Table 2.

Loss of function (LOF) and deleterious variants (classified by Meta Likelihood Ratio Prediction [LRP]) in pancreatic cancer patients

Gene	Chrom	Location	rsID	Ref	Var	AA/protein change	Allele freq#	CDKN2A carrier	History of smoking: yes/no/unk	Family/Patient ID
Loss of function [stopgain, frameshift] variants:
ATM	chr11	108155142		AG		E1313fs	0	no	no	M595
ATM	chr11	108183151	rs587779852	G	T	E1978*	1.05E-04	no	unk	AJ7379
BRCA2	chr13	32914288	rs80359537	AT		H1932fs	0	no	yes	P153
PALB2	chr16	23646627	rs180177100	G	A	R414*	0	no	unk	AJ7379
Deleterious missense or inframe deletion variants classified by Meta LRP:
MSH2	chr2	47630331	rs267607911	A	G	M1V	0	yes	no^	LUMC6_019
MSH2	chr2	47637248	rs145649774	C	G	L128V	0.000349	yes	no	P147
MSH2	chr2	47641430	rs34136999,,	C	T	A272V	0.000581	no	no	P149
MSH6	chr2	48026852	rs376220212	G	A	R577H	0.000116	yes	no	P176
PMS2	chr7	6013076		G	A	P848L	0	no	unk	P1
PMS2	chr7	6022617	rs587780046	G	A	T671M	6.34E-04	no	yes	P282
CFTR	chr7	117171037	rs201958172	G	A	A120T	1.36E-04	yes	no	M402
CFTR	chr7	117171152	rs397508725	G	C	S158T	1.73E-05	yes	no	P61
CFTR	chr7	117243784	rs151048781	G	C	M952I	1.20E-04	no	yes	P115
CFTR	chr7	117250625	rs149279509	A	G	Y1014C	0.001	yes	unk	K_1001, K_1002
ATM	chr11	108122581		T	G	L542W	0	no	no	P268
ATM	chr11	108196797	rs567060474	G	A	A2274T	0.001	no	yes	P115
FANCA	chr16	89858430		CTT		E377del	0	no	yes	P282
TP53	chr17	7576911	rs145151284	G	C	T312S	8.99E-05	no	no	P268
BRCA1	chr17	41256266	rs28897673	T	C	Y105C	0.000116	yes	no, yes	LUMC19_013, LUMC19_016

^#Maximum allele frequency from public databases (see Supplemental Table 4 for details)

^{^}Extensive passive smoking exposure

Chrom, chromosome; Ref, referent allele; Var, variant allele; AA, amino acid; freq, frequency; unk, unknown