Table 2 Pathogenic/likely pathogenic mutations and gene copy-number variations identified in pancreatic ITPN and associated invasive carcinoma.

From: Integrative characterization of intraductal tubulopapillary neoplasm (ITPN) of the pancreas and associated invasive adenocarcinoma

ID case	Histology	TMB	MSI	Clinically relevant SNV					CNV
ID case	Histology	TMB	MSI	Gene	Variation	Mutation type	Freq (%)	Class	Gene	Variation	# of copies
1	Tubular	5.6	MSS	none					FGFR1	Gain	3.0
									RAD50	LOH	1.0
	Papillary	5.6	MSS	RNF43	c.571+1G>A	Substitution – splice site	13	4	FGFR1	Gain	3.4
									RAD50	LOH	1.0
2	Tubular	3.9	MSS	SMAD4	p.D415fs*20	Deletion – frameshift	27	5	NOTCH1	Gain	3.6
									CCNE1	Ampl	5.0
	Papillary	2.8	MSS	none					FGFR4	Gain	3.5
									CCNE1	Ampl	5.5
3	Tubular	11.7	MSS	EP300	c.3591-1G>A	Splice site variation	48	4	none
3	Papillary	13.9	MSS	EP300	c.3591-1G>A	Splice site variation	25	4	none
4	Tubular	10.0	MSS	none					NTRK1	Ampl	5.0
4	Papillary	10.0	MSS	none					NTRK1	Ampl	5.0
5	Tubular	7.8	MSS	TP53	p.Y220C	Substitution – missense	48	5	TP53	LOH	1.0
									NOTCH3	Ampl	5.0
									CCNE1	Ampl	29.0
	Papillary	7.2	MSS	TP53	p.Y220C	Substitution – missense	24	5	TP53	LOH	1.0
									NOTCH3	Gain	4.0
									CCNE1	Ampl	29.0
6	Tubular	6.6	MSS	none					None
6	Papillary	6.1	MSS	none					None
7a^a	Tubular	11.7	MSS	BRAF	p.V600E	Substitution – missense	35	5	NTRK1	Ampl	6.0
				APC	p.E1544*	Substitution – nonsense	5	5	STK11	LOH	1.0
				STK11	p.Q159*	Substitution – nonsense	51	5
	Papillary	11.7	MSS	BRAF	p.V600E	Substitution – missense	35	5	NTRK1	Ampl	8.0
				APC	p.E1544*	Substitution – nonsense	45	5	STK11	LOH	1.0
				STK11	p.Q159*	Substitution – nonsense	47	5
7b^a	AC	11.4	MSS	BRAF	p.V600E	Substitution – missense	21	5	NTRK1	Ampl	13.1
7b^a				STK11	p.Q159*	Substitution – nonsense	20	5	STK11	LOH	0.9
8	Tubular	11.6	MSS	none					MDM2	Gain	4.0
8	AC	11.0	MSS	none					MDM2	Gain	4.0
9	Tubular	5.6	MSS	KRAS	p.G12S	Substitution – missense	11	5	STK11	LOH + gain	3.1
				RUNX1	p.S318Ffs*282	Deletion – frameshift	12	5
				STK11	c.921-1G>C	Substitution – splice site	68	5
	Papillary	6.1	MSS	KRAS	p.G12S	Substitution – missense	14	5	STK11	LOH + gain	3.0
				RUNX1	p.S318Ffs*282	Deletion – frameshift	3	5
				STK11	c.921-1G>C	Substitution – splice site	57	5
	AC	6.7	MSS	KRAS	p.G12S	Substitution – missense	15	5	STK11	LOH + gain	3.0
				STK11	c.921-1G>C	Substitution – splice site	66	5
				ARID2	p.S1476Cfs*26	Deletion – frameshift	3	4
10	Tubular	3.9	MSS	POLE	c.4149+2dupT	Insertion – splice site	40	4
	Papillary	3.9	MSS	POLE	c.4149+2dupT	Insertion – splice site	42	4
	AC	3.3	MSS	POLE	c.4149+2dupT	Insertion – splice site	44	4
11	Tubular	7.2	MSS	KRAS	p.G12D	Substitution – missense	34	5	FGFR3	Ampl	6.5
				TP53	p.R248W	Substitution – missense	55	5	APC	LOH	1.0
				SMAD4	p.R445*	Substitution – nonsense	55	5	ERBB2	Ampl	10.3
									STAT3	Ampl	8.2
									AKT2	Ampl	14.6
	Papillary	8.3	MSS	KRAS	p.G12D	Substitution – missense	35	5	FGFR3	Ampl	6.5
				TP53	p.R248W	Substitution – missense	65	5	APC	LOH	1.0
									ERBB2	Ampl	9.6
									STAT3	Ampl	7.3
									AKT2	Ampl	9.9
	AC	9.4	MSS	KRAS	p.G12D	Substitution – missense	41	5	FGFR3	Gain	4.0
				TP53	p.R248W	Substitution – missense	47	5	APC	LOH	1.0
				ASXL1	p.Q1074*	Substitution – nonsense	5	4	ERBB2	Ampl	8.6
									STAT3	Ampl	6.5
									AKT2	Ampl	7.6
12	Tubular	12.7	MSS	KRAS	p.G12V	Substitution – missense	24	5	None
				TP53	p.L194H	Substitution – missense	59	5
				PALB2	p.E13K	Substitution – missense	22	4
				RB1	c.138-1G>T	Substitution – splice site	70	4
	Papillary	10.1	MSS	KRAS	p.G12V	Substitution – missense	11	5	NOTCH1	Gain	4.0
				TP53	p.L194H	Substitution – missense	60	5
				PALB2	p.E13K	Substitution – missense	21	4
				RB1	c.138-1G>T	Substitution – splice site	45	4
	AC	11.1	MSS	KRAS	p.G12V	Substitution – missense	20	5	None
				TP53	p.L194H	Substitution – missense	35	5
				PALB2	p.E13K	Substitution – missense	28	4
				RB1	c.138-1G>T	Substitution – splice site	52	4
13	Tubular	6.6	MSS	KRAS	p.G12D	Substitution – missense	34	5	CCND3	Ampl	9.0
				TP53	p.Y220C	Substitution – missense	35	5	NOTCH4	Ampl	9.0
									MDM2	Ampl	5.0
	Papillary	6.6	MSS	KRAS	p.G12D	Substitution – missense	44	5	CCND3	Ampl	9.0
				TP53	p.Y220C	Substitution – missense	42	5	NOTCH4	Ampl	9.0
									MDM2	Ampl	5.0
	AC	5	MSS	KRAS	p.G12D	Substitution – missense	10	5	CCND3	Ampl	9.0
				TP53	p.Y220C	Substitution – missense	10	5	NOTCH4	Ampl	9.0
									MDM2	Ampl	5.0
14	Tubular	6.5	MSS	BRCA2	p.Q2960*	Stop gain	85	5	MAX	Hom del	0.0
	Papillary	8.1	MSS	BRCA2	p.Q2960*	Stop gain	93	5	MAX	Hom del	0.0
	AC	6.7	MSS	BRCA2	p.Q2960*	Stop gain	54	5	NA^b
15	Tubular	8.3	MSS	BRAF	p.V600E	Substitution – missense	32	5	STK11	LOH	1.0
									NOTCH3	LOH	1.0
									JAK3	Gain	3.0
	AC	7.8	MSS	BRAF	p.V600E	Substitution – missense	32	5	STK11	LOH	1.0
									NOTCH3	LOH	1.0
									JAK3	Gain	3.0
16	Tubular	4.3	MSS	none					None
	Papillary	4.3	MSS	none					None
	AC	5.4	MSS	PBRM1	p.D554fs*4	Deletion – frameshift	13	4	None
	Liver met.	4.3	MSS	none					None

TMB tumor mutational burden, MSI microsatellite instability, MSS microsatellite stable, SNV single nucleotide variants, CNV copy number variations, AC adenocarcinoma, N/A not available, LOH loss of heterozygosity (1 copy), Gain >2 copies, Ampl amplification (>4 copies), met metastasis, Class clinical Impact class according to AMGP/AMP guidelines (5: pathogenic; 4: likely pathogenic; Richards et al. Genet Med 2015).
^a7a pancreatic resection for ITPN; 7b: local relapse as adenocarcinoma.
^bNeoplastic cellularity was too low for CNV analysis.

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Table 2 Pathogenic/likely pathogenic mutations and gene copy-number variations identified in pancreatic ITPN and associated invasive carcinoma.

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