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Table 3
Comparison of prediction programs with 15 functional variants
Chromosome	Nucleotide position	Reference nucleotide	Variant nucleotide	Gene	rs ID number	Amino acid change^a	PolyPhen-2	SIFT	MAPP	VarioWatch	Loss of function

2	138476119	C	T	HNMT	rs11558538	T105I	D	D	D	D	Yes
4	26092552	C	T	CCKAR	rs52795588	V365I	D	T	T	D	Yes
4	165337896	A	G	ANP32C	NA	Y140H	D	D	D	D	Yes
5	7923973	A	G	MTRR	rs1801394	I49M	D	D	D	D	Yes
7	5993056	C	T	PMS2	rs1805324	M622I	T	T	D	T	Yes
7	5993133	T	A	PMS2	rs1805318	T597S	T	T	D	T	Yes
7	127041823	G	A	PAX4	NA	R121W	D	D	D	D	Yes
7	127042702	G	A	PAX4	rs35155575	R37W	D	D	D	D	Yes
10	42930125	G	A	RET	rs1799939	G691S	D	T	D	D	No
10	72030393	G	A	PRF1	rs35947132	A91V	D	D	D	D	Yes
12	38989178	G	A	LRRK2	rs7133914	R1398H	D	T	T	T	Yes
12	39000112	G	C	LRRK2	rs33949390	R1628P	D	D	T	D	Yes
12	39043595	G	A	LRRK2	rs34778348	G2385R	T	T	D	D	No
13	32911463	A	G	BRCA2	rs1799944	N991D	T	T	D	D	Yes
19	15851431	C	T	CYP4F2	rs2108622	V433M	D	D	T	D	Yes

Correct predictions							11/15	10/15	9/15	10/15

This table highlights the 15 variants that were a gold standard in a functional study. ^a Position of the amino acid change associated with the nucleotide change.
Jaffe et al. BMC Proceedings 2011 5(Suppl 9):S13 doi:10.1186/1753-6561-5-S9-S13

Table 3