A Comprehensive In Silico Analysis of the Functional and Structural Impact of Nonsynonymous SNPs in the ABCA1 Transporter Gene

Table 1

Structural and functional properties used by MutPred and PolyPhen2.

	PolyPhen2	MutPred
Sequence based properties
Bond annotation	X
Functional site annotation	X	X
Region annotation	X	X
PHAT score	X
PSIC score	X
SIFT score		X
Evolutionary attributes	X	X
Structural properties
Secondary structure	X	X
Solvent-accessible surface area	X	X
Phi-psi dihedral angles	X
Normalized accessible surface area	X
Change in accessible surface propensity	X
Change in residue side chain volume	X
Region of the phi-psi map (Ramachandran map)	X
Normalized B-factor	X	X
Ligand contacts	X
Interchain contacts	X
Functional site contacts	X
Molecular Recognition Fragments (MoRFs)		X