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Table 3 Significant exonic or splice site non-synonymous mutations of KEGG cell cycle genes by MutSigCV in KIT mutant GIST samples

From: Genomic aberrations in cell cycle genes predict progression of KIT-mutant gastrointestinal stromal tumors (GISTs)

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