Accurate Prediction of the Functional Significance of Single Nucleotide Polymorphisms and Mutations in the ABCA1 Gene

Abstract

The human genome contains an estimated 100,000 to 300,000 DNA variants that alter an amino acid in an encoded protein. However, our ability to predict which of these variants are functionally significant is limited. We used a bioinformatics approach to define the functional significance of genetic variation in the ABCA1 gene, a cholesterol transporter crucial for the metabolism of high density lipoprotein cholesterol. To predict the functional consequence of each coding single nucleotide polymorphism and mutation in this gene, we calculated a substitution position-specific evolutionary conservation score for each variant, which considers site-specific variation among evolutionarily related proteins. To test the bioinformatics predictions experimentally, we evaluated the biochemical consequence of these sequence variants by examining the ability of cell lines stably transfected with the ABCA1 alleles to elicit cholesterol efflux. Our bioinformatics approach correctly predicted the functional impact of greater than 94% of the naturally occurring variants we assessed. The bioinformatics predictions were significantly correlated with the degree of functional impairment of ABCA1 mutations (r 2 = 0.62, p = 0.0008). These results have allowed us to define the impact of genetic variation on ABCA1 function and to suggest that the in silico evolutionary approach we used may be a useful tool in general for predicting the effects of DNA variation on gene function. In addition, our data suggest that considering patterns of positive selection, along with patterns of negative selection such as evolutionary conservation, may improve our ability to predict the functional effects of amino acid variation.

Disclosure of Selective Advantages in the “modern” Sublineage of the Mycobacterium tuberculosis Beijing Genotype Family by Quantitative Proteomics

“…Prediction of Protein Stability upon Mutation-Three independent algorithms were used to predict the effect of a previously described mutation (30) on the stability of Rv3283/sseA: PolyPhen-2 (58), I-Mutant3.0 (sequence mode) (59), and (Protein ANalysis THrough Evolutionary Relationships) PANTHER (60). The respective protein sequence was derived from tbdb.org (61), using the conversion of a glutamic acid residue to a lysine residue in position 276.…”

“…Functional Prediction of Amino Acid Residue Substitution in Rv3283/sseA-To investigate if the observed lower protein abundance of the protein Rv3283/sseA in modern Beijing strains could be caused by destabilization of the protein stucture by the altered amino acid at position 276, because of the nsSNP, reported to be specific for modern Beijing lineage strains (30), we applied the protein stability prediction programs, PolyPhen-2 (58) and I-Mutant3.0 (59) and the protein functionality prediction program PANTHER (60).…”

“…Finally, we predicted the functionality of the mutant and wild-type version of Rv3283/sseA using PANTHER (60). This software considers site-specific variation between evolutionary related proteins to calculate substitution position-specific evolutionary conservation (subPSEC) score.…”

The proportion of mutations predicted to have a deleterious effect differs between gain and loss of function genes in neurodegenerative disease

“…To convert the Panther results, a score of 0 to -3 is considered to be tolerated and a score from -3 to -10 is not tolerated. The value of -3 was chosen because it represents a probability of 0.5 of being damaging (Brunham, et al, 2005). Statistical analysis was performed using the SPSS version 11.0.1 software.…”

“…Another study used the SIFT database to examine whether mutations that were either supported or not by functional evidence were predicted to be tolerated or damaging (Ng and Henikoff, 2002). As well, the Panther program was used to analyze variants in the ABCA1 gene (MIM# 600046) (Brunham, et al, 2005). This gene has several common SNPs as well as causative variants which were assayed for functionality based on cholesterol efflux.…”