Table. Nonrecurrent Extreme-pLI Gene Deletion Frequencies.
| Gene | No. (%)a |
|---|---|
| MAPK8 b | 56 (0.013) |
| THOC1 | 20 (0.0046) |
| TJP1 | 19 (0.0044) |
| RANBP2 | 17 (0.0039) |
| INTS6, NXN | 13 (0.0030) |
| BCAR1 | 12 (0.0028) |
| CNOT7, FNDC3A | 11 (0.0026) |
| RB1 b | 10 (0.0023) |
| COL6A1, SMCHD1 | 9 (0.0021) |
| DOPEY1, ELFN1,b TTYH3 | 8 (0.0019) |
| DAAM2, KDM5A, UHRF2, ZNF496 | 7 (0.0016) |
| DLGAP2,b INTS10, PDIA3, PELP1, PRPF39, TRIP13, WNK1 | 6 (0.0014) |
| DLGAP1,b FMN2, LZTS3, NCOR1, SIM1, SMARCA2,c TENM3 | 5 (0.0012) |
| BANP, CACTIN, CSMD1, CSNK1G1, FAM131B, FLT4, FZR1, GSE1, KIAA0947, LMX1A, PTGS2, RAB11FIP3, TERT | 4 (0.0009) |
| AJAP1, ATP13A3, ATP6V1B2, BHLHE40, BMPR1B, CCNA2, CECR2, CENPB, CFLAR, CHRM3,b COL11A1, CPE, DBF4, DCUN1D5, DLC1, EFEMP1, FAM160A2, FNIP1, GLG1, GMPS, GNB2L1, GRIK2,b GSPT1,b HECTD1, IVNS1ABP, KIF26B, KIF3C, LRCH1, MICAL3, NCOA5, PDE10A,b PLXNA1, PLXNB2, PLXND1, PRICKLE1, PSME4, PTBP1, PTPRA,b RERE,c RSPRY1, SH3GLB1, SLC6A3,b SMARCAD1, SMC2, SUGP2, TPR, TTBK2 | 3 (0.0007) |
| ACTR3B, ADAM10,b AFF3, AGFG1, AHCYL2, AHR, ARHGAP42, ASXL2, ATRN, BRINP2,b BRWD1, C17orf85, CADM4, CAND1, CAPZA2, CCNL1, CELF5, CEP170B, CHAMP1,c CHD3,c CNTNAP5, COG3, CPSF6, CUL4A, CUX1,b DKFZP761J1410, DLL4, DMXL1, DNAJC2, DYRK2, EDNRA, EIF5B, ELMSAN1, ETS2, EXOC8, EXT1, EYA3, FAM135A, FBXO38,b FLNC, FRMD5, FRY, FURIN, GGA1, GRID2,b GRM7,b HCN1, HIC2, INO80, INPP4A, ISY1, ISY1-RAB43, ITGB8, ITPR1,c JAG2, JPH3, KCNN2,b KDM6B,c KIF1B,b KLHL2, LRP2, LRRC8B, MAN1A2, MDM2, MKL2, NAV2, NCOA1,c NFAT5, NRIP1, PBX2, PCIF1, PICALM,b PIK3R1, PITPNM3, PRKCD,b PRKG1,b PRPF8, PRR14L, PRRC2B, PSIP1, PSMC2, PSMD11, PSMD13, PTPN12, RBM26, REV1, RFX3,c RFX4, RFX7, RIC8B, ROR1,b SBF1, SEMA6A,b SIPA1L2, SLC12A5,b SLC44A1, SLTM, SMAP1, SRGAP1, STIM2, SYVN1, TERF2, TIPARP, TMEM259, TP63, TRAF6, TRIM2, UBE4B, USP15, USP8, VPS54, XPO4, YAP1, ZBTB44, ZC3H13, ZMYND8,c ZNF654 | 2 (0.0005) |
| ABCA2, ADAMTS6, ADD2, AFTPH, AGO2, AGPAT3, AGPS, AHCTF1, AMBRA1, ANKIB1, ANKRD52, ANKS1B, AP1B1, AP2B1, APPBP2, AQR, ARFGEF2,b ARHGAP29, ARHGAP5, ARHGEF12, ARID2,c ARID3A, ARNT2, ASAP1, ASAP2, ASIC2, ASTN1, ASTN2, ATAD2B, ATP2C1, B4GALT5, BAI3, BAZ2A, BOD1L1, BTBD11, C11orf84, C7orf60, CACNA1I,b CAD, CAMTA2, CASKIN2, CBLL1, CCDC88A, CCNC, CCT2, CDH11, CEP350, CEPT1, CHD1, CHD5, CHD6, CHRM1,b CLASP1,c CLASP2,b CLCN3, CLOCK, CNNM2, COL1A2, COL3A1, CORO1C, CPSF7, CREB1, CSE1L, CSNK1G2, CSNK1G3, CTCF,c CTR9, CUL1, CUL3,c DACH1, DAGLA,b DAPK1, DCAF15, DCC,b DDB1, DDX21, DDX4, DNAJC13, DNAJC6, DNM2, DPF2, DPYSL5,b EED, EEF1G, EIF3D, EIF4ENIF1, ELL2, EP400, EPB41L4B, EPHA7,b ERBB4,b ERP44, ESRP1, EWSR1, EZH2,b FAM160B1, FAM208A, FAT4, FBN2, FBXL17, FBXL5, FBXO33, FBXO41, FBXW2, FBXW7, FGFR2, FNDC3B, FOXJ2, FOXO1, FOXP1,c FRS2, FRYL, GABBR1,b GABRA2,b GALNT13, GANAB, GCLM, GIT2, GNAL, GPS1, GRIN2D,b GRM5,b HGF, HIPK1, HIVEP1, HMBOX1, HMGCR, HMGCS1, HNRNPUL2, HOOK3, HTT, ING3, IPO5, ITPKB, JAK1, JAKMIP2, KCNB1,c KCNH2,b KCNH3,b KDM3A, KDM4B, KDR, KIAA0368, KIAA1429, KIF13A, KIF2A,b KIRREL, KMT2C,c KPNA1, L3MBTL3, LARP4B,c LATS1, LEPR, LPHN1, LPHN2, LRRC4,b MAGI2, MAP1A,c MAP2,b MAP2K4, MAP3K1, MAP4K5, MAPK8IP2,b MAPK8IP3,b MAPKAPK2, MARK2,b MAT2A, MCMBP, MGA, MGAT5, MINK1, MKLN1, MKRN1, MLLT4, MLLT6, MORC2, MPPED2, MRC1L1, MSL1, MTA1, MTF2,c MTMR12, MTMR3, MTPAP, MUC5B, MYCBP2,b MYH10, MYH9, MYO16, NAP1L1, NASP, NCAM1,b NCKAP1,c NELL2, NEURL4, NF2, NFATC3, NFIA, NFKB1, NFKB2, NFKBIA, NISCH, NOL6, NOTCH2,b NRBP1, NRF1, NTNG2,b OLFM1, PACS1,c PACS2,c PAIP1, PAPOLG,c PBRM1, PCGF1, PDS5B, PDZD2, PHC1, PHF19, PHF3,c PIAS2, PIK3CD, PITPNM2, PKN2, PLCG2, PLK2,b PLXNA4, PLXNC1, PNISR, POLR1A, PPARGC1A, PPM1A, PPP1R16B, PPP3CA, PPP3CB, PPP6R3, PPRC1, PRDM16, PREX1, PRKAG2, PRKCG,b PRPF40B, PRPF4B, PSMC6, PSPC1, PTK2,b PTPN4, PTPRM,b PTPRT,b RABL6, RAD21, RALGAPB, RANBP3, RAPGEF6, RB1CC1, RBM14, RBM17, RBM4, REL, RELN,c REST, RFWD2, RFX2, RNF111, RNF2, RNF31, RORB,c RP11-159G9.5, RPL5, RPS6KA5, SART3, SENP6, SERBP1, SF3B2, SF3B3, SFSWAP, SGIP1, SIK2, SKIDA1,c SLC4A4, SLC8A1, SLIT2, SMARCA5, SMARCB1, SMG7, SNAP91, SOX30, SRP54, SSH2, ST18, ST7, STAT1, STAU1, STK39, STXBP5, SUFU, SVEP1, SWT1, TAF5, TBX21, TBX5, TEK,c TENM2,b TEX10, TFAP4, TFCP2L1, TFDP2, THBS1, TLK1, TMEM108, TMEM201, TMEM57, TNIK,b TOP1, TOPBP1, TP53BP1, TP73, TRAF2, TRAPPC10, TRAPPC8, TRIM27, TRIM28, TRIM71, TRIM8, TRIP12,c TRPS1, TSKS, UBN2, UBP1, UCHL1,b ULK1, UNK, USP1, USP42, WDR18, WNK2, WWP1, XPO7, XPOT, XPR1, YLPM1, YTHDC1, YTHDC2, ZBTB16, ZBTB21, ZBTB38, ZC3H12C, ZC3H18, ZC3H7A, ZCCHC6, ZFHX4, ZFR, ZMYND11,c ZNF131, ZNF236, ZNF445, ZNF541, ZNF638, ZNF770, ZNF800, ZNFX1, ZRANB1 | 1 (0.0002) |
Abbreviations: CNV, copy number variant; pLI, probability of loss-of-function intolerance.
a
Number and percentage of participants for each individual extreme-pLI gene at a nonrecurrent CNV locus. Frequencies are lower than true population prevalences due to the UK Biobank’s healthy participant bias and the exclusion of participants with diagnosed neurodevelopmental disorders.
b
Manually annotated genes of special interest (eg, ion channel genes, neurotransmitter receptors/transporters, genes involved in neurodevelopment).
c
Neurodevelopmental disorder genes are listed in the eMethods in the Supplement.