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. 2010 Jan 25;11(1):370–385. doi: 10.3390/ijms11010370

Table 2.

PolyPhen and TreeSAAP results for each missense polymorphisms used in the study. Each rare variant is defined by which part of the triglyceride phenotype distribution it was found (H = high, M = Middle, L= Low) according to Romeo et al. [3]. For the five common missense variants, Significant and NonSig (Nonsignificant) refers to phenotypic associations from the Treescan analyses. The Biological Assay column refers to assays in Table 3 of Romeo et al. [4]. A “-“ means no tests were performed. All significant PolyPhen predictions are in bold. All TreeSAAP properties considered significant with a score of 6 or more [13] are reported, all with an extreme value of 8 are in bold. The TreeSAAP property symbol key is provided below.

Missense Variant Phenotype Distribution Biological Assay PolyPhen Score PolyPhen Prediction TreeSAAP Property
M-1-T M - NA benign
P-5-L M - NA benign αc, αn, K0, Hp
E-40-K Significant - 1.424 benign pHi
M-41-I NonSig - 1.16 benign
S-67-R M - 1.563 possibly damaging
R-72-L M - 1.958 possibly damaging H, Hnc, αn
E-167-K L LPL Inhib 0.194 benign pHi
P-174-S M - 1.715 possibly damaging
E-190-Q NonSig - 0.243 benign
E-196-K M - 1.541 possibly damaging pHi, El
G-223-R L Secretion 2.065 probably damaging E’sm
R-230-C M - 2.792 probably damaging pHi, E’sm, Et, Br, Ns, C
F-237-V M - 2.51 probably damaging
P-251-T H Nothing 1.781 possibly damaging
T-266-M NonSig - 0.783 benign K0, Ht
R-278-Q Significant - 0.644 benign pHi
V-291-M M - 1.012 benign
L-293-M M - 1.236 benign
E-296-V M - 2.057 probably damaging Ns, , Br, H, Ra
P-307-S M - 0.955 benign αc
V-308-M M - 1.199 benign
R-336-C L Secretion 2.255 probably damaging Br, pHi, Et, Ns, C, Ca, Hnc
D-338-E M - 1.626 possibly damaging
W-349-C L Secretion 3.677 probably damaging
Ca, E’sm, Mv, Mw, Hnc, V0,
G-361-R L Secretion 2.274 probably damaging μ
R-371-Q H Nothing 1.558 possibly damaging pHi
R-384-W L Secretion 2.304 probably damaging Br, Ht
TreeSAAP Property Key
Alpha-helical tendency Molecular weight Mw
Average # of surrounding residues Ns Normalized hydrophobicity Hnc
Beta-structure tendency Partial specific volume V0
Buriedness Br Power to be at the C-terminal αc
Composition C Power to be at the N-terminal αn
Compressibility K0 Refractive index μ
Helical contact Ca Short-range & medium-range nonbonded energy E’sm
Hydropathy H Solvent accessible reduction ratio Ra
Isoelectric point pHi Surrounding hydrophobicity Hp
Long-range nonbonded energy El Thermodyn. transfer hydrophobicity Ht
Molecular volume Mv Total non-bonded energy Et