Mutation analysis of related genes in hamartoma polyp tissue of Peutz-Jeghers syndrome

Table 5 Prediction of protein function changes caused by MSH6 and other gene mutations

Case No.	Gene	Polyphen-2_HDIV		Mutation Taster		FATHMM		M-CAP
		Score	prediction	Score	Prediction	Score	Prediction	Score	Prediction
3	MUTYH	0.069	Benign	1	Pathogenic	-2.41	Damaging	0.084	Damaging
3	MLH1	1	Probably_damaging	1	Pathogenic	-2.66	Damaging	/	/
3	PMS2	0.03	Benign	1	Polymorphism	1.06	Tolerable	/	/
4	MSH6	1	Probably_damaging	1	Pathogenic	-2.52	Damaging	0.292	Damaging
4	MLH1	1	Probably_damaging	1	Pathogenic	-2.66	Damaging	/	/
4	PMS2	0.239	Benign	1	Polymorphism	1.06	Tolerable	/	/
7	MLH3	1	Probably_damaging	1	Pathogenic	-2.37	Damaging	0.137	Damaging
7	AXIN2	0.121	Benign	0.997	Polymorphism	-0.25	Tolerable	/	/
9	MSH6	0.67	Probably_damaging	1	Pathogenic	-2.12	Damaging	/	/
9	APC	0.156	Benign	0.737	Pathogenic	-2.47	Damaging	0.046	Damaging
10	MSH2	0	Benign	1	Polymorphism	-2.29	Damaging	0.028	Damaging
10	MSH6	/	/	/	/	/	/	/	/
10	APC	1	Probably_damaging	1	Pathogenic	-1.53	Damaging	0.033	Damaging
14	MSH2	0.042	Benign	1	Pathogenic	-2.47	Damaging	0.075	Damaging
14	MSH2	/	/	/	/	/	/	/	/
14	PMS1	/	/	1	Pathogenic	/	/	/	/
14	PMS1	0.329	Benign	0.996	Pathogenic	-1.34	Tolerable	0.03	Damaging
15	PTEN	0.956	Probably_damaging	0.999	Pathogenic	/	/	/	/
19	MSH2	0.148	Benign	1	Pathogenic	-3.07	Damaging	/	/
20	MLH1	1	Probably_damaging	1	Pathogenic	-1.91	Damaging	0.247	Damaging