pair gene chrom pos ref alt consequence impact hgvsc hgvsp tx tumor_vaf tumor_dp tumor_sq normal_vaf normal_dp gnomad_af cgc_tier cgc_role cosmic_n cancer_hotspot clinvar_pathogenic vid cytoband ucla_T1_organoid CDH11 chr16 64988302 - C frameshift_variant HIGH NM_001797.4:c.853dup NP_001788.2:p.(Glu285GlyfsTer9) NM_001797.4 0.5288 104 173.4 0.0 66 0.0 1.0 TSG,fusion 3 False False 16-64988302-T-TC 16q21 ucla_T1_organoid CDH11 chr16 64998674 CCGA ATTTG frameshift_variant HIGH NM_001797.4:c.408_411delinsCAAAT NP_001788.2:p.(Arg137LysfsTer17) NM_001797.4 0.5244 82 164.7 0.0 74 0.0 1.0 TSG,fusion 3 False False 16-64998674-CCGA-ATTTG 16q21 ucla_T1_organoid CDH11 chr16 64988279 T C missense_variant MODERATE NM_001797.4:c.877A>G NP_001788.2:p.(Lys293Glu) NM_001797.4 0.6729 107 195.7 0.0 66 0.0 1.0 TSG,fusion 4 False False 16-64988279-T-C 16q21 ucla_T1_organoid CDH11 chr16 64988217 C T missense_variant MODERATE NM_001797.4:c.939G>A NP_001788.2:p.(Met313Ile) NM_001797.4 0.4875 80 122.2 0.0 56 0.0 1.0 TSG,fusion 3 False False 16-64988217-C-T 16q21 ucla_T1_organoid CDH11 chr16 64988212 GA AG missense_variant MODERATE NM_001797.4:c.943_944delinsCT NP_001788.2:p.(Ser315Leu) NM_001797.4 0.4444 72 104.7 0.0 54 0.0 1.0 TSG,fusion 5 False False 16-64988212-GA-AG 16q21 ucla_T1_organoid CDH11 chr16 64988223 AT GG missense_variant MODERATE NM_001797.4:c.932_933delinsCC NP_001788.2:p.(Asp311Ala) NM_001797.4 0.3836 73 101.1 0.0 53 0.0 1.0 TSG,fusion 2 False False 16-64988223-AT-GG 16q21 ucla_T1_organoid CDH11 chr16 64998836 AGA GGC missense_variant MODERATE NM_001797.4:c.247_249delinsGCC NP_001788.2:p.(Ser83Ala) NM_001797.4 0.3333 60 81.2 0.0 58 0.0 1.0 TSG,fusion 0 False False 16-64998836-AGA-GGC 16q21 ucla_T1_organoid CDH11 chr16 64988234 CA TG missense_variant MODERATE NM_001797.4:c.921_922inv NP_001788.2:p.(Val308Ile) NM_001797.4 0.2747 91 73.5 0.0 58 0.0 1.0 TSG,fusion 2 False False 16-64988234-CA-TG 16q21 ucla_T1_organoid RNF213 chr17 80327830 TAC - inframe_deletion MODERATE NM_001256071.3:c.3211_3213del NP_001243000.2:p.(Leu1071del) NM_001256071.3 0.2121 66 64.6 0.0 78 0.0 1.0 fusion 0 False False 17-80327830-ATAC-A 17q25.3 ucla_T1_organoid ETV6 chr12 11869812 C GCACTCG inframe_insertion MODERATE NM_001987.5:c.852delinsGCACTCG NP_001978.1:p.(His283_Ser284dup) NM_001987.5 0.0545 55 58.4 0.0 57 0.0 1.0 TSG,fusion 4 False False 12-11869812-C-GCACTCG 12p13.2 ucla_T1 RNF213 chr17 80327830 TAC - inframe_deletion MODERATE NM_001256071.3:c.3211_3213del NP_001243000.2:p.(Leu1071del) NM_001256071.3 0.1282 78 44.5 0.0 78 0.0 1.0 fusion 0 False False 17-80327830-ATAC-A 17q25.3 ucla_T1_organoid DDX6 chr11 118786140 T G missense_variant MODERATE NM_004397.6:c.112A>C NP_004388.2:p.(Thr38Pro) NM_004397.6 0.1364 44 38.8 0.0 63 0.0 1.0 fusion 0 False False 11-118786140-T-G 11q23.3 ucla_T1_organoid CDH11 chr16 64988239 T C missense_variant MODERATE NM_001797.4:c.917A>G NP_001788.2:p.(Asn306Ser) NM_001797.4 0.1158 95 36.8 0.0 56 7e-06 1.0 TSG,fusion 0 False False 16-64988239-T-C 16q21 ucla_T1_organoid DDX6 chr11 118786169 G C missense_variant MODERATE NM_004397.6:c.83C>G NP_004388.2:p.(Thr28Ser) NM_004397.6 0.1591 44 34.9 0.0 62 0.0 1.0 fusion 0 False False 11-118786169-G-C 11q23.3 ucla_T1_organoid CDH11 chr16 64988200 G T missense_variant MODERATE NM_001797.4:c.956C>A NP_001788.2:p.(Thr319Lys) NM_001797.4 0.1111 72 34.9 0.0 58 0.0 1.0 TSG,fusion 1 False False 16-64988200-G-T 16q21 ucla_T1_organoid DDX6 chr11 118786166 C G missense_variant MODERATE NM_004397.6:c.86G>C NP_004388.2:p.(Gly29Ala) NM_004397.6 0.1591 44 34.6 0.0 61 0.0 1.0 fusion 0 False False 11-118786166-C-G 11q23.3 ucla_T1_organoid RBM15 chr1 110339490 C T missense_variant MODERATE NM_022768.5:c.85C>T NP_073605.4:p.(Arg29Trp) NM_022768.5 0.1 50 34.4 0.0 77 1e-06 1.0 fusion 1 False False 1-110339490-C-T 1p13.3 ucla_T1_organoid BCL11B chr14 99257816 CG TA missense_variant MODERATE NM_138576.4:c.81_82delinsTA NP_612808.1:p.(Ala28Thr) NM_138576.4 0.125 48 34.3 0.0 67 0.0 1.0 TSG,oncogene,fusion 3 False False 14-99257816-CG-TA 14q32.2 ucla_T1_organoid SALL4 chr20 51802368 G C missense_variant MODERATE NM_020436.5:c.41C>G NP_065169.1:p.(Ser14Trp) NM_020436.5 0.1081 37 34.0 0.0 65 0.0 1.0 oncogene 0 False False 20-51802368-G-C 20q13.2 ucla_T1_organoid CEBPA chr19 33302389 G A missense_variant MODERATE NM_004364.5:c.26C>T NP_004355.2:p.(Ala9Val) NM_004364.5 0.1591 44 32.6 0.0 55 0.0 1.0 TSG,oncogene 1 False False 19-33302389-G-A 19q13.11 ucla_T1_organoid CDKN1B chr12 12718144 C T missense_variant MODERATE NM_004064.5:c.305C>T NP_004055.1:p.(Pro102Leu) NM_004064.5 0.0794 63 32.1 0.0 79 7e-06 1.0 TSG,oncogene 0 False False 12-12718144-C-T 12p13.1 ucla_T1_organoid SETBP1 chr18 44953248 A T missense_variant MODERATE NM_015559.3:c.3908A>T NP_056374.2:p.(Tyr1303Phe) NM_015559.3 0.1042 48 32.0 0.0 57 0.0 1.0 fusion,oncogene 1 False False 18-44953248-A-T 18q12.3 ucla_T1_organoid ACVR1 chr2 157765997 TGGT GGAC missense_variant MODERATE NM_001111067.4:c.987_990delinsGTCC NP_001104537.1:p.(Pro330Ser) NM_001111067.4 0.0811 37 31.9 0.0 81 0.0 1.0 oncogene 1 False False 2-157765997-TGGT-GGAC 2q24.1 ucla_T1_organoid SETBP1 chr18 44953223 G A missense_variant MODERATE NM_015559.3:c.3883G>A NP_056374.2:p.(Val1295Met) NM_015559.3 0.1163 43 31.0 0.0 62 0.00019 1.0 fusion,oncogene 1 False False 18-44953223-G-A 18q12.3 ucla_T1_organoid BCL9 chr1 147624277 G C missense_variant MODERATE NM_004326.4:c.3599G>C NP_004317.2:p.(Gly1200Ala) NM_004326.4 0.0769 65 30.7 0.0 68 1e-06 1.0 oncogene,fusion 1 False False 1-147624277-G-C 1q21.2 ucla_T1_organoid FAT4 chr4 125316691 TCC GCT missense_variant MODERATE NM_001291303.3:c.280_282delinsGCT NP_001278232.1:p.(Ser94Ala) NM_001291303.3 0.0769 52 30.3 0.0 67 0.0 1.0 TSG 0 False False 4-125316691-TCC-GCT 4q28.1 ucla_T1_organoid SETBP1 chr18 44953226 A G missense_variant MODERATE NM_015559.3:c.3886A>G NP_056374.2:p.(Ser1296Gly) NM_015559.3 0.1136 44 30.1 0.0 60 0.0 1.0 fusion,oncogene 0 False False 18-44953226-A-G 18q12.3 ucla_T2 IGHG1 chr14 105741794 CCTGTAGGGACAGAGGTTGGTACAGCGGTCACTCTCAGGGCAGAGGGTGGGCCGAGCCGGCCTCTGTCCATGTGGCCCTCGCACCCCACGGGTCCCA - splice_donor_variant;splice_acceptor_variant;coding_sequence_variant;intron_variant HIGH ENST00000390548.6:c.670+2_671del ENST00000390548.6 0.4463 298 189.8 0.0 81 0.0 0 False False 14-105741794-CCCTGTAGGGACAGAGGTTGGTACAGCGGTCACTCTCAGGGCAGAGGGTGGGCCGAGCCGGCCTCTGTCCATGTGGCCCTCGCACCCCACGGGTCCCA-C 14q32.33 ucla_T1 MAP2 chr2 209694769 CTGGGCTACTGTGTGTTCAATAAGTACACAGT AGGG frameshift_variant HIGH NM_001375505.1:c.2599_2630delinsAGGG NP_001362434.1:p.(Leu867ArgfsTer39) NM_001375505.1 0.3663 101 122.2 0.0 80 0.0 0 False False 2-209694769-CTGGGCTACTGTGTGTTCAATAAGTACACAGT-AGGG 2q34 ucla_T1_organoid GAPDH chr12 6537761 - T frameshift_variant HIGH NM_002046.7:c.704dup NP_002037.2:p.(Thr237HisfsTer20) NM_002046.7 0.3814 97 95.4 0.0 63 0.0 0 False False 12-6537761-G-GT 12p13.31 ucla_T1_organoid GAPDH chr12 6537765 CCACTG TAACC frameshift_variant HIGH NM_002046.7:c.707_712delinsTAACC NP_002037.2:p.(Pro236LeufsTer10) NM_002046.7 0.3542 96 94.8 0.0 67 0.0 0 False False 12-6537765-CCACTG-TAACC 12p13.31 personalis MAP2 chr2 209694769 CTGGGCTACTGTGTGTTCAATAAGTACACAGT AGGG frameshift_variant HIGH NM_001375505.1:c.2599_2630delinsAGGG NP_001362434.1:p.(Leu867ArgfsTer39) NM_001375505.1 0.5556 18 92.1 0.0 53 0.0 0 False False 2-209694769-CTGGGCTACTGTGTGTTCAATAAGTACACAGT-AGGG 2q34 ucla_T1_organoid MAP2 chr2 209694769 CTGGGCTACTGTGTGTTCAATAAGTACACAGT AGGG frameshift_variant HIGH NM_001375505.1:c.2599_2630delinsAGGG NP_001362434.1:p.(Leu867ArgfsTer39) NM_001375505.1 0.3077 52 86.0 0.0 80 0.0 0 False False 2-209694769-CTGGGCTACTGTGTGTTCAATAAGTACACAGT-AGGG 2q34 ucla_T2 MAP2 chr2 209694769 CTGGGCTACTGTGTGTTCAATAAGTACACAGT AGGG frameshift_variant HIGH NM_001375505.1:c.2599_2630delinsAGGG NP_001362434.1:p.(Leu867ArgfsTer39) NM_001375505.1 0.1938 129 68.7 0.0 77 0.0 0 False False 2-209694769-CTGGGCTACTGTGTGTTCAATAAGTACACAGT-AGGG 2q34 personalis SRGAP3 chr3 9104715 G A stop_gained HIGH NM_014850.4:c.388C>T NP_055665.1:p.(Gln130Ter) NM_014850.4 0.35 60 67.8 0.0 41 0.0 0 False False 3-9104715-G-A 3p25.3 ucla_T1_organoid ABTB3 chr12 107642169 C T stop_gained;splice_region_variant HIGH NM_001018072.2:c.2920C>T NP_001018082.1:p.(Gln974Ter) NM_001018072.2 0.2157 51 64.3 0.0 81 0.0 1 False False 12-107642169-C-T 12q23.3 personalis ABTB3 chr12 107642169 C T stop_gained;splice_region_variant HIGH NM_001018072.2:c.2920C>T NP_001018082.1:p.(Gln974Ter) NM_001018072.2 0.5 14 61.4 0.0 36 0.0 1 False False 12-107642169-C-T 12q23.3 ucla_T1 PIP5K1A chr1 151242178 G - frameshift_variant HIGH NM_001135638.2:c.1421del NP_001129110.1:p.(Gly474AlafsTer22) NM_001135638.2 0.1685 89 55.2 0.0 75 0.0 0 False False 1-151242178-AG-A 1q21.3 ucla_T1_organoid PIP5K1A chr1 151242178 G - frameshift_variant HIGH NM_001135638.2:c.1421del NP_001129110.1:p.(Gly474AlafsTer22) NM_001135638.2 0.1493 67 47.7 0.0 75 0.0 0 False False 1-151242178-AG-A 1q21.3 ucla_T1 DOT1L chr19 2214506 G A stop_gained HIGH NM_032482.3:c.1833G>A NP_115871.1:p.(Trp611Ter) NM_032482.3 0.1905 63 47.6 0.0 52 0.0 1 False False 19-2214506-G-A 19p13.3 ucla_T1 ABTB3 chr12 107642169 C T stop_gained;splice_region_variant HIGH NM_001018072.2:c.2920C>T NP_001018082.1:p.(Gln974Ter) NM_001018072.2 0.1304 69 46.0 0.0 81 0.0 1 False False 12-107642169-C-T 12q23.3 ucla_T1_organoid GLIS3 chr9 3856152 ATGTGGTGA T frameshift_variant HIGH NM_001042413.2:c.2322_2330delinsA NP_001035878.1:p.(His775GlnfsTer81) NM_001042413.2 0.1875 48 43.5 0.0 51 0.0 0 False False 9-3856152-ATGTGGTGA-T 9p24.2 personalis ADAM17 chr2 9521241 C A stop_gained HIGH NM_003183.6:c.919G>T NP_003174.3:p.(Glu307Ter) NM_003183.6 0.2195 41 43.1 0.0 40 0.0 1 False False 2-9521241-C-A 2p25.1 ucla_T1_organoid DOT1L chr19 2214506 G A stop_gained HIGH NM_032482.3:c.1833G>A NP_115871.1:p.(Trp611Ter) NM_032482.3 0.1667 48 41.5 0.0 52 0.0 1 False False 19-2214506-G-A 19p13.3 ucla_T1_organoid SPAG1 chr8 100213209 G - frameshift_variant HIGH NM_003114.5:c.1220del NP_003105.2:p.(Gly407AlafsTer42) NM_003114.5 0.1525 59 40.2 0.0 55 0.0 0 False False 8-100213209-CG-C 8q22.2 ucla_T1_organoid CNTRL chr9 121115135 G T stop_gained HIGH NM_007018.6:c.1390G>T NP_008949.4:p.(Glu464Ter) NM_007018.6 0.1475 61 39.5 0.0 56 0.0 1 False False 9-121115135-G-T 9q33.2 ucla_T2 DOT1L chr19 2214506 G A stop_gained HIGH NM_032482.3:c.1833G>A NP_115871.1:p.(Trp611Ter) NM_032482.3 0.1308 130 38.5 0.0 52 0.0 1 False False 19-2214506-G-A 19p13.3 ucla_T1 SPAG1 chr8 100213209 G - frameshift_variant HIGH NM_003114.5:c.1220del NP_003105.2:p.(Gly407AlafsTer42) NM_003114.5 0.1325 83 38.1 0.0 55 0.0 0 False False 8-100213209-CG-C 8q22.2 ucla_T1 CGNL1 chr15 57451531 ATTGGAACAGAAAAGCA - frameshift_variant HIGH NM_032866.5:c.1837_1853del NP_116255.2:p.(Leu613ValfsTer7) NM_032866.5 0.1605 81 37.1 0.0 42 0.0 0 False False 15-57451531-TATTGGAACAGAAAAGCA-T 15q21.3 ucla_T2 PIP5K1A chr1 151242178 G - frameshift_variant HIGH NM_001135638.2:c.1421del NP_001129110.1:p.(Gly474AlafsTer22) NM_001135638.2 0.0921 152 36.7 0.0 75 0.0 0 False False 1-151242178-AG-A 1q21.3 ucla_T1 TECPR1 chr7 98241127 G - frameshift_variant HIGH NM_015395.3:c.774del NP_056210.1:p.(Thr259HisfsTer77) NM_015395.3 0.1077 65 36.6 0.0 74 0.0 0 False False 7-98241127-TG-T 7q21.3 ucla_T1 CNTRL chr9 121115135 G T stop_gained HIGH NM_007018.6:c.1390G>T NP_008949.4:p.(Glu464Ter) NM_007018.6 0.1111 108 36.4 0.0 56 0.0 1 False False 9-121115135-G-T 9q33.2 ucla_T1_organoid TAF7L chrX 101286650 T - frameshift_variant;splice_region_variant HIGH NM_001168474.2:c.69del NP_001161946.1:p.(Glu23AspfsTer9) NM_001168474.2 0.2 30 36.3 0.0 38 0.0 0 False False X-101286650-GT-G Xq22.1 ucla_T2 ADCYAP1 chr18 907775 C - frameshift_variant HIGH NM_001099733.2:c.230del NP_001093203.1:p.(Pro77ArgfsTer82) NM_001099733.2 0.0882 102 34.8 0.0 80 0.0 0 False False 18-907775-GC-G 18p11.32 ucla_T2 TAF7L chrX 101286650 T - frameshift_variant;splice_region_variant HIGH NM_001168474.2:c.69del NP_001161946.1:p.(Glu23AspfsTer9) NM_001168474.2 0.1528 72 33.6 0.0 38 0.0 0 False False X-101286650-GT-G Xq22.1 ucla_T1 BAZ1B chr7 73498699 C A splice_acceptor_variant HIGH NM_032408.4:c.370-1G>T NM_032408.4 0.1143 70 33.2 0.0 50 0.0 1 False False 7-73498699-C-A 7q11.23 ucla_T2 GABBR1 chr6 29630494 G A stop_gained HIGH NM_001470.4:c.439C>T NP_001461.1:p.(Gln147Ter) NM_001470.4 0.0809 173 33.2 0.0 71 0.0 1 False False 6-29630494-G-A 6p22.1 ucla_T1 CDHR18P chr3 63770421 C T splice_acceptor_variant;non_coding_transcript_variant HIGH ENST00000430831.6:n.698-1G>A ENST00000430831.6 0.1019 108 32.8 0.0 52 0.0 0 False False 3-63770421-C-T 3p14.2 ucla_T2 CDKN2B-AS1 chr9 22056251 G T splice_acceptor_variant;non_coding_transcript_variant HIGH ENST00000650946.1:n.303-1G>T ENST00000650946.1 0.1373 102 31.7 0.0 39 0.0 0 False False 9-22056251-G-T 9p21.3 ucla_T1_organoid CDHR18P chr3 63770421 C T splice_acceptor_variant;non_coding_transcript_variant HIGH ENST00000430831.6:n.698-1G>A ENST00000430831.6 0.1071 56 31.6 0.0 52 0.0 0 False False 3-63770421-C-T 3p14.2 ucla_T1_organoid MGA chr15 41766833 GAAC - frameshift_variant HIGH NM_001400225.1:c.8899_8902del NP_001387154.1:p.(Glu2967GlnfsTer16) NM_001400225.1 0.0816 49 31.5 0.0 74 0.0 0 False False 15-41766833-AGAAC-A 15q15.1 ucla_T1_organoid SFN chr1 26863755 C A stop_gained HIGH NM_006142.5:c.543C>A NP_006133.1:p.(Tyr181Ter) NM_006142.5 0.093 43 31.3 0.0 63 0.0 0 False False 1-26863755-C-A 1p36.11 ucla_T1 SRGAP3 chr3 9104715 G A stop_gained HIGH NM_014850.4:c.388C>T NP_055665.1:p.(Gln130Ter) NM_014850.4 0.092 87 31.3 0.0 58 0.0 0 False False 3-9104715-G-A 3p25.3 ucla_T1_organoid TTN chr2 178570552 TC - frameshift_variant HIGH NM_001267550.2:c.75578_75579del NP_001254479.2:p.(Arg25193IlefsTer10) NM_001267550.2 0.125 48 30.9 0.0 59 0.0 0 False False 2-178570552-ATC-A 2q31.2 ucla_T1_organoid PCBP1 chr2 70088718 GC AT stop_gained HIGH NM_006196.4:c.975_976delinsAT NP_006187.2:p.(Gln326Ter) NM_006196.4 0.0833 60 30.9 0.0 65 0.0 1 False False 2-70088718-GC-AT 2p13.3 ucla_T1 GLIS3 chr9 3856152 ATGTGGTGA T frameshift_variant HIGH NM_001042413.2:c.2322_2330delinsA NP_001035878.1:p.(His775GlnfsTer81) NM_001042413.2 0.1013 79 30.8 0.0 54 0.0 0 False False 9-3856152-ATGTGGTGA-T 9p24.2 ucla_T1_organoid HSPA12A chr10 116679535 - ATAGGGTCAGAACTCGGGGCAAGCCAACTTACTTGCTCTTCCTCAATGCATGCTCCACGCTGTGG stop_gained;frameshift_variant HIGH NM_025015.3:c.1253_1254insCCACAGCGTGGAGCATGCATTGAGGAAGAGCAAGTAAGTTGGCTTGCCCCGAGTTCTGACCCTAT NP_079291.2:p.(Asn429LysfsTer2) NM_025015.3 0.093 43 30.7 0.0 65 0.0 0 False False 10-116679535-C-CATAGGGTCAGAACTCGGGGCAAGCCAACTTACTTGCTCTTCCTCAATGCATGCTCCACGCTGTGG 10q25.3 ucla_T1_organoid TTN chr2 178570559 - CC frameshift_variant HIGH NM_001267550.2:c.75571_75572dup NP_001254479.2:p.(Arg25193LysfsTer6) NM_001267550.2 0.125 48 30.4 0.0 57 0.0 3 False False 2-178570559-T-TCC 2q31.2 ucla_T1_organoid PIEZO2 chr18 10708373 T CGGGG frameshift_variant HIGH NM_001378183.1:c.5490delinsCCCCG NP_001365112.1:p.(Glu1830AspfsTer5) NM_001378183.1 0.0727 55 30.1 0.0 74 0.0 0 False False 18-10708373-T-CGGGG 18p11.22 personalis ZNF436 chr1 23362762 G C missense_variant MODERATE NM_001077195.2:c.620C>G NP_001070663.1:p.(Ser207Cys) NM_001077195.2 0.6667 33 133.3 0.0 52 0.0 2 False False 1-23362762-G-C 1p36.12 ucla_T1_organoid GAPDH chr12 6537665 CT GC missense_variant MODERATE NM_002046.7:c.607_608delinsGC NP_002037.2:p.(Leu203Ala) NM_002046.7 0.6032 126 131.6 0.0 56 0.0 3 False False 12-6537665-CT-GC 12p13.31 ucla_T1_organoid ZNF436 chr1 23362762 G C missense_variant MODERATE NM_001077195.2:c.620C>G NP_001070663.1:p.(Ser207Cys) NM_001077195.2 0.3571 56 104.2 0.0 82 0.0 2 False False 1-23362762-G-C 1p36.12 ucla_T1 ZNF436 chr1 23362762 G C missense_variant MODERATE NM_001077195.2:c.620C>G NP_001070663.1:p.(Ser207Cys) NM_001077195.2 0.3167 60 94.8 0.0 82 0.0 2 False False 1-23362762-G-C 1p36.12 ucla_T1 DBH chr9 133652279 C T missense_variant MODERATE NM_000787.4:c.1369C>T NP_000778.3:p.(His457Tyr) NM_000787.4 0.2632 76 81.1 0.0 76 0.0 1 False False 9-133652279-C-T 9q34.2 ucla_T1_organoid GTF3C5 chr9 133057893 GAGGAGGAGGAA - inframe_deletion MODERATE NM_012087.4:c.1485_1496del NP_036219.2:p.(Glu496_Glu499del) NM_012087.4 0.2877 73 80.1 0.0 67 1.9e-05 1 False False 9-133057893-GGAGGAGGAGGAA-G 9q34.13 personalis LCE1B chr1 152812486 C T missense_variant MODERATE NM_178349.2:c.40C>T NP_848126.1:p.(Pro14Ser) NM_178349.2 0.4 35 69.7 0.0 41 0.0 4 False False 1-152812486-C-T 1q21.3 ucla_T1_organoid DBH chr9 133652279 C T missense_variant MODERATE NM_000787.4:c.1369C>T NP_000778.3:p.(His457Tyr) NM_000787.4 0.2453 53 69.7 0.0 76 0.0 1 False False 9-133652279-C-T 9q34.2 ucla_T1 GTF3C5 chr9 133057893 GAGGAGGAGGAA - inframe_deletion MODERATE NM_012087.4:c.1485_1496del NP_036219.2:p.(Glu496_Glu499del) NM_012087.4 0.25 72 67.6 0.0 64 1.9e-05 1 False False 9-133057893-GGAGGAGGAGGAA-G 9q34.13 ucla_T2 DBH chr9 133652279 C T missense_variant MODERATE NM_000787.4:c.1369C>T NP_000778.3:p.(His457Tyr) NM_000787.4 0.155 129 56.1 0.0 76 0.0 1 False False 9-133652279-C-T 9q34.2 ucla_T1_organoid PPP1CC chr12 110722539 A G missense_variant MODERATE NM_002710.4:c.680T>C NP_002701.1:p.(Phe227Ser) NM_002710.4 0.1923 52 55.5 0.0 72 0.0 5 False False 12-110722539-A-G 12q24.11 ucla_T1_organoid TIAM1 chr21 31266586 AGT TGA missense_variant MODERATE NM_001353694.2:c.385_387delinsTCA NP_001340623.1:p.(Thr129Ser) NM_001353694.2 0.1961 51 51.3 0.0 70 0.0 1 False False 21-31266586-AGT-TGA 21q22.11 ucla_T1 ACE chr17 63497361 T A missense_variant MODERATE NM_000789.4:c.3916T>A NP_000780.1:p.(Ser1306Thr) NM_000789.4 0.1731 52 50.1 0.0 69 0.0 3 False False 17-63497361-T-A 17q23.3 ucla_T1 FZD9 chr7 73434684 G A missense_variant MODERATE NM_003508.3:c.677G>A NP_003499.1:p.(Arg226His) NM_003508.3 0.1667 72 49.6 0.0 64 0.0 2 False False 7-73434684-G-A 7q11.23 ucla_T1_organoid CDV3 chr3 133587953 T G missense_variant MODERATE NM_017548.5:c.684T>G NP_060018.1:p.(Asp228Glu) NM_017548.5 0.2 60 49.4 0.0135 74 1.1e-05 2 False False 3-133587953-T-G 3q22.1 ucla_T2 ZNF436 chr1 23362762 G C missense_variant MODERATE NM_001077195.2:c.620C>G NP_001070663.1:p.(Ser207Cys) NM_001077195.2 0.122 123 49.3 0.0 82 0.0 2 False False 1-23362762-G-C 1p36.12 personalis KIF1C chr17 5007293 G A missense_variant MODERATE NM_006612.6:c.1366G>A NP_006603.2:p.(Glu456Lys) NM_006612.6 0.3636 11 48.5 0.0 45 7e-06 2 False False 17-5007293-G-A 17p13.2 personalis KDM3B chr5 138391529 C T missense_variant MODERATE NM_016604.4:c.1897C>T NP_057688.3:p.(Pro633Ser) NM_016604.4 0.2571 35 48.4 0.0 42 1e-06 1 False False 5-138391529-C-T 5q31.2 ucla_T1_organoid HECTD1 chr14 31129172 C G missense_variant MODERATE NM_015382.4:c.4199G>C NP_056197.3:p.(Gly1400Ala) NM_015382.4 0.1607 56 46.4 0.0 70 0.0 10 False False 14-31129172-C-G 14q12 ucla_T1_organoid XKR4 chr8 55102627 GA AC missense_variant MODERATE NM_052898.2:c.139_140delinsAC NP_443130.1:p.(Glu47Thr) NM_052898.2 0.2642 53 46.0 0.0 49 0.0 1 False False 8-55102627-GA-AC 8q12.1 ucla_T1_organoid AMD1 chr6 110893500 G T missense_variant MODERATE NM_001634.6:c.889G>T NP_001625.2:p.(Ala297Ser) NM_001634.6 0.1525 59 45.9 0.0 74 1e-06 1 False False 6-110893500-G-T 6q21 ucla_T1_organoid WWC1 chr5 168399513 T G missense_variant MODERATE NM_015238.3:c.536T>G NP_056053.1:p.(Val179Gly) NM_015238.3 0.1698 53 45.8 0.0 59 0.0 1 False False 5-168399513-T-G 5q34 ucla_T1_organoid LCP1 chr13 46146964 C T missense_variant MODERATE NM_002298.5:c.1118G>A NP_002289.2:p.(Arg373Lys) NM_002298.5 0.225 40 45.7 0.0 55 1e-06 2 False False 13-46146964-C-T 13q14.13 ucla_T1_organoid AMD1 chr6 110893520 A C missense_variant MODERATE NM_001634.6:c.909A>C NP_001625.2:p.(Glu303Asp) NM_001634.6 0.1864 59 45.6 0.0 75 0.0 1 False False 6-110893520-A-C 6q21 ucla_T1 WWC1 chr5 168399513 T G missense_variant MODERATE NM_015238.3:c.536T>G NP_056053.1:p.(Val179Gly) NM_015238.3 0.1579 95 45.1 0.0 59 0.0 1 False False 5-168399513-T-G 5q34 ucla_T2 ROBO2 chr3 77607853 C A missense_variant MODERATE NM_001395656.1:c.3204C>A NP_001382585.1:p.(Asn1068Lys) NM_001395656.1 0.1447 152 43.8 0.0 55 1e-06 1 False False 3-77607853-C-A 3p12.3 ucla_T1_organoid H1-2 chr6 26055824 CCTTGGGCTTAGCGG - inframe_deletion MODERATE NM_005319.4:c.590_604del NP_005310.1:p.(Ala197_Lys201del) NM_005319.4 0.1486 74 43.6 0.0 62 3.4e-05 9 False False 6-26055824-ACCTTGGGCTTAGCGG-A 6p22.2 ucla_T1_organoid WDR20 chr14 102209703 GC AT missense_variant MODERATE NM_144574.4:c.1533_1534delinsAT NP_653175.2:p.(Pro512Ser) NM_144574.4 0.1475 61 43.0 0.0 73 0.0 1 False False 14-102209703-GC-AT 14q32.31 ucla_T1_organoid LCE1B chr1 152812486 C T missense_variant MODERATE NM_178349.2:c.40C>T NP_848126.1:p.(Pro14Ser) NM_178349.2 0.1356 59 41.4 0.0 65 0.0 4 False False 1-152812486-C-T 1q21.3 ucla_T1_organoid MEF2D chr1 156479733 GT TG missense_variant MODERATE NM_005920.4:c.459_460delinsCA NP_005911.1:p.(Leu154Met) NM_005920.4 0.1404 57 40.6 0.0 60 0.0 1 False False 1-156479733-GT-TG 1q22 ucla_T1 TMEM139 chr7 143286139 G T missense_variant MODERATE NM_001282876.2:c.182G>T NP_001269805.1:p.(Trp61Leu) NM_001282876.2 0.1449 69 40.2 0.0 53 0.0 1 False False 7-143286139-G-T 7q34 ucla_T1_organoid ODC1 chr2 10444170 TTA CTG missense_variant MODERATE NM_002539.3:c.372_374delinsCAG NP_002530.1:p.(Asn125Ser) NM_002539.3 0.1385 65 40.1 0.0 69 0.0 1 False False 2-10444170-TTA-CTG 2p25.1 personalis GTF3C5 chr9 133057893 GAGGAGGAGGAA - inframe_deletion MODERATE NM_012087.4:c.1485_1496del NP_036219.2:p.(Glu496_Glu499del) NM_012087.4 0.25 16 40.0 0.0 48 1.9e-05 1 False False 9-133057893-GGAGGAGGAGGAA-G 9q34.13 ucla_T1_organoid KIFC1 chr6 33405368 G A missense_variant MODERATE NM_002263.4:c.1273G>A NP_002254.2:p.(Gly425Arg) NM_002263.4 0.1625 80 39.9 0.0 61 1e-06 1 False False 6-33405368-G-A 6p21.32 ucla_T1 CTSE chr1 206022947 C A missense_variant MODERATE NM_001910.4:c.179G>T NP_001901.1:p.(Cys60Phe) NM_001910.4 0.14 100 39.8 0.0 51 0.0 1 False False 1-206022947-C-A 1q32.1 ucla_T2 GTF3C5 chr9 133057893 GAGGAGGAGGAA - inframe_deletion MODERATE NM_012087.4:c.1485_1496del NP_036219.2:p.(Glu496_Glu499del) NM_012087.4 0.1128 133 39.4 0.0 64 1.9e-05 1 False False 9-133057893-GGAGGAGGAGGAA-G 9q34.13 ucla_T1_organoid ABCA13 chr7 48410588 C T missense_variant MODERATE NM_152701.5:c.12139C>T NP_689914.3:p.(Leu4047Phe) NM_152701.5 0.1304 46 39.1 0.0 67 1e-06 1 False False 7-48410588-C-T 7p12.3 ucla_T1_organoid LHFPL1 chrX 112671169 AT GG missense_variant MODERATE NM_178175.4:c.221_222delinsCC NP_835469.1:p.(Asn74Thr) NM_178175.4 0.25 20 38.2 0.0 33 0.0 1 False False X-112671169-AT-GG Xq23 ucla_T1 TRMO chr9 97910412 C T missense_variant MODERATE NM_016481.5:c.614G>A NP_057565.3:p.(Gly205Glu) NM_016481.5 0.1132 106 38.1 0.0 64 0.0 1 False False 9-97910412-C-T 9q22.33 ucla_T1_organoid TMEM139 chr7 143286139 G T missense_variant MODERATE NM_001282876.2:c.182G>T NP_001269805.1:p.(Trp61Leu) NM_001282876.2 0.1379 58 37.8 0.0 53 0.0 1 False False 7-143286139-G-T 7q34 ucla_T1_organoid CSDE1 chr1 114737987 GAGG ATGT missense_variant MODERATE NM_001007553.3:c.282_285delinsACAT NP_001007554.1:p.(Leu95His) NM_001007553.3 0.1321 53 37.5 0.0 71 0.0 1 False False 1-114737987-GAGG-ATGT 1p13.2 ucla_T1_organoid EEF2 chr19 3982273 T C missense_variant MODERATE NM_001961.4:c.764A>G NP_001952.1:p.(Asp255Gly) NM_001961.4 0.1148 61 37.4 0.0 68 1.3e-05 3 False False 19-3982273-T-C 19p13.3 ucla_T1 LCE1B chr1 152812486 C T missense_variant MODERATE NM_178349.2:c.40C>T NP_848126.1:p.(Pro14Ser) NM_178349.2 0.1071 84 36.8 0.0 65 0.0 4 False False 1-152812486-C-T 1q21.3 ucla_T2 ABCA13 chr7 48410588 C T missense_variant MODERATE NM_152701.5:c.12139C>T NP_689914.3:p.(Leu4047Phe) NM_152701.5 0.1 110 36.8 0.0 67 1e-06 1 False False 7-48410588-C-T 7p12.3 ucla_T1_organoid ZBED4 chr22 49885684 TT CC missense_variant MODERATE NM_014838.3:c.2022_2023delinsCC NP_055653.2:p.(Phe675Leu) NM_014838.3 0.1346 52 36.3 0.0 80 0.0 2 False False 22-49885684-TT-CC 22q13.33 ucla_T1_organoid TWIST1 chr7 19117079 ACA TCC missense_variant MODERATE NM_000474.4:c.241_243delinsGGA NP_000465.1:p.(Cys81Gly) NM_000474.4 0.1552 58 36.2 0.0 61 0.0 1 False False 7-19117079-ACA-TCC 7p21.1 ucla_T1 PPP6R3 chr11 68601969 G T missense_variant;splice_region_variant MODERATE NM_001164161.2:c.2299G>T NP_001157633.1:p.(Ala767Ser) NM_001164161.2 0.0909 66 36.2 0.0 82 0.0 1 False False 11-68601969-G-T 11q13.2 ucla_T1_organoid CAMSAP1 chr9 135882932 CG TA missense_variant MODERATE NM_015447.4:c.306_307delinsTA NP_056262.3:p.(Ala103Thr) NM_015447.4 0.1364 66 35.9 0.0 70 0.0 3 False False 9-135882932-CG-TA 9q34.3 ucla_T1_organoid PRPH2 chr6 42722185 A T missense_variant MODERATE NM_000322.5:c.150T>A NP_000313.2:p.(Asp50Glu) NM_000322.5 0.1077 65 35.9 0.0 66 1e-06 1 False False 6-42722185-A-T 6p21.1 ucla_T1_organoid FDPS chr1 155309905 AC GT missense_variant MODERATE NM_002004.4:c.116_117inv NP_001995.1:p.(Tyr39Cys) NM_002004.4 0.1304 69 35.7 0.0 60 0.0 2 False False 1-155309905-AC-GT 1q22 ucla_T1_organoid OGFRL1 chr6 71301505 C T missense_variant MODERATE NM_024576.5:c.812C>T NP_078852.3:p.(Thr271Ile) NM_024576.5 0.125 48 35.6 0.0 57 0.0 1 False False 6-71301505-C-T 6q13 ucla_T1_organoid RNF103 chr2 86604464 T G missense_variant MODERATE NM_005667.4:c.1437A>C NP_005658.1:p.(Glu479Asp) NM_005667.4 0.1167 60 35.6 0.0 59 0.0 5 False False 2-86604464-T-G 2p11.2 ucla_T1 H1-2 chr6 26055824 CCTTGGGCTTAGCGG - inframe_deletion MODERATE NM_005319.4:c.590_604del NP_005310.1:p.(Ala197_Lys201del) NM_005319.4 0.1034 116 35.5 0.0 62 3.4e-05 9 False False 6-26055824-ACCTTGGGCTTAGCGG-A 6p22.2 ucla_T1_organoid TULP4 chr6 158503746 G T missense_variant MODERATE NM_020245.5:c.4083G>T NP_064630.2:p.(Glu1361Asp) NM_020245.5 0.1471 68 35.1 0.0167 60 0.0 1 False False 6-158503746-G-T 6q25.3 ucla_T1_organoid ANK2 chr4 113359291 AT GA missense_variant MODERATE NM_001148.6:c.10673_10674delinsGA NP_001139.3:p.(His3558Arg) NM_001148.6 0.093 43 35.1 0.0 83 0.0 1 False False 4-113359291-AT-GA 4q26 ucla_T1_organoid SH3BP4 chr2 235042898 G A missense_variant MODERATE NM_014521.3:c.2129G>A NP_055336.1:p.(Arg710Lys) NM_014521.3 0.1132 53 34.9 0.0 77 0.0 1 False False 2-235042898-G-A 2q37.2 ucla_T1_organoid COL6A3 chr2 237379144 CA GG missense_variant MODERATE NM_004369.4:c.1988_1989delinsCC NP_004360.2:p.(Met663Thr) NM_004369.4 0.1143 35 34.2 0.0 63 0.0 1 False False 2-237379144-CA-GG 2q37.3 ucla_T1_organoid CBLL1 chr7 107758605 AAA CAG missense_variant MODERATE NM_024814.4:c.903_905delinsCAG NP_079090.2:p.(Asn302Ser) NM_024814.4 0.1071 56 34.1 0.0 78 0.0 1 False False 7-107758605-AAA-CAG 7q22.3 ucla_T1_organoid SYS1 chr20 45366966 T C missense_variant MODERATE NM_033542.4:c.322T>C NP_291020.1:p.(Phe108Leu) NM_033542.4 0.0962 52 34.0 0.0 70 1e-06 1 False False 20-45366966-T-C 20q13.12 ucla_T1_organoid USP1 chr1 62450577 ACA GCC missense_variant MODERATE NM_003368.5:c.1954_1956delinsGCC NP_003359.3:p.(Thr652Ala) NM_003368.5 0.1053 38 33.7 0.0 65 0.0 1 False False 1-62450577-ACA-GCC 1p31.3 ucla_T1_organoid FZD9 chr7 73434684 G A missense_variant MODERATE NM_003508.3:c.677G>A NP_003499.1:p.(Arg226His) NM_003508.3 0.1042 48 33.7 0.0 64 0.0 2 False False 7-73434684-G-A 7q11.23 ucla_T1_organoid CDAN1 chr15 42735960 C T missense_variant MODERATE NM_138477.4:c.688G>A NP_612486.2:p.(Ala230Thr) NM_138477.4 0.082 61 33.7 0.0 78 1e-06 1 False False 15-42735960-C-T 15q15.2 ucla_T1_organoid SFMBT2 chr10 7284110 C T missense_variant MODERATE NM_001387889.1:c.566G>A NP_001374818.1:p.(Gly189Asp) NM_001387889.1 0.1154 52 33.6 0.0 55 0.0 2 False False 10-7284110-C-T 10p14 ucla_T1_organoid ACE chr17 63497361 T A missense_variant MODERATE NM_000789.4:c.3916T>A NP_000780.1:p.(Ser1306Thr) NM_000789.4 0.0943 53 33.5 0.0 69 0.0 3 False False 17-63497361-T-A 17q23.3 ucla_T1_organoid OTUD7B chr1 149944445 TG AA missense_variant MODERATE NM_020205.4:c.1943_1944delinsTT NP_064590.2:p.(Ala648Val) NM_020205.4 0.0893 56 33.4 0.0 72 0.0 1 False False 1-149944445-TG-AA 1q21.2 ucla_T1_organoid USP1 chr1 62450617 C G missense_variant MODERATE NM_003368.5:c.1994C>G NP_003359.3:p.(Ala665Gly) NM_003368.5 0.1163 43 33.2 0.0 63 0.0 2 False False 1-62450617-C-G 1p31.3 ucla_T1_organoid WDR20 chr14 102209846 G C missense_variant MODERATE NM_144574.4:c.1676G>C NP_653175.2:p.(Gly559Ala) NM_144574.4 0.102 49 33.0 0.0 80 0.0 1 False False 14-102209846-G-C 14q32.31 ucla_T1_organoid YY1 chr14 100239420 - CGG inframe_insertion MODERATE NM_003403.5:c.183_185dup NP_003394.1:p.(Gly64dup) NM_003403.5 0.1538 52 32.9 0.0 48 0.0 1 False False 14-100239420-A-ACGG 14q32.2 ucla_T1_organoid INA chr10 103277362 T A missense_variant MODERATE NM_032727.4:c.151T>A NP_116116.1:p.(Ser51Thr) NM_032727.4 0.1282 39 32.9 0.0 49 0.0 1 False False 10-103277362-T-A 10q24.33 ucla_T1 ROBO2 chr3 77607853 C A missense_variant MODERATE NM_001395656.1:c.3204C>A NP_001382585.1:p.(Asn1068Lys) NM_001395656.1 0.096 125 32.8 0.0 55 1e-06 1 False False 3-77607853-C-A 3p12.3 ucla_T1_organoid FZD5 chr2 207768053 GGCA CGGG missense_variant MODERATE NM_003468.4:c.684_687delinsCCCG NP_003459.2:p.(Ala229Pro) NM_003468.4 0.1163 43 32.7 0.0 58 0.0 1 False False 2-207768053-GGCA-CGGG 2q33.3 ucla_T1_organoid COPS7B chr2 231807579 CG TA missense_variant MODERATE NM_022730.4:c.729_730delinsTA NP_073567.1:p.(Ala244Thr) NM_022730.4 0.1111 36 32.5 0.0 74 0.0 2 False False 2-231807579-CG-TA 2q37.1 ucla_T2 EPPK1 chr8 143870409 CC AA missense_variant MODERATE NM_031308.4:c.2844_2845delinsTT NP_112598.3:p.(Gln948_Ala949delinsHisSer) NM_031308.4 0.0932 118 32.5 0.0 63 0.0 2 False False 8-143870409-CC-AA 8q24.3 ucla_T1_organoid ROBO2 chr3 77607853 C A missense_variant MODERATE NM_001395656.1:c.3204C>A NP_001382585.1:p.(Asn1068Lys) NM_001395656.1 0.12 50 32.4 0.0 55 1e-06 1 False False 3-77607853-C-A 3p12.3 ucla_T1_organoid GJC1 chr17 44805008 C A missense_variant MODERATE NM_005497.4:c.810G>T NP_005488.2:p.(Glu270Asp) NM_005497.4 0.0976 41 32.4 0.0 65 0.0 2 False False 17-44805008-C-A 17q21.31 ucla_T1_organoid CNTNAP5 chr2 124527414 A G missense_variant MODERATE NM_001367498.1:c.1607A>G NP_001354427.1:p.(Asn536Ser) NM_001367498.1 0.0952 42 32.4 0.0 65 1e-06 1 False False 2-124527414-A-G 2q14.3 personalis MBD4 chr3 129437921 C T missense_variant MODERATE NM_001276270.2:c.134G>A NP_001263199.1:p.(Arg45Lys) NM_001276270.2 0.1273 55 32.3 0.0 48 0.0 1 False False 3-129437921-C-T 3q21.3 ucla_T1_organoid TRMO chr9 97910412 C T missense_variant MODERATE NM_016481.5:c.614G>A NP_057565.3:p.(Gly205Glu) NM_016481.5 0.0943 53 32.3 0.0 64 0.0 1 False False 9-97910412-C-T 9q22.33 ucla_T1_organoid MBD5 chr2 148469063 G A missense_variant MODERATE NM_001378120.1:c.1120G>A NP_001365049.1:p.(Val374Ile) NM_001378120.1 0.093 43 32.3 0.0 66 0.0 12 False False 2-148469063-G-A 2q23.1 ucla_T1_organoid IRS1 chr2 226795213 CA TC missense_variant MODERATE NM_005544.3:c.3525_3526delinsGA NP_005535.1:p.(Asn1175_Gly1176delinsLysSer) NM_005544.3 0.122 41 32.2 0.0 50 0.0 1 False False 2-226795213-CA-TC 2q36.3 ucla_T1_organoid CTSE chr1 206022947 C A missense_variant MODERATE NM_001910.4:c.179G>T NP_001901.1:p.(Cys60Phe) NM_001910.4 0.1132 53 32.1 0.0 51 0.0 1 False False 1-206022947-C-A 1q32.1 ucla_T1_organoid WAC chr10 28535670 G A missense_variant MODERATE NM_016628.5:c.187G>A NP_057712.2:p.(Asp63Asn) NM_016628.5 0.1064 47 32.1 0.0 58 2e-05 1 False False 10-28535670-G-A 10p12.1 ucla_T1_organoid RNF103 chr2 86604661 A T missense_variant MODERATE NM_005667.4:c.1240T>A NP_005658.1:p.(Ser414Thr) NM_005667.4 0.0943 53 32.1 0.0 63 0.0 1 False False 2-86604661-A-T 2p11.2 personalis H1-2 chr6 26055824 CCTTGGGCTTAGCGG - inframe_deletion MODERATE NM_005319.4:c.590_604del NP_005310.1:p.(Ala197_Lys201del) NM_005319.4 0.1413 92 32.0 0.0 37 3.4e-05 9 False False 6-26055824-ACCTTGGGCTTAGCGG-A 6p22.2 ucla_T1_organoid DPP4 chr2 161995345 T G missense_variant MODERATE NM_001935.4:c.2080A>C NP_001926.2:p.(Asn694His) NM_001935.4 0.1111 36 31.9 0.0 55 0.0 5 False False 2-161995345-T-G 2q24.2 ucla_T1_organoid KL chr13 33016930 GTC ACT missense_variant MODERATE NM_004795.4:c.490_492delinsACT NP_004786.2:p.(Val164Thr) NM_004795.4 0.1333 45 31.7 0.0 53 0.0 1 False False 13-33016930-GTC-ACT 13q13.1 ucla_T1_organoid CILP chr15 65198796 C G missense_variant MODERATE NM_003613.4:c.1490G>C NP_003604.4:p.(Ser497Thr) NM_003613.4 0.1228 57 31.6 0.0 70 0.0 1 False False 15-65198796-C-G 15q22.31 ucla_T1_organoid HPCAL1 chr2 10419865 G T missense_variant MODERATE NM_002149.4:c.108G>T NP_002140.2:p.(Lys36Asn) NM_002149.4 0.1194 67 31.5 0.0 56 0.0 2 False False 2-10419865-G-T 2p25.1 ucla_T1_organoid ETV1 chr7 13895928 C T missense_variant MODERATE NM_004956.5:c.1372G>A NP_004947.2:p.(Ala458Thr) NM_004956.5 0.1132 53 31.3 0.0 48 8e-06 1 False False 7-13895928-C-T 7p21.2 ucla_T1_organoid MTMR14 chr3 9697842 C A missense_variant MODERATE NM_001077525.3:c.1745C>A NP_001070993.1:p.(Pro582Gln) NM_001077525.3 0.1087 46 31.3 0.0 52 0.0 1 False False 3-9697842-C-A 3p25.3 ucla_T1_organoid TMPO chr12 98547744 T G missense_variant MODERATE NM_001032283.3:c.1251T>G NP_001027454.1:p.(Ile417Met) NM_001032283.3 0.0976 41 31.3 0.0 59 1e-06 1 False False 12-98547744-T-G 12q23.1 ucla_T1_organoid LRBA chr4 150599123 A C missense_variant MODERATE NM_001364905.1:c.5930T>G NP_001351834.1:p.(Leu1977Arg) NM_001364905.1 0.08 50 31.2 0.0 68 0.0 3 False False 4-150599123-A-C 4q31.3 ucla_T1_organoid SMG6 chr17 2299304 GAC AAT missense_variant MODERATE NM_017575.5:c.1447_1449delinsATT NP_060045.4:p.(Val483Ile) NM_017575.5 0.0943 53 31.1 0.0 59 0.0 1 False False 17-2299304-GAC-AAT 17p13.3 ucla_T1_organoid RPRD2 chr1 150472601 T C missense_variant MODERATE NM_015203.5:c.3653T>C NP_056018.2:p.(Val1218Ala) NM_015203.5 0.0921 76 31.1 0.0 75 0.0 2 False False 1-150472601-T-C 1q21.2 ucla_T1_organoid EOMES chr3 27717710 GA TT missense_variant MODERATE NM_001278182.2:c.1477_1478delinsAA NP_001265111.1:p.(Ser493Asn) NM_001278182.2 0.0862 58 31.1 0.0 64 0.0 2 False False 3-27717710-GA-TT 3p24.1 personalis SAMD9 chr7 93101611 C T missense_variant MODERATE NM_017654.4:c.4487G>A NP_060124.2:p.(Gly1496Glu) NM_017654.4 0.1304 69 31.0 0.0 37 0.0 4 False False 7-93101611-C-T 7q21.2 ucla_T1_organoid HDAC9 chr7 18762236 A G missense_variant MODERATE NM_178425.4:c.2123A>G NP_848512.1:p.(Asn708Ser) NM_178425.4 0.1042 48 31.0 0.0 69 0.0 8 False False 7-18762236-A-G 7p21.1 ucla_T1_organoid TUBA1A chr12 49185444 G A missense_variant MODERATE NM_006009.4:c.922C>T NP_006000.2:p.(Arg308Cys) NM_006009.4 0.0968 62 31.0 0.0 66 0.0 2 False True 12-49185444-G-A 12q13.12 ucla_T1_organoid SLC6A17 chr1 110198169 G A missense_variant MODERATE NM_001010898.4:c.1909G>A NP_001010898.1:p.(Val637Ile) NM_001010898.4 0.0909 44 30.9 0.0 63 5e-05 1 False False 1-110198169-G-A 1p13.3 ucla_T1_organoid UBP1 chr3 33439831 CT AC missense_variant MODERATE NM_014517.5:c.17_18delinsGT NP_055332.3:p.(Lys6Ser) NM_014517.5 0.087 69 30.9 0.0 64 0.0 2 False False 3-33439831-CT-AC 3p22.3 ucla_T1_organoid RFX7 chr15 56093757 C T missense_variant MODERATE NM_022841.7:c.3971G>A NP_073752.6:p.(Gly1324Asp) NM_022841.7 0.1026 39 30.8 0.0 71 0.000963 1 False False 15-56093757-C-T 15q21.3 ucla_T1_organoid CRIM1 chr2 36356312 A G missense_variant MODERATE NM_016441.3:c.20A>G NP_057525.1:p.(Asp7Gly) NM_016441.3 0.1525 59 30.7 0.0 48 0.0 1 False False 2-36356312-A-G 2p22.2 ucla_T1 DYNC1H1 chr14 102030200 G T missense_variant MODERATE NM_001376.5:c.9801G>T NP_001367.2:p.(Gln3267His) NM_001376.5 0.0723 83 30.7 0.0 72 0.0 1 False False 14-102030200-G-T 14q32.31 ucla_T1_organoid KIF1A chr2 240757380 C T missense_variant MODERATE NM_001244008.2:c.2797G>A NP_001230937.1:p.(Ala933Thr) NM_001244008.2 0.14 50 30.6 0.0175 57 1.3e-05 3 False False 2-240757380-C-T 2q37.3 ucla_T1_organoid TIAM1 chr21 31182595 CGT TAC missense_variant MODERATE NM_001353694.2:c.2711_2713delinsGTA NP_001340623.1:p.(Asp904_Ala905delinsGlyThr) NM_001353694.2 0.0943 53 30.6 0.0 62 0.0 3 False False 21-31182595-CGT-TAC 21q22.11 ucla_T1_organoid TAF7 chr5 141319471 C T missense_variant MODERATE NM_005642.3:c.574G>A NP_005633.2:p.(Ala192Thr) NM_005642.3 0.0833 48 30.6 0.0 64 9e-06 1 False False 5-141319471-C-T 5q31.3 ucla_T2 LCE1B chr1 152812486 C T missense_variant MODERATE NM_178349.2:c.40C>T NP_848126.1:p.(Pro14Ser) NM_178349.2 0.0797 138 30.6 0.0 64 0.0 4 False False 1-152812486-C-T 1q21.3 ucla_T1_organoid NCOA6 chr20 34741679 T C missense_variant MODERATE NM_014071.5:c.4577A>G NP_054790.2:p.(Lys1526Arg) NM_014071.5 0.0755 53 30.6 0.0 72 7e-06 1 False False 20-34741679-T-C 20q11.22 ucla_T1_organoid NPAS4 chr11 66424895 G A missense_variant MODERATE NM_178864.4:c.2005G>A NP_849195.2:p.(Asp669Asn) NM_178864.4 0.1064 47 30.5 0.0 66 1.4e-05 2 False False 11-66424895-G-A 11q13.2 ucla_T1_organoid FN1 chr2 215380920 T G missense_variant MODERATE NM_212482.4:c.5325A>C NP_997647.2:p.(Glu1775Asp) NM_212482.4 0.1053 38 30.5 0.0 52 7e-06 1 False False 2-215380920-T-G 2q35 ucla_T1_organoid RAB11FIP5 chr2 73089096 TAT CAG missense_variant MODERATE NM_001371272.1:c.649_651delinsCTG NP_001358201.1:p.(Ile217Leu) NM_001371272.1 0.0889 45 30.4 0.0 61 0.0 1 False False 2-73089096-TAT-CAG 2p13.2 ucla_T1_organoid GPR75 chr2 53853958 CA TG missense_variant MODERATE NM_006794.4:c.798_799inv NP_006785.1:p.(Ala267Thr) NM_006794.4 0.1017 59 30.2 0.0 66 0.0 1 False False 2-53853958-CA-TG 2p16.2 ucla_T1_organoid RFX7 chr15 56093748 T C missense_variant MODERATE NM_022841.7:c.3980A>G NP_073752.6:p.(Asn1327Ser) NM_022841.7 0.1 40 30.2 0.0 70 2e-05 3 False False 15-56093748-T-C 15q21.3 ucla_T1_organoid TGFB3 chr14 75980716 T A missense_variant MODERATE NM_003239.5:c.178A>T NP_003230.1:p.(Thr60Ser) NM_003239.5 0.0727 55 30.2 0.0 68 0.0 2 False False 14-75980716-T-A 14q24.3 ucla_T1_organoid NUFIP2 chr17 29286212 T G missense_variant MODERATE NM_020772.3:c.1782A>C NP_065823.1:p.(Glu594Asp) NM_020772.3 0.069 58 30.2 0.0 70 0.0 1 False False 17-29286212-T-G 17q11.2 ucla_T1_organoid ASXL2 chr2 25743447 T A missense_variant MODERATE NM_018263.6:c.2890A>T NP_060733.4:p.(Met964Leu) NM_018263.6 0.0833 36 30.1 0.0 67 0.0 1 False False 2-25743447-T-A 2p23.3 ucla_T1_organoid RNF114 chr20 49941680 C T missense_variant MODERATE NM_018683.4:c.260C>T NP_061153.1:p.(Thr87Ile) NM_018683.4 0.08 50 30.1 0.0 64 1.3e-05 1 False False 20-49941680-C-T 20q13.13 ucla_T1_organoid MAP1A chr15 43522167 C G missense_variant MODERATE NM_002373.6:c.694C>G NP_002364.5:p.(Pro232Ala) NM_002373.6 0.069 58 30.0 0.0 87 0.0 1 False False 15-43522167-C-G 15q15.3 personalis PLK4 chr4 127886717 C T synonymous_variant LOW NM_014264.5:c.1347C>T NP_055079.3:p.(Asn449=) NM_014264.5 0.1915 47 38.3 0.0 37 0.0 0 False True 4-127886717-C-T 4q28.1 ucla_T1_organoid PLK4 chr4 127886717 C T synonymous_variant LOW NM_014264.5:c.1347C>T NP_055079.3:p.(Asn449=) NM_014264.5 0.122 41 35.6 0.0 63 0.0 0 False True 4-127886717-C-T 4q28.1 ucla_T1 PLK4 chr4 127886717 C T synonymous_variant LOW NM_014264.5:c.1347C>T NP_055079.3:p.(Asn449=) NM_014264.5 0.0991 111 35.4 0.0 63 0.0 0 False True 4-127886717-C-T 4q28.1 ucla_T1_organoid ARCN1 chr11 118583290 T C synonymous_variant LOW NM_001655.5:c.379T>C NP_001646.2:p.(Leu127=) NM_001655.5 0.0833 48 32.4 0.0 73 7e-06 0 False True 11-118583290-T-C 11q23.3