Disease phenotypes and defects in function can be traced to nonsynonymous single nucleotide polymorphisms (nsSNPs), which are important indicators of action sites and effective potential therapeutic approaches. Identification of deleterious nsSNPs is crucial to characterize the genetic basis of diseases, assess individual susceptibility to disease, determinate molecular and therapeutic targets, and predict clinical phenotypes. In this study using PolyPhen2 and MutPred in silico algorithms, we analyzed the genetic variations that can alter the expression and function of the ABCA1 gene that causes the allelic disorders familial hypoalphalipoproteinemia and Tangier disease. Predictions were validated with published results from in vitro, in vivo, and human studies. Out of a total of 233 nsSNPs, 80 (34.33%) were found deleterious by both methods. Among these 80 deleterious nsSNPs found, 29 (12.44%) rare variants resulted highly deleterious with a probability >0.8. We have observed that mostly variants with verified functional effect in experimental studies are correctly predicted as damage variants by MutPred and PolyPhen2 tools. Still, the controversial results of experimental approaches correspond to nsSNPs predicted as neutral by both methods, or contradictory predictions are obtained for them. A total of seventeen nsSNPs were predicted as deleterious by PolyPhen2, which resulted neutral by MutPred. Otherwise, forty two nsSNPs were predicted as deleterious by MutPred, which resulted neutral by PolyPhen2. 1. Introduction Nonsynonymous single nucleotide polymorphisms (nsSNPs) are single base changes in coding regions that cause an amino acid substitution in the correspondent proteins. These missense variants constitute the most identifiable group of SNPs represented by a small (<1%) proportion [1]. The nsSNPs might alter structure, stability, and function of proteins and produce the least conservative substitutions with drastic phenotypic consequences [2–5]. Studies suggest that about 60% of Mendelian diseases are caused by amino acid exchanges [6]. Thousands of associations between Mendelian and complex diseases reveal a phenotypic code that links each complex disorder to a unique set of Mendelian loci [7]. Discriminating disease-associated from neutral variants would help to understand the genotype/phenotype relation and to develop diagnosis and treatment strategies for diseases. Nonetheless, the most important application is the evaluation of functional effect and impact of genomic variation, relating interactions with phenotypes translating the finding
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