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