Table 2. All novel somatic SNVs and INDELs detected in metastatic KIT-mutated GISTs and predicted deleterious with at least one predictor.
| GENE | exon | cDNA mutation | Protein mutation | Alteration type | Chr. | Genomic coordinate | Reference Base | Altered Base | Coverage Ratio Tumor RNA seq | SNPs&GO prediction | PROVEAN prediction |
|---|---|---|---|---|---|---|---|---|---|---|---|
| GIST_11 | |||||||||||
| KIT | 11 | c.1669_1673del | p.557_558del | Non frameshift deletion | 4 | 55593601 | AGTGGA | - | 0.43 | NA | Deleterious |
| DDT | 2 | c.G280A | p.D94N | SNV | 22 | 24315961 | C | T | 0.72 | Deleterious | Deleterious |
| GNAI3 | 3 | c.G299C | p.R100T | SNV | 1 | 110116655 | G | C | 0.34 | Neutral | Deleterious |
| GIST_124 | |||||||||||
| KIT | 11 | c.1765-1766ins | p.589insQLPYDHWEFPRNR | Non frameshift insertion | 4 | 55593601 | - | CAACTATTCTATGACCACTGGGAATTTCCTAGGAACAGG | - | NA | Deleterious |
| CDKN2A | 2 | c.C247T | p.H83Y | SNV | 9 | 21971111 | G | A | 1.00 | Deleterious | Deleterious |
| FAM21C | 9 | c.T746C | p.M249T | SNV | 10 | 46245557 | T | C | 0.52 | Neutral | Deleterious |
| PCTP | 2 | c.G188A | p.C63Y | SNV | 17 | 53844742 | G | A | 0.59 | Deleterious | Deleterious |
| TRIM28 | 4 | c.T658C | p.F220L | SNV | 19 | 59058814 | T | C | 0.38 | Neutral | Deleterious |
| UBR1 | 32 | c.A3614G | p.N1205S | SNV | 15 | 43294798 | T | C | 0.59 | Neutral | Deleterious |
| AUP1 | 2 | c.75delG | p.L25fs | Frameshift deletion | 2 | 74756602 | C | - | 0.54 | NA | frameshift |
| GIST_131 | |||||||||||
| KIT | 11 | c.1706_1735del | p.569_578del | Non frameshift deletion | 4 | 55593638 | TGTTTACATAGACCCAACACAACT | - | 0.52 | NA | Deleterious |
| ZCCHC11 | 26 | c.A3965C | p.K1321T | SNV | 1 | 52902624 | T | G | 0.96 | Neutral | Deleterious |
| ALDOB | 5 | c.C524A | p.A175D | SNV | 9 | 104189780 | G | T | 0.55 | Deleterious | Deleterious |
| NRP1 | 5 | c.G800A | p.S267N | SNV | 10 | 33545258 | C | T | 0.45 | Deleterious | Neutral |
| POTEE | 15 | c.2387_2409del | p.796_803del | Frameshift deletion | 2 | 132021415 | TGGCTCCCGAGGAGCACCCCATC | - | 0.55 | NA | frameshift |
| GIST_150 | |||||||||||
| KIT | 11 | c.1651_1663del | p.551_554del | Non frameshift deletion | 4 | 55593583 | AACCCATGTATG | - | 0.99 | NA | Deleterious |
| ASUN | 9 | c.G923C | p.G308A | SNV | 12 | 27070633 | C | G | 0.60 | Neutral | Deleterious |
| KEAP1 | 4 | c.G1385A | p.G462E | SNV | 19 | 10600470 | C | T | 0.42 | Deleterious | Deleterious |
| KIAA0564 | 16 | c.C1874T | p.P625L | SNV | 13 | 42390907 | G | A | 0.50 | Neutral | Deleterious |
| TMEM8A | 4 | c.G509C | p.G170A | SNV | 16 | 427163 | C | G | 0.36 | Neutral | Deleterious |
| FNBP4 | 10 | c.1607_1608 ins | p.T536fs | Frameshift insertion | 11 | 47755656 | - | T | 0.94 | NA | frameshift |
| CSAD | 8 | c.745delC | p.L249fs | Frameshift deletion | 12 | 53552333 | G | - | 0.60 | NA | frameshift |
| GIST_174 | |||||||||||
| KIT | 11 | c.T1727C | p.L576P | SNV | 4 | 55593661 | T | C | 1.00 | Deleterious | Deleterious |
| LATS2 | 8 | c.C2809T | p.Q937X | Stop gained | 13 | 21549467 | G | A | 0.40 | Deleterious | Deleterious |
| PRPF31 | 12 | c.G1153C | p.E385Q | SNV | 19 | 54632438 | G | C | 0.47 | Neutral | Deleterious |
| PTEN | 7 | c.C697T | p.R233X | Stop gained | 10 | 89717672 | C | T | 0.69 | Deleterious | Deleterious |
| TOMM70A | 2 | c.T357A | p.N119K | SNV | 3 | 100105790 | A | T | 0.91 | Neutral | Deleterious |
| ZNF12 | 6 | c.C1864T | p.P660S | SNV | 7 | 6730595 | G | A | 0.71 | Neutral | Deleterious |
| GIST_178 | |||||||||||
| KIT | 11 | c.T1676A | p.V559D | SNV | 4 | 55593610 | T | A | 0.63 | Deleterious | Deleterious |
| CES1 | 7 | c.C852G | p.H284Q | SNV | 16 | 55853498 | G | C | 1.00 | Neutral | Deleterious |
| SGSM2 | 11 | c.A1247G | p.Y416C | SNV | 17 | 2268594 | A | G | 0.32 | Neutral | Deleterious |
| IL17RC | 19 | c.1835_1839del | p.612_613del | Frameshift deletion | 3 | 9974736 | CGCTG | - | 0.68 | NA | frameshift |
| GIST_188 | |||||||||||
| KIT | 11 | c.1690_1728del | p.564_576del | Non frameshift deletion | 4 | 55593609 | AATGGAAACAATTA.....CATAGACCCAACACAACTT | - | 0.51 | NA | Deleterious |
| KIT | 17 | c.T2466G | p.N822K | SNV | 4 | 55599340 | T | G | 0.46 | Deleterious | Deleterious |
| EAF1 | 2 | c.T155C | p.V52A | SNV | 3 | 15471471 | T | C | 0.54 | Neutral | Deleterious |
| HSPA1L | 2 | c.C1472T | p.T491I | SNV | 6 | 31778278 | G | A | 0.64 | Neutral | Deleterious |
| SHC1 | 5 | c.C368T | p.T233I | SNV | 1 | 154941023 | G | A | 0.42 | Neutral | Deleterious |
| TAPT1 | 14 | c.G1600T | p.E534X | Stop gained | 4 | 16165035 | C | A | 0.59 | Deleterious | Deleterious |
| TEF | 4 | c.G758A | p.R283H | SNV | 22 | 41791900 | G | A | 0.97 | Deleterious | Deleterious |
| CDKN1B | 2 | c.479delC | p.S160fs | Frameshift deletion | 12 | 12871762 | C | - | 0.85 | NA | frameshift |
| EIF4G3 | 9 | c.1277_1279del | p.426_427del | Non frameshift deletion | 1 | 21268200 | GAG | - | 0.97 | NA | Deleterious |
| TIMM22 | 4 | c.568_569ins | p.D190insDY | Non frameshift insertion | 17 | 904311 | - | ATT | 0.26 | NA | Deleterious |
NA=analysis not available for insertion or deletion