-04 |
| CTNNB1 | 0 | 11 | 0 | 1 | 0.97 | 0 | 1 | 1.90E-02 | N | – |
| TCF12 | 1 | 2 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | N | – |
| KANSL1 | 0 | 8 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | Y | – |
| MEIS2 | 0 | 2 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | N | – |
| EIF4A2 | 1 | 1 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | N | – |
| WHSC1 | 0 | 3 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | N | – |
| KAT6B | 0 | 8 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | Y | – |
| MAP2 | 0 | 2 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | N | – |
| CUL3 | 0 | 2 | 0 | 1 | 0.97 | 0 | 1 | 2.21E-02 | N | – |
| ARID1B | 0 | 30 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | N | – |
| KAT6A | 0 | 8 | 0 | 1 | 0.97 | 0 | 0 | 1.00E+00 | N | – |
| NSD1 | 1 | 7 | 0 | 1 | 0.96 | 0 | 2 | 7.82E-04 | Y | 1.30E-04 |
| EP300 | 3 | 12 | 0 | 1 | 0.96 | 0 | 0 | 1.00E+00 | N | – |
| CACNA1A | 5 | 0 | 0 | 1 | 0.95 | 0 | 0 | 1.00E+00 | N | – |
| MEA1 | 0 | 1 | 0 | 1 | 0.95 | 0 | 0 | 1.00E+00 | N | – |
| ZNF623 | 0 | 1 | 0 | 1 | 0.94 | 0 | 0 | 1.00E+00 | N | – |
| GANAB | 2 | 0 | 1 | 1 | 0.94 | 0 | 0 | 1.00E+00 | N | – |
| COL4A3BP | 4 | 0 | 1 | 0 | 0.92 | 0 | 0 | 1.00E+00 | N | – |
| LZTR1 | 2 | 1 | 1 | 0 | 0.91 | 1 | 0 | 2.65E-02 | N | – |
| RABGAP1L | 0 | 1 | 1 | 1 | 0.9 | 0 | 0 | 1.00E+00 | N | – |
| MED13L | 5 | 13 | 1 | 0 | 0.89 | 0 | 0 | 1.00E+00 | Y | – |
| TLK2 | 2 | 0 | 0 | 1 | 0.87 | 0 | 0 | 1.00E+00 | N | – |
| ARID1A | 1 | 2 | 1 | 0 | 0.87 | 0 | 0 | 1.00E+00 | Y | – |
| SRRM2 | 0 | 2 | 0 | 1 | 0.87 | 0 | 0 | 1.00E+00 | N | – |
| CHD4 | 5 | 1 | 1 | 0 | 0.86 | 1 | 0 | 7.30E-02 | Y | – |
| SMAD2 | 0 | 0 | 1 | 1 | 0.8 | 0 | 0 | 1.00E+00 | N | 1.60E-04 |
These 33 genes are prioritized by mTADA using the information of undiagnosed developmental disorders (DD). Columns ‘dn_LoF/MiD’ describe the number of loss-of-function/missense damaging de novo mutations. mTADA was applied to the DD and the CHD data in the 2nd, 3rd, 4th and 5th columns. The column ‘PP’ describes the posterior probabilities of these genes from mTADA’s analyses. Columns ‘dn_MiD_CHD2018’ and ‘dn_LoF_CHD2018’ are data from an independent dataset. Column ‘pPoisson’ describes p values of the Poisson test for the independent dataset. Column ‘Known gene’ shows whether a gene is in the list of known genes (Yes/Y) or not (No/N). The last column shows p-values calculated by Jin et al.23 for their top significant genes.