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Table 1 Summary of common polymorphisms and rare variants used for in vitro study

From: Resequencing the susceptibility gene, ITGAM, identifies two functionally deleterious rare variants in systemic lupus erythematosus cases

Variant Chromosomes from resequencing study with minor allele (total = 146) PolyPhen-2 SIFT
M441T 21 Benign (0) Tolerated (0.63)
A858V 33 Benign (0.001) Tolerated (0.35)
F941V 1 Probably damaging (1.00) Damaging (0)
G1145S 1 Benign (0.319) Tolerated (0.5)
  1. PolyPhen-2 [30] categorizes mutations as benign, possibly damaging, or probably damaging, based on pairs of false-positive rate (FPR) thresholds. SIFT [31] predicts variants to be deleterious, given an output value <0.05.