Table 3 Significant exonic or splice site non-synonymous mutations of KEGG cell cycle genes by MutSigCV in KIT mutant GIST samples
Hugo symbol | Number of patients | Samples | Variant classification | Variant type | Genome_change | Exon | Codon change | Protein change | Gene p value | Mean VAF | Range VAF |
|---|---|---|---|---|---|---|---|---|---|---|---|
RB1 | 1 | 17A | Splice_Site | DEL | g.chr13:48953728_48953729delAG | 14 | c.e14-1 | 1.31E−06 | 0.50 | 0.50 | |
RB1 | 1 | 10A, 10B | Splice_Site | SNV | g.chr13:49030485G > A | 19 | c.(1960–1962)Gtg > Atg | p.V654 M | 1.31E−06 | 0.52 | 0.18–0.86 |
RB1 | 1 | 14B | Nonsense_Mutation | SNV | g.chr13:48954195G > T | 15 | c.(1396–1398)Gaa > Taa | p.E466* | 1.31E−06 | 1.00 | 1 |
CUL1 | 1 | 14A, 14B, 14C | Missense_Mutation | SNV | g.chr7:148451142C > T | 3 | c.(214–216)tCg > tTg | p.S72L | 3.11E−04 | 0.54 | 0.41–0.54 |
TP53 | 1 | 2A, 2B | Missense_Mutation | SNV | g.chr17:7577548C > T | 7 | c.(733–735)Ggc > Agc | p.G245S | 3.66E−04 | 0.92 | 0.89–0.92 |
TP53 | 1 | 20A | Missense_Mutation | SNV | g.chr17:7573984A > G | 10 | c.(1042–1044)tTg > tCg | p.L348S | 3.66E−04 | 0.50 | 0.5 |
TP53 | 1 | 20A | Missense_Mutation | SNV | g.chr17:7577548C > A | 7 | c.(733–735)Ggc > Tgc | p.G245C | 3.66E−04 | 0.41 | 0.41 |
CDC27 | 1 | 8A | Missense_Mutation | SNV | g.chr17:45266534G > A | 1 | c.(4–6)aCg > aTg | p.T2 M | 2.00E−03 | 0.33 | 0.33 |
ANAPC1 | 1 | 15A | Frame_Shift_Del | DEL | g.chr2:112622408_112622409delCA | 8 | c.(805–807)tggfs | p.W269 fs | 7.36E−03 | 0.50 | 0.5 |
E2F3 | 1 | 10A, 10B | Missense_Mutation | SNV | g.chr6:20486985T > C | 5 | c.(949–951)gTt > gCt | p.V317A | 2.23E−02 | 0.34 | 0.19–0.49 |
GADD45A | 1 | 21A | Missense_Mutation | SNV | g.chr1:68153434G > A | 4 | c.(475–477)Gtg > Atg | p.V159 M | 4.88E−02 | 0.42 | 0.42 |
MAD2L2 | 1 | 15A | Missense_Mutation | SNV | g.chr1:11735761G > C | 9 | c.(454–456)aCg > aGg | p.T152R | 4.97E−02 | 0.77 | 0.77 |