Detection and analysis of common pathogenic germline mutations in Peutz-Jeghers syndrome

Table 10 Prediction of protein function changes caused by other gene mutations

Gene	SIFT		PolyPhen		Mutation Assessor
	Score	Prediction	Score	Prediction	Score	Prediction
BARD1	0	Deleterious	0.144	Benign	0.66939; 2.045	Medium
EGFR	0.4	Tolerated	0.956	Probably damaging	0.33485; 1.01	Low
GEN1	0	Deleterious	0.999	Probably damaging	0.34521; 1.04	Low
BRCA1	0.02	Deleterious	0.775	Probably damaging	0.78223; 2.4	Medium
NTRK1	0.01	Deleterious	0.639	Probably damaging	0.02685; -0.53	Neutral
PDGFRA	0.1	Tolerated	0.05	Benign	0.38838; 1.175	Low
TSC2	0.15	Tolerated	0.327	Benign	0.57536; 1.79	Low
MSH6	0.45	Tolerated	0.176	Benign	0.08118; 0	Neutral
EGFR	0	Deleterious	0.814	Possibly damaging	0.83953; 2.67	Medium
MTUS1	0.09	Tolerated	0.044	Benign	0.27053; 0.805	Low
PTCH1	0	Deleterious	0.7	Possibly damaging	0.88377; 2.95	Medium
SDHA	0.01	Deleterious low confidence	0.078	Benign	0.49699; 1.58	Low
MTUS1	0.01	Deleterious	0.096	Benign	0.29908; 0.895	Low
RECQL4	/	/	/	/	/	/
RECQL4	/	/	/	/	/	/
ATM	0	Deleterious	0.294	Benign	0.67953; 2.075	Medium
TSC2	0.01	Deleterious	0.226	Benign	0.08118; 0	Neutral
FANCG	0.03	Deleterious	0.018	Benign	0.14661; 0.345	Neutral
SBDS	0.12	Tolerated	0.051	Benign	0.71920; 2.185	Medium
VHL	0.06	Tolerated	0.012	Benign	0.19112; 0.55	Neutral
FANCA	0.24	Tolerated	0	Benign	0.02315; -0.6	Neutral
TP53	0.03	Deleterious	0.386	Benign	0.45228; 1.405	Low
FANCA	0.79	Tolerated	0.007	Benign	0.52573; 1.65	Low
PALLD	0.7	Tolerated	0.159	Benign	0.00602; -1.34	Neutral
MLH3	0.47	Tolerated	0	Benign	0.55103; 1.725	Low
SMARCA4	0.05	Deleterious	0.007	Benign	0.29908; 0.895	Low
NF1	0.62	Tolerated	0.015	Benign	0.08118; 0	Neutral
PTCH1	0	Deleterious	0.626	Possibly damaging	0.88377; 2.95	Medium
GALNT12	0.11	Tolerated	0.007	Benign	0.51422; 1.61	Low
ATR	0	Deleterious	0.998	Probably damaging	0.65975; 2.015	Medium
VEGFA	0.25	Tolerated low confidence	0.695	Probably damaging	0.08118; 0	Neutral
DIS3L2	0.05	Tolerated	0.996	Probably damaging	0.87328; 2.875	Medium
TSC1	/	/		/	0.00621; -1.32	Neutral
PTCH1	0.03	Deleterious low confidence	0.259	Benign	0.36672; 1.1	Low
BRIP1	/	/	/	/	/	/
WRN	0.59	Tolerated	0.164	Benign	0.70595; 2.14	Medium
RECQL	0.5	Tolerated	0.005	Benign	0.41079; 1.255	Low
BARD1	0.4	Tolerated	0	Benign	0.08118; 0	Neutral
USHBP1	0.05	Tolerated	0.521	Possibly damaging	0.56769; 1.78	Low
APC	0.16	Tolerated	0.82	Possibly damaging	0.46157; 1.445	Low
DICER1	0.29	Tolerated	0.664	Possibly damaging	0.34521; 1.04	Low
FANCM	1	Tolerated	0	Benign	0.40543; 1.245	Low
APC	0.57	Tolerated low confidence	0.003	Benign	0.14661; 0.345	Neutral
NSD1	0.03	Deleterious	0.684	Possibly damaging	0.66939; 2.045	Medium
SDHA	0.02	Deleterious low confidence	0.02	Benign	0.20574; 0.59	Neutral
MTUS1	0.87	Tolerated	0	Benign	0.12746; 0.255	Neutral
EXT2	0.03	Deleterious	0.993	Possibly damaging	0.82323; 2.585	Medium
ATM	0.58	Tolerated	0.007	Benign	0.56769; 1.78	Low
BRCA2	0.09	Tolerated	0.003	Benign	0.08118; 0	Neutral
TP53	0.94	Tolerated	0	Benign	0.03608; -0.345	Neutral
FLCN	0.03	Deleterious	0	Benign	0.47716; 1.5	Low
MSH2	0.25	Tolerated	0.023	Benign	0.39692;1.235	Low
KIT	0.15	Tolerated	0.472	Possibly damaging	0.03608; -0.345	Neutral
BAP1	0	Deleterious low confidence	0.968	Possibly damaging	0.59436; 1.845	Low
TSC2	0.02	Deleterious	0.446	Possibly damaging	0.75777; 2.31	Medium