Table 2:
Genes enriched for de novo variation in 10,927 ASD/ID/DD patients in denovo-db v.1.5.
| Significance Category | Genes |
|---|---|
| LGD | ADNP*†, AHDC1*†, ANK2†, ANKRD11*†, ANP32A*, ARID1B*†, ARID2†, ASH1L*†, ASXL1†, ASXL3*†, AUTS2†, BCL11A*†, BRPF1†, CAPRIN1*†, CASZ1†, CDC42BPB†, CDKL5†, CHAMP1*†, CHD7†, CHD8*†, CLTC†, CNKSR2*†, CNOT3†, CTNNB1*†, CUL3*†, DLG4*†, DSCAM†, DVL3†, EBF3†, EHMT1*†, ENO3*†, EP300*†, FAM200A†, FAM200B†, FOSL2, FOXP2†, GATAD2B*†, HIST1H1E†, HIVEP2†, HIVEP3*†, HNRNPD†, IRF2BPL†, KANSL1*†, KAT6A*†, KAT6B*†, KCNS3†, KDM5B*†, KDM6A†, KDM6B†, KIAA2022*†, KIF11†, KMT2A*†, KMT2C†, LARP4B†, LEO1*†, MBD5*†, MEIS2*†, MSL3*†, NAA15*†, NFE2L3†, NONO*†, NSD1*†, ODC1†, PDHA1†, PHF12†, PHF21A†, PHF3†, PHIP†, POU3F3†, PPM1D*†, PRR12†, PTCHD1†, QRICH1*†, RAI1†, RPL26†, SET*†, SETBP1*†, SETD2†, SETD5*†, SHANK3*†, SIN3A†, SKIDA1†, SMC1A*†, SON†, SOX5*†, SPAST†, SPEN†, SPRY2†, SRCAP*†, SRRM2, SRSF11†, STARD9†, SUV420H1*†, SYNCRIP*†, SYNGAP1*†, TAB2†, TBR1†, TCF12†, TCF20*†, TNRC6B, TRA2B†, TRIP12*†, UPF3B*†, USP9X*†, VEZF1, WAC*†, WDFY3†, WDR45*†, WDR87†, WHSC1†, YTHDF3†, ZBTB18*†, ZBTB7A†, ZC4H2†, ZNF292† |
| LGD & Missense | CHD2*†, CREBBP*†, DYRK1A*†, FBXO11†, FOXG1*†, FOXP1*†, HNRNPU*†, MEF2C*†, MYT1L*†, NFIX*†, POGZ*†, PTEN*†, PURA*†, TLK2*†, WDR26*† |
| LGD & MIS30 | TCF7L2† |
| LGD & Missense & MIS30 | CASK*†, DDX3X*†, HDAC8*†, IQSEC2*†, MECP2*†, MED13L*†, PPP2R5D*†, PUF60*†, SATB2*†, SCN2A*†, SLC6A1*†, STXBP1*†, TBL1XR1*†, TCF4*† |
| Missense | ABI2†, ACHE†, ADAP1*†, AGAP2†, AGO1†, AGO4*†, AQP10†, BRAF*†, BTF3†, C2orf42†, CABP7†, CAPN15*†, CBL†, CHD4†, CLASP1†, DEAF1†, DLX3*†, DNM1†, EGLN2†, GABRB2*†, GABRB3†, GLRA2†, GNAI1*†, HMGXB3†, HUWE1†, ITPR1*†, KCNC1†, KCNJ6†, MAPK3†, MTF2†, MYO1E†, PBX1†, PLAC8L1†, PLK5†, PPP1CB*†, PRKCA†, PRKD1†, PRPF18†, PSMG4†, PTPN11*†, RAC1*†, RFX8†, RRP8†, RYR2†, SETD1B†, SF3B1†, SHISA6†, SMAD4†, SMARCD1*†, SMC3†, SNAPC5*†, SNX5*†, SUSD4†, SYT1†, TAOK1†, TMEM178A*†, TMEM42†, TNPO3†, TRAF7†, TRRAP†, UNC80†, VAMP2†, WDFY4†, YWHAG† |
| MIS30 | ACTC1†, AGO3†, CACNA1E†, FAM104A†, HIST1H2AC†, KIF5C†, PACS2*†, PAPOLG†, PDK2†, SEPT10†, STC1†, TAF1*†, TNPO2*†, U2AF2† |
| Missense & MIS30 | CDK13*†, CHD3*†, COL4A3BP*†, CSNK2A1*†, CTCF*†, DNMT3A*†, DYNC1H1*†, EEF1A2*†, EFTUD2*†, GNAO1*†, GRIN2B*†, HECW2*†, KCND3†, KCNH1*†, KCNQ2*†, KCNQ3*†, KIF1A*†, MAP2K1*†, NAA10*†, NR2F1†, NR4A2†, PACS1*†, PIK3CA*†, PPP2R1A*†, RAB11A†, SCN8A*†, SMARCA2*†, SMARCA4*†, TRIO*†, ZMYND11*† |
Listing of genes reaching significance for excess of DNM in n = 10,927 independent samples at an FDR of 5% by either the denovolyzeR or CH model (union) for each mutational category (LGD, Missense, MIS30).
†
Gene also in the intersection set.
*
Gene in FWER exome-wide significance (p<5e-7) set.