Table 1 Somatic genetic variants detected using Exome sequencing
From: Proto-oncogene mutations in middle ear cholesteatoma contribute to its pathogenesis
sample | Gene | Locus (hg19) | Reference allele | Alternative allele | Variant allele frequency | Function | Variant | Accession number |
|---|---|---|---|---|---|---|---|---|
chole04 | ADAM32 | chr8:39027505–39,027,505;G > A | 85 | 12 | 0.12 | exonic | c.G904A:p.G302R | ENST00000519315.1 |
chole02 | ARHGEF19 | chr1:16534478–16,534,478;C > T | 41 | 9 | 0.18 | exonic | c.G655A:p.A219T | ENST00000270747.3 |
chole04 | ARHGEF7 | chr13:111920009–111,920,009;G > A | 170 | 28 | 0.14 | exonic | c.G235A:p.G79R | ENST00000544132.1 |
chole04 | C21orf91 | chr21:19190626–19,190,626;C > T | 299 | 39 | 0.12 | exonic | c.G10A:p.E4K | ENST00000400558.3 |
chole04 | C6orf120 | chr6:170103003–170,103,003;C > G | 317 | 48 | 0.13 | exonic | c.C448G:p.P150A | ENST00000332290.2 |
chole04 | EFCAB6 | chr22:44068144–44,068,144;G > C | 257 | 33 | 0.11 | exonic | c.C1461G:p.F487L | ENST00000262726.7 |
chole05 | EIF4G2 | chr11:10825526–10,825,526;A > T | 344 | 41 | 0.11 | exonic | c.T622A:p.L208M | ENST00000396525.2 |
chole05 | EPSTI1 | chr13:43462434–43,462,434;->TTAGG | 190 | 38 | 0.17 | exonic | c.1184_1185insCCTAA:p.E395fs | ENST00000313640.7 |
chole04 | GNB4 | chr3:179143948–179,143,948;A > C | 149 | 20 | 0.12 | exonic | c.T41G:p.L14R | ENST00000232564.3 |
chole06 | HRASLS | chr3:192959038–192,959,038;G > T | 0 | 2 | 1.00 | exonic | c.G31T:p.A11S | ENST00000264735.2 |
chole04 | HS3ST3B1 | chr17:14248860–14,248,860;A > G | 206 | 29 | 0.12 | exonic | c.A1070G:p.H357R | ENST00000360954.2 |
chole02 | JAG1 | chr20:10639143–10,639,143;C > G | 214 | 54 | 0.20 | exonic | c.G667C:p.G223R | ENST00000254958.5 |
chole04 | KCNA4 | chr11:30033739–30,033,739;C > T | 164 | 22 | 0.12 | exonic | c.G487A:p.G163S | ENST00000328224.6 |
chole04 | KMT2D | chr12:49421623–49,421,623;A>- | 417 | 57 | 0.12 | exonic | c.14606delT:p.L4869fs | ENST00000301067.7 |
chole04 | LY75-LY75-CD302 | chr2:160734945–160,734,945;T > A | 368 | 57 | 0.13 | exonic | c.A1664T:p.Y555F | ENST00000553424.1 |
chole02 | MID1 | chrX:10,417,566–10,417,566;C > T | 251 | 43 | 0.15 | exonic | c.G1846A:p.A616T | ENST00000453318.2 |
chole02 | MYC | chr8:128750683–128,750,683;C > G | 242 | 45 | 0.16 | exonic | c.C220G:p.P74A | ENST00000377970.2 |
chole04 | NETO1 | chr18:70526220–70,526,220;G > A | 338 | 38 | 0.10 | exonic | c.C307T:p.R103X | ENST00000397929.1 |
chole04 | NOTCH1 | chr9:139402705–139,402,705;C > A | 97 | 33 | 0.25 | exonic | c.G3304T:p.E1102X | ENST00000277541.6 |
chole05 | NOTCH1 | chr9:139412233–139,412,233;A > G | 187 | 49 | 0.21 | exonic | c.T1412C:p.I471T | ENST00000277541.6 |
chole02 | NSMCE2 | chr8:126194499–126,194,499;->T | 125 | 20 | 0.14 | splicing | c.418 + 1->T | ENST00000287437.3 |
chole05 | PLA2G15 | chr16:68279402–68,279,402;A > G | 306 | 39 | 0.11 | exonic | c.A73G:p.M25V | ENST00000566188.1 |
chole05 | PSMC4 | chr19:40485876–40,485,876;G > A | 419 | 59 | 0.12 | exonic | c.G826A:p.D276N | ENST00000157812.2 |
chole02 | SCN2A | chr2:166226663–166,226,663;C > T | 138 | 37 | 0.21 | exonic | c.C3703T:p.R1235X | ENST00000357398.3 |
chole05 | UBR5 | chr8:103307283–103,307,283;T > C | 243 | 31 | 0.11 | exonic | c.A4097G:p.N1366S | ENST00000521922.1 |