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A comprehensive in silico analysis of the functional and structural impact of nonsynonymous SNPs in the ABCA1 transporter gene.

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 mis-sense 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 into medical practices.

ATP-binding cassette transporter ABCA1 gene also known as the cholesterol efflux regulatory protein (CERP) encodes a 220 kDa protein [8]. This protein is crucial for reverse cholesterol transport and is considered as an important target in antiatherosclerosis treatment. ABCA1 mediates the efflux of cholesterol and phospholipids to lipid-poor apolipoproteins (apoA1 and apoE), which form nascent high-density lipoproteins (HDL). ABCA1 resides on the cell membrane and has an extensive intracellular pathway, with rapid movement of the transporter between the cell membrane and intracellular vesicles [9]. ABCA1 is present in higher quantities in tissues that transfer or are involved in the turnover of lipids such as the liver, the small intestine, and adipose tissue [10-12]. As well, lipid export activity of ABCA1 improves the function of pancreatic cells and ameliorates insulin release [13], reduces biliary cholesterol content protecting against gallstone [14], and plays a key role in lipid homeostasis in the lung [15]. Besides, evidence suggest a causal link-between ABCA1 as cholesterol transporter and its antitumor activity [16,17], as well as its implication in brain cholesterol homeostasis [15-20] founding lipid and myelin abnormalities in schizophrenia and Alzheimer's disease [18-20].

Although theentireABCA1 protein 3D-structure remains unknown electron microscopic studies suggest a structural model consisting of a transmembrane domain (TMD) and a nucleotide-binding domain (NBD) (Figure 1) [14, 21, 22], where an NBD-TMD dimer is the minimum unit required for transport function [22, 23]. Also, X-ray structures are available for different domains in the C-terminus protein essential for lipid efflux activity [24, 25]. Many variants disrupting the normal ABCA1 protein function result in modest or no circulating HDL [26-32]. Cholesterol accumulated within cells produces a toxicity that impairs cell function leading to a diversity of phenotypes, from severe disease states to mild impacts on health. In fact, the ABCA1 variability is associated with myocardial infarction, cancer, type 2 diabetes, and metabolic syndrome [33]. Heterozygous states, nearly one-third of them, are associated with hypoalphalipoproteinemia, known as familial HDL deficiency syndrome (FHA). Two copies cause a more severe syndrome Tangier disease (TD) [34-38] described by reduced HDL-c plasma level (<5%), impaired cholesterol efflux, and a trend to accumulate intracellular cholesterol [34-43]. Indeed, loss of function of ABCA1 mutations in TD patients has a major impact on lipoprotein metabolism. A failure to acquire apolipoproteins leads to a rapid catabolism of lipid-poor apoA1 and accumulation of lipids in macrophages, intestinal cells, platelet, and hepatocytes [34-38, 44]. Compared with unaffected family members, heterozygotes and homozygotes have a more prevalent, premature, and severe atherosclerosis [42].

Because high levels of HDL-c are atheroprotective there is considerable interest in developing agents that act to increase ABCA1 expression and thereby raise plasma HDL-c levels. The nsSNPs are important indicators of action sites and effective potential therapeutic approaches. Therefore, it is crucial to identify deleterious nsSNPs to characterize the genetic basis of diseases, assess individual susceptibility to these diseases, determinate molecular and therapeutic targets, and predict clinical phenotypes. Beyond the genetic level, a disease depends on the sequence and the structural location of the nsSNPs of the protein. While the nsSNPs occur all through the ABCA1 gene, they tend to cluster in the extracellular loops, the NBD, and the COOH-terminal region (Figure 1). In fact, three structural motifs have been functionally associated with disease: the ARA motif, an interface between NBD and TMD that forms a partially buried a-helix able to interact with the transmembrane helices, the conserved-loop 1, a allosteric loop between the membrane and globular domains, and the conserved-loop 2, an interaction surface for intracellular partners, critical in ATP-binding.

Even though many of nsSNP (rare or common) found in human ABCA1 have been identified, mainly in the HapMap project (http://hapmap.ncbi.nlm.nih.gov/), the molecular bases relating these variants and the caused phenotypes have not been studied in detail. To explore the effect of the large number of nsSNPs ABCA1 by experimental approaches would be extremely time-consuming and with low statistical chance. Alternatively, bioinformatic approaches, based on the biophysical severity of the amino acid exchange and the protein sequence and structural information, can offer a more feasible phenotype prediction. As such, MutPred (mutation prediction) [45] andPolyPhen2 (polymorphism phenotyping 2) algorithms [46], were used in this study to investigate the impact of all known nsSNPs on ABCA1 protein function. Besides, based on the results of in vitro, in vivo, and human studies of this gene in the literature we validated the predictions made by reviewing the effect of the most critical nsSNPs in ABCA1 gene and its pathological consequences.

2. Methods

Figure 2 shows the workflow designed to predict the nsSNPs effect on ABCA1 protein. ABCA1 human gene variants including SNPs, short insertions, and deletions were retrieved from Ensemble Variation 72 database 3141. Mutations were annotated using the SnpEff v3.2 toolbox [47] based on the human genome assembly GRCh37.68. Only variants found on the canonical transcript were considered for functional effect prediction, for what we used two different algorithms. PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/) algorithm uses a naive Bayesian classifier to predict allele function based on a combination of sequence and structure-based attributes (if available) [46]. It calculates the probability for a given mutation to be benign, possibly damaging, or probably damaging. Then, we used MutPred (http://mutpred.mutdb.org/) [45] based upon SIFT algorithm [48] and a gain/loss of 14 predicted structural and functional properties. The predicted mutation outcome is based on a random forest (RF) classifier. The MutPred output includes the top 5 property scores and a general score (RF) equal to the probability of amino acid exchange is either deleterious or disease-associated. The ROC curves for both methods were generated using R programming language and the ROCR package (Figure 3) by a variation dataset obtained from VariBench (http://structure.bmc.lu.se/VariBench/) that contains mutations affecting protein tolerance including a neutral set of mutations comprising 17393 human coding nsSNPs and a pathogenic set of 14610 missense mutations obtained by manual curation from the PhenCode database.

Prediction accuracy accomplished by MutPred and PolyPhen2 depends on their specific criterion. Twelve structural and six sequence-based properties were used in this study (Table 1). About 28% of validated nsSNPs in the Human Genome Variation Database are predicted to affect protein function [49]. Similarly, about 25% of nsSNPs affecting protein activity was predicted by PolyPhen2 [49]. MutPred offers classification accuracy with respect to human disease mutations. Considering conservative thresholds on the predicted disruption of molecular function, MutPred generates accurate and reliable hypotheses on the molecular basis of disease for about 11% of known inherited disease-causing mutations [45].

Our MutPred and PolyPhen2 predictions were validated by comparing them with previously obtained results from in vitro, in vivo, and human studies of ABCA1 gene in the databases and literature. When a given nsSNP found experimentally to be associated with a remarkable change of phenotype such as altered transporting activity or a disease was predicted by in silico methods as deleterious, it was considered that the prediction on this nsSNPs was correct. The prediction was defined as an error if such a deleterious nsSNP was predicted as tolerant.

3. Results and Discussion

The importance of ABCA1 in cholesterol efflux was demonstrated by the identification of ABCA1 mutations in TD and FHA families [34-38]. This has produced extensive research into the possibility to provide protection from atherosclerosis by increasing ABCA1 expression and thereby to raise plasma HDL-c levels. The identification of the large number of alleles for this transporter gene as target directly involved in HDL-c regulation constitutes a significant therapeutic strategy in reducing the risk for atherosclerosis.

3.1. Accuracy of the Prediction of the Functional Impact of nsSNPs. Out of a total of 3141 SNPs in ABCA1 gene retrieved from dbSNP, we found 233 nsSNPs, 126 sSNPs, 59 mRNA 37UTR SNPs, 12 mRNA 5'-UTR SNPs, and 2543 intronic SNPs (Figure 4). Among the 233 nsSNPs, MutPred (RF score > 0.5) predicted 122 (52.36%) as deleterious whereas PolyPhen2 (pph2_prob > 0.5) identified 97 (41.63%) as potentially damaging and damaging. Then, once that MutPred was used to predict the nsSNP disease-association probability, the damaging probability of nsSNPs was validated by PolyPhen2. A total of 80 (34.33%) nsSNPs were found to be deleterious by both methods. Among these 80 deleterious nsSNPs, the 29 (12.44%) targeted (MAF/NA) that resulted with high pathological phenotype (probability > 0.8) are C1477R, W590L, W590S, A1046D, N1611D, M1091T, F2009S, N935H, R2081W, R1068H, N935S, R1068C, D1099Y, D1099N, W1699C, W840R, A937V, I1517R, C1660R, R1680W, P1065S, R1615P, T929I, Y2206D, L1379F, T940M, G1216V, Y2178H, and R1680Q. As shown in Table 2, a good correlation index was obtained between the scores observed from the evolutionary-based approach MutPred and the structural-based approach PolyPhen2. As shown in Figure 5, the overall correlation of the predictions made by both methods is high (~0.57). The majority of mutations classified as pathogenic by PolyPhen2 with the highest score (=1) are also classified as pathogenic by MutPred but within a score range between 0.51 and 1. The prediction accuracy depends not only by limitations of the in silico algorithms such as false positive error and interference of redundant motifs but also by the phenotype data from experimental studies [3].

Equally important is to consider the incorrect predictions in order to know the limitations of both algorithms and to suggest how they might be improved. Where MutPred predicts P2150L variant as deleterious, PolyPhen2 indicates a benign amino acid exchange. Conversely, MutPred predicted P85L to be probably damaging, while PolyPhen2 indicates it as neutral. Conflicting results were observed for a few other nsSNPs included in Table 2. A total of seventeen deleterious nsSNPs predicted by PolyPhen2 resulted neutral by MutPred. In contrast, forty two deleterious nsSNPs by MutPred result neutral by PolyPhen2. We have observed (Figure 5, Table 2) that some mutational characteristics of nsSNPs such as C1477F, R666Q, P1475S, G616V, Q2210H, V1806M, and V304M show high PolyPhen2 values but very low MutPred scores due, at least in part, to loss or gain of catalytic residues and disorder and gain of ubiquitination and phosphorylation to the protein. On the other hand, some mutational characteristics of nsSNPs included T459P, A2028V, T774P, Q1279K, N1185K, D917N, E1005K, C887F, D1289N, Q188K, D462G, M1012I, R965C, S1181F, A255T, D457E, R496W, R1341T, R1925Q, R230C, L184S, R999L, and K1974R with low PolyPhen2 values but high MutPred scores produce, however loss of solvent accessibility and of disorder, gain of phosphorylation, and both loss and gain of molecular recognition features (MoRFs) binding, loss and gain of methylation, and loss and gain of helix structure. Both, loss and gain of catalytic residues are actively involved in human inherited disease. Also, the small ubiquitin--a 76 residue [beta]-grasp protein--is about 95% conserved from yeast to human. Overall, both gain and loss of a phosphorylation site in a target protein may be important features for predicting cancer-causing mutations and may represent a molecular cause of disease for a number of inherited and somatic mutations. Changes in secondary structure impair large functional alterations, as well as the solvent accessibility degree. Therefore, inaccurate predictions occurred at these sites could be explicated not only for the limited effects of genetic variant but also for gene-environment interactions. Since the MutPred is based on a predicted structure of the protein under study rather than a solved structure as PolyPhen2 and considering the fact that nowadays the ABCA1 protein structure is only partially solved, it makes sense to prioritize the MutPred predictions. This fact was confirmed after evaluating the performance of both methods using a curated nsSNPs dataset with known outcome as a benchmark as shown in Figure 3. We have also observed that mostly, nsSNPs with verified functional effect in experimental studies are correctly predicted as damage variants by MutPred and PolyPhen2 tools. Still, controversial experimental data are obtained for those nsSNPs predicted as neutral by both of these methods.

3.2. Functional Assessment of ABCA1 Variants. Disease-causing variants are under strong selective constraints, which determines if mutation frequency will increase, decrease, or change randomly during evolution. Most alterations are delseterious and so are finally removed during purifying selection. Benign mutations can sweep through the population and become fixed contributing to species differentiation. The ABCA1 gene is highly conserved between species. Human ABCA1 is 95.2% identical to mouse, 85.3% to chicken, 25.5% to drosophila, 21.6% to C. elegans, and 10.2% identical to fugu. In humans, there is an abundance of common nsSNPs that disrupt sites highly conserved across species and likely to be deleterious [50]. The information of nsSNPs can be used to outline the migration patterns of ancient humans and the ancestry of modern humans. Causal nsSNPs in single gene disorders are sufficient to impart large effects. Instead, complex traits are due to a much more complicated system of causative mechanisms that in aggregate increase the probability of disease. Genome-wide association studies reveal common genetic variants effects (common disease/common variant hypothesis) in complex traits. However, where common nsSNPs account for a relatively slight heritability of the traits, rare variants might produce large effects on the phenotype (rare variant/common disease hypothesis). The frequency range includes alleles that are exceptionally rare and even unique to an individual genome to be extremely common. Most deleterious nsSNPs are retained at low-population frequencies due to negative selection. Thus, variants with large effect tend to be rare and those that exert weak effects are more common. It is worthy to note that rare alleles can also have weak effect or no effect. A specific locus may contain numerous rare alleles, so there may be many rare variants with large effect and a few common variants with weak effects. Although it has not yet been possible to determine whether other variables are associated with specific nsSNPs frequencies, variants within metabolic genes are not randomly distributed along the human population but follow diverse ethnic and/or geographic-specific patterns. It has been reported [51] that a significant proportion (~16%) of individuals with low HDL-c from the general population has the rare sequence of 25 variants in ABCA1 gene (Table 2, MAF [less than or equal to] 0.01). However, consistent with MutPred and PolyPhen2 only nine of them, N1800H, W590L, S1731C, C1477R, D1706N, R1615P, R638Q, T2073A, and A1670T, are predicted as functionally impaired. Some deleterious mutations from some other genes have reached intermediate to high frequencies. Specifically, the ancestral APOE4 allele, remains higher in populations like Pygmies (0.41), Khoi San (0.37), Papuans (0.37), some Native Americans (0.28), Lapps (0.31) and aborigines of Malaysia (0.24), and Australia (0.26) [52]. The exposure of APOE4 to the current environmental conditions could have rendered it a susceptibility allele for cardiovascular and Alzheimer diseases. However, the prediction for variant within ABCA1 gene indicates lack of harmful alleles to MAF [greater than or equal to] 0.01. Therefore we have evaluated and contrasted the predictions made for nsSNPs (rare/common) most widely studied for their role in cholesterol pathway by reviewing the effect of the most significant nsSNPs in ABCA1 gene and its pathological consequences.

3.2.1. Accurate Prediction of the Functionally Deleterious nsSNPs in the ABCA1 Gene. The N1800H ABCA1 has been fully characterized showing a complete lack of protein function in terms of cholesterol efflux and HDL production [53, 54]. Unlike the WT (wild-type), which is found at the endoplasmic reticulum and plasma membrane, N1800H is accumulated intracellularly [54]. Even similar physicochemical properties (polar, medium size) of exchanged residues the N1800H nsSNP, located between transmembrane domains [54], is a critical site for protein function. Scores from in silico methods predict the N1800H variant as highly deleterious.

The W590L was never studied, but the W590S ABCA1 variant affecting the same position is extensively known [54]. Distribution of W590S is identical to WT [55] as well as apoA1 binding activity [54-57]; however it shows defective lipid transport [54, 56, 58, 59]. Since multiple alignments often show a leucine residue in this position, it could be assumed that W590L had a similar behavior or even a lower impact than W590S on the protein function. Both W590S and W590L were predicted as deleterious nsSNPs with loss of functionality.

Studies indicate that S1731C variant alters the activity of ABCA1 protein [27, 51, 60]. This allele is present in French-Canadian families with low HDL-c levels [27] but not in subjects with normal [60] or high 51] HDL-c levels. Compared with WT, heterozygous show decreased ~60% the cholesterol efflux activity [27, 51, 61]. Interestingly, some but not all families harboring S1731C also carried the 2144X stop mutation [60] able to produce the most severe effects on HDL-c levels and on cholesterol efflux [62]. These data along with our in silico predictions indicate that conserved S1731C is highly likely to affect protein function.

S1506L, Q597R, are linked to TD variants are linked to TD and FHA and found in tumor cancer [54]. Normal function of ABCA1 inhibits tumor growth in human cancer cells [54]. However, although expressed to similar levels as WT, these alleles show deficient cellular cholesterol efflux and HDL production and do not decrease tumor growth [17]. The three are located intracellularly but C1477R is also found in membrane [54], which indicates that membrane localization is essential but not sufficient for apoA1 binding [54, 63]. In fact, ApoA1 binds to ABCA1 protein oligomers but not with monomers [64]. Thus, conformation changes in binding sites might be produced by these nsSNPs found as deleterious by our in silico analysis.

The R587W reaches the cell surface but reduces the apoA1 binding efficiency ~50% [56]. Others studies indicate that this allele is mainly retained intracellularly decreasing cholesterol efflux and apoA1 binding ~75% [54]. Severe HDL deficiency [34] and premature CVD is caused by R587W [65]. This variant is highly conserved during evolution, and the in silico analysis predicts it as strongly damaging and disease-associated. Besides to be related with TD, the R587W as well as W590S variants are linked to AD. As the WT, these mutants significantly reduce A[beta]-peptide synthesis ~45% [66], but increase by ~2-fold (R587W) and by 25% (W590S) amyloid precursor protein intracellular domain, a major cytotoxic of AD [66].

The A1046D, localized between conserved motifs [54, 67], shows an intermediate phenotype caused by its limited presence in the plasma membrane. This variant shows reduced apoA1 binding efficacy, poor HDL-c, and folding protein alteration. Both in silico methods predict A1046D as a functional residue with a probability to be deleterious very close to 1.

According to literature, N1611D is associated to probable atherosclerosis [62, 68]. The mutated protein expression was comparable to WT although cholesterol efflux from the cells was markedly reduced. Our theoretical results indicate very high probabilities of this nsSNP being deleterious, which indicate an adverse and potential harmful effect on ABCA1 function.

The M1091T variant exerts a dominant-negative impact on ABCA1 function with severe phenotype observed in subjects carrying this variant [42, 54, 62]. It is retained intracellularly preventing the protein from reaching the membrane [54]. In heterozygous, M1091T is lowered by 50% HDL and inhibits apoA1 binding and cholesterol efflux [54]. From evolutionary path, the inherited residue at this position has been methionine. Among related homologues ABCA2 and ABCA4 share a methionine at this position, while ABCA7 substitutes a leucine. Consistent with this fact, ABCA1 and ABCA7 are functionally divergent, with ABCA7 easing the efflux of phospholipids but not cholesterol [69]. Despite the modest conservation at this position, located in a critical cluster at the C-terminal region, in silico data suggest a severe-negative impact.

The F2009S is conserved between human and mouse, that along with the exchange from large size and aromatic (F) to small size and polar (S) explicates its reduced cholesterol efflux, low HDL-c, andapoA1 levels [70]. The functional effect produced by F2009S variant is consistent with our prediction made by PolyPhen2 and MutPred indicating a deleterious mutant.

The N935S variant is found intracellularly [54] in subjects without risk of premature atherosclerosis but with extremely low levels of HDL and signs of severe dementia and amyloid depositions in the brain [71,72]. This variant was predicted as deleterious by the used methods.

R1068H mutation is located within the first ATP-binding domain. It is identified in TD homozygous [73]. Since the R1068H mutation is likely to produce a dysfunctional protein, one would expect it to be associated with FHA in the heterozygous state [73]. Residue R1068 is located in an [alpha]-helix of the Walker B motif in the NBD, vulnerable to interaction with D1092 and E1093 [74]. Homology modeling of the ABCA1 protein showed that the R1068H mutation disrupts the conformation of NBD. Functional studies of R1068H showed a lack of cholesterol efflux activity due to defective transference to the plasma membrane, mainly caused by impaired oligomerization [74]. The in silico analysis predicts a high possibility for R1068H to be damaging. Besides, a different mutation of this position, R1068C, predicted as a deleterious by our methods, has been reported in a compound heterozygote with almost no HDL [31].

D1099Y is located at possible interaction site and exchanges the medium size and acidic residue to the large and aromatic tyrosine. Surface residues not at defined interfaces are usually preserved. Still, a moderate to highly conserved domain on the surface of the structure includes this nsSNP, which is associated to familial HDL deficiency [70, 75] and predicted as deleterious in our analysis.

The W1699C, located within the transmembrane domain, is accumulated within the cytoplasm and a small proportion reaches the plasma membrane [76]. It introduces a cysteine residue, which stimulates the formation of a new disulphide bridge able to disrupt the ABCA1 protein structure preventing its oligomerization and transference to the plasma membrane. Probably, W1699C retains some residual functions, as shown by the plasma HDL-c levels found in members carrying this mutation which were not as low as might be expected in carriers [76]. In silico analysis with PolyPhen2 and MutPred indicate a deleterious effect of this nsSNP on ABCA1 function.

3.2.2. Controversial Results for Prediction of the Neutral nsSNPs in the ABCA1 Gene. The mutant R1897W that induces a change from basic (R) to aromatic (W) is predicted functionally neutral in this analysis. This variant was identified in the mother and the brother of an FHA patient, who had plasma HDL levels in the lower range of the normal values 77].

Both the D1289N and P2150L variants identified in TD patients are considered as disease causative [42, 78, 79]. Further experimental evidences disagreeing with these results suggest that both could be nonfunctional variants [51,54,80]. Indeed, they showed a lipid transport activity, apoA1 binding, and distribution similar to WT [54,80]. Interestingly, P2150L is only found in patients who also harbor a second variant, the deleterious R587W described above [54]. Besides, TD patients with D1289N variant were homozygous for a second mutation R2081W that could cause the shown pathological phenotype [79]. R2081W is missed at the plasma membrane and instead accumulated intracellularly [54]. Our results suggest that mutations R2081W and R587W are highly deleterious. For D1289N and P2150L variants, PolyPhen2 predicts a neutral impact on protein function contrary to MutPred predictions that indicates a high probability for these mutants to be deleterious. The positions 1289 and 2150 are conserved among all ABCA1 orthologs but with the close-related ABCA7 and ABCA4. Since conservation patterns in ABCA1 protein endure for a relatively short time in evolutionary path, it is hard to determine if the conservation at these positions is due to functional constraint or simply reflects random chance. Along with experimental data, this suggests that R2081W is a major responsible of ABCA1 protein dysfunction found in TD patients.

The rare R219K polymorphism is located on an N-terminal extracellular loop, which mediates ABCA1 protein interaction with apoA1 [39, 56, 58, 59]. Despite high number of case-control studies conducted to investigate the functionality of R219K variant the results have been inconclusive [60, 81-83]. While some reports suggest an association of R219K is with risk of CVD [84], other research indicates a decreased atherosclerosis progression in general population [60, 85]. Conversely, large prospective studies found no association with HDL-c levels or atherosclerosis susceptibility [82,86]. A meta-analysis indicates that R219K polymorphism is protective against CVD in Asians but not in Caucasians [87]. Unexpectedly, the K219 allele was associated with a decreased risk of myocardial infarction [18, 60, 84]. Also, this variant has effect on triglycerides [60] but not with HDL-c [84] or with apoAl levels [85]. Otherwise, a study indicates that blood lipid levels do not seem to be R219K dependent [88]. Whether this variant confers major susceptibility to CVD is for clarification. The association of R219K variant to risk of AD has been studied in diverse ethnic groups [18-20, 89, 90]. Although conflicting results were noted, a study observed a protective dependence in delaying the risk of late-onset AD [18]. Equal to other cases, experimental results inconclusive and contradictories result prediction of the R219K polymorphism was predicted to be neutral in our in silico analysis.

Some studies [60, 91-93] but not all 39, 94] indicate that I883M variant severely increases the risk of atherosclerosis and AD [20]. The I883M has been reported as a milder phenotype with a significant reduction of HDL-c and cholesterol efflux (~70% of WT) [51]. In contrast, others studies [28, 60, 82, 83, 88] did not find any difference in lipid levels in I883M carriers. Studies among different healthy people [95, 96] as well as population with T2D [97] correlated the I883M variant with higher HDL-c concentration. Also, a stepwise regression approach identified I883M as one the key predictors of ischemic heart disease, whereas additive effects were found for V771M/I883M and I883M/E1172D pairs [82, 98]. As well, several studies have reported associations between V825I/I883M and increased plasma HDL-c levels [39,67,99]. Despite the controversial experimental results on the influence on cholesterol efflux activity observed of this polymorphism, our data predict that the I883M variant is functionally neutral. Interestingly, both alleles are found in the human population and the minor allele, methionine, is likely to be the ancestral allele at this position. Along with the human ABCA1orthologs, murine aligns valine at this position and the chimpanzee sequence aligns methionine. This divergence could explain why a simple conservation-based approach predicts the I883M change as neutral.

The R1851Q variant exchanges the large size and basic arginine (R) residue to medium size and polar glutamine predicted deleterious by MutPred and neutral by PolyPhen2. R1851Q occurs within the extracellular loop proximal to the transmembrane [68, 100]. Heterozygotes states show low HDL-c and apoA1 levels compared with those related to WT protein.

The R230C variant, found in Native American groups but not in European, Asian, or African individuals, has been associated with low levels of HDL-c and apoA1 [101]. These results are confirmed after adjusting for gender, BMI, and waist circumference [102]. Besides, the C230 allele is associated with obesity, metabolic syndrome, and T2D in Mexican population [101]. Still, R230C may have conferred resistance against certain infectious diseases [101]. R230C has been reported as a rare variant causing FHA in an Oji-Cree individual [67]. MutPred predicts a high probability of functional impairment of R230C, while that the PolyPhen2 program predicts the variant as neutral. Other facts that suggest functionally damage are (1) R230C occurs at the first extracellular loop, where TD and FHA mutations are clustered; (2) the arginine at position 230 is conserved between species; and (3) very different nature of residues involved; whereas arginine is basic and hydrophilic, the hydrophobic cysteine is vulnerable to disulfide bond.

The variants, R1901S that induces a change from large size and basic (R) to small size and polar (S); Q2196H that exchanges residues with similar physicochemical property (medium size, polar); and E284K that exchanges a medium size and acidic (E) to large size and basic (K), are predicted to be deleterious by MutPred and neutral by PolyPhen2. The R1901S and Q2196H variants occur within the C-terminal domain, close to the NBD, and E284K was located in the first extracellular loop, all of them associated to FHA [76]. The A594T, I659V, T1512M, and R2004K polymorphisms display different degrees of mislocalization to the plasma membrane and slight impacts on cholesterol efflux [103]. These nsSNPs were identified in low-HDL subjects [29]. The A594T, I659V, and T1512M were predicted to be functionally neutral and the R2004K mutation possibly damaging [29]. Finally, the novel mutation (P85L) in ABCA1 was identified in one family with low HDL but was not detected in over 400 chromosomes of healthy subjects [104]. Our in silico prediction indicated this variant as possible damaging by MutPred and neutral by PolyPhen2.

4. Conclusion and Future Directions

The practice of medicine, including health promotion and disease prevention, is primarily based on phenotype-based approaches. Most of them are proximal phenotypes achieved through biochemical markers. Finding genetic determinants of the phenotypes could not only clarify biological and functional consequence of variants but also might translate and extend to clinical phenotype. This focus would consider the large locus heterogeneity and numerous nongenetic factors to contribute to the phenotype. Since high levels of HDL-c are atheroprotective, there is extensive interest in developing agents that enhance ABCA1 expression and thereby raise plasma HDL-c levels. Amino acid exchange variants are crucial indicators of action sites and effective potential therapeutic approaches. In fact, nsSNPs represent disease modifiers capable of altering drug/nutrient response and potential targets vulnerable to environmental factors.

Evaluation of 233 nsSNPs (rare or common) found in ABCA1 transporter indicates that the rare 29 (12.44%) of them resulted to be highly deleterious with a probability >0.8. From 20 sequence variants found in about 16% of individuals with low HDL cholesterol only nine of them, D1706N, R1615P, W590L, C1477R, N1800H, R638Q, T2073A, A1670T, and S1731C, were predicted by MutPred and PolyPhen2 as functionally impaired. We have observed that mostly nsSNPs with verified functional effect in all experimental studies made are correctly predicted as damage variants by MutPred and PolyPhen2 tools. However, controversial experimental data are obtained for those nsSNPs predicted as neutral by both methods. Presumably clinical phenotype is the result of the additive effects and interactions among multiple alleles with different effect degree. Multiple rare alleles in ABCA1 contribute to plasma HDL-c levels in the general population.

Predicting the phenotypic consequence of nsSNPs using computational algorithms provides a better understanding of genetic differences in susceptibility to diseases and drug/ nutrient response. These methods predict whether an amino acid altering mutation is deleterious or disease-causing based on physicochemical properties, population frequency, protein structure, and cross-species conservation. However, computational prediction tools are generally based on machine learning algorithms, which need to be trained before classifying a mutation as either neutral or deleterious. A major obstacle of these approaches is the lack of experimentally validated and impartial data sets. A further complication is that mutations in highly conserved sequences do not always produce phenotypes that are easily noticeable. Besides, knowledge of protein structure is crucial to accurately predict functional nsSNPs and understand their linkage with disease. Severe limitation arises thus when protein 3D-structure is not available as the ABCA1 case. Thus, an accurate, efficient, and generally applicable approach is needed to establish a genotype/phenotype correlation. Whole genome sequencing is likely to become a commodity that could be readily available at a reasonable cost and be easily accommodated into the decision making tree of health care of every individual. The challenging task will be to identify variants that are disease-causing or likely disease-causing and develop strategies to prevent and attenuate the evolving phenotype. Likewise, various complementary studies, genetic and biological, would be necessary to discern the associated alleles from the true disease-causing variants. Moreover a better understanding of genome components, such as functional, large intergenic noncoding RNAs, small non-coding RNAs, and primary transcripts, would be essential. An integrated approach that utilizes genomics, transcriptomic, proteomics, and metabolomic would be expected to facilitate identification and characterization of the mechanisms involved in the pathogenesis of the phenotype.

http://dx.doi.org/10.1155/2014/639751

Conflict of Interests

The authors declare that there is no conflict of interests regarding the publishing of this paper.

Acknowledgment

This work has been supported by European Union Structural Funds.

References

[1] E. Pennisi, "ENCODE project writes eulogy for junk DNA," Science, vol. 337, no. 6099, pp. 1159-1161, 2012.

[2] C. M. Yates and M. J. E. Sternberg, "The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on proteinprotein interactions," Journal of Molecular Biology, vol. 425, no. 21, pp. 3949-3969, 2013.

[3] P. C. Ng and S. Henikoff, "Predicting the effects of amino acid substitutions on protein function," Annual Review of Genomics and Human Genetics, vol. 7, pp. 61-80, 2006.

[4] M. Gonzalez-Castejon, F. Marin, C. Soler-Rivas, G. Reglero, F. Visioli, and A. Rodriguez-Casado, "Functional non-synonymous polymorphisms prediction methods: current approaches and future developments," Current Medicinal Chemistry, vol. 18, no. 33, pp. 5095-5103, 2011.

[5] A. Rodriguez-Casado, "In silico investigation of functional nsSNPs an approach to rational drug design," Research and Reports in Medicinal Chemistry, vol. 2, pp. 31-42, 2012.

[6] D. Botstein and N. Risch, "Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease," Nature Genetics, vol. 33, pp. 228-237, 2003.

[7] D. R. Blair, C. S. Lyttle, and J. M. Mortensen, "A non-degenerate code of deleterious variants in Mendelian loci contributes to complex disease risk," Cell, vol. 155, no. 1, pp. 70-80, 2013.

[8] J. F. Oram, "HDL apolipoproteins and ABCA1 partners in the removal of excess cellular cholesterol," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 23, no. 5, pp. 720-727, 2003.

[9] S. Santamarina-Fojo, A. T. Remaley, E. B. Neufeld, and H.B. Brewer Jr., "Regulation and intracellular trafficking of the ABCA1 transporter," Journal of Lipid Research, vol. 42, no. 9, pp. 1339-1345, 2001.

[10] L. R. Brunham, J. K. Kruit, J. Iqbal et al., "Intestinal ABCA1 directly contributes to HDL biogenesis in vivo," Journal of Clinical Investigation, vol. 116, no. 4, pp. 1052-1062, 2006.

[11] J. M. Timmins, J. Lee, E. Boudyguina et al., "Targeted inactivation of hepatic Abca1 causes profound hypoalphalipoproteinemia and kidney hypercatabolism of apoA-I," Journal of Clinical Investigation, vol. 115, no. 5, pp. 1333-1342, 2005.

[12] L. R. Brunham, R. R. Singaraja, M. Duong et al., "Tissue-specific roles of ABCA1 influence susceptibility to atherosclerosis," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 29, no. 4, pp. 548-554, 2009.

[13] L. R. Brunham, J. K. Kruit, T. D. Pape et al., "[beta]-cell ABCA1 influences insulin secretion, glucose homeostasis and response to thiazolidinedione treatment," Nature Medicine, vol. 13, no. 3, pp. 340-347, 2007.

[14] J. Lee, A. Shirk, J. F. Oram, S. P. Lee, and R. Kuver, "Polarized cholesterol and phospholipid efflux in cultured gall-bladder epithelial cells: evidence for an ABCA1-mediated pathway," Biochemical Journal, vol. 364, no. 2, pp. 475-484, 2002.

[15] J. McNeish, R. J. Aiello, D. Guyot et al., "High density-lipoprotein deficiency and foam cell accumulation in mice with targeted disruption of ATp-binding cassette transporter-1," Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 8, pp. 4245-4250, 2000.

[16] T. Sjoblom, S. Jones, and L. D. Wood, "The consensus coding sequences of human breast and colorectal cancers," Science, vol. 314, no. 5797, pp. 268-274, 2006.

[17] B. Smith and H. Land, "Anticancer activity of the cholesterol exporter ABCA1 gene," Cell Reports, vol. 2, no. 3, pp. 580-590, 2012.

[18] M. A. Wollmer, J. R. Streffer, D. LUtjohann et al., "ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease," Neurobiology of Aging, vol. 24, no. 3, pp. 421-426, 2003.

[19] P. D. Sundar, E. Feingold, R. L. Minster, S. T. DeKosky, and M. I. Kamboh, "Gender-specific association of ATP-binding cassette transporter 1 (ABCA1) polymorphisms with the risk of late-onset Alzheimer's disease," Neurobiology of Aging, vol. 28, no. 6, pp. 856-862, 2007.

[20] M. Ota, T. Fujii, K. Nemoto et al., "A polymorphism of the ABCA1 gene confers susceptibility to schizophrenia and related brain changes," Progress in Neuro-Psychopharmacology and Biological Psychiatry, vol. 35, no. 8, pp. 1877-1883, 2011.

[21] M. F. Rosenberg, R. Callaghan, R. C. Ford, and C. F. Higgins, "Structure of the multidrug resistance p-glycoprotein to 2.5 nm resolution determined by electron microscopy and image analysis," The Journal of Biological Chemistry, vol. 272, no. 16, pp. 10685-10694,1997.

[22] M. Dean, Y. Hamon, and G. Chimini, "The human ATP-binding cassette (ABC) transporter superfamily," Journal of Lipid Research, vol. 42, no. 7, pp. 1007-1017, 2001.

[23] M. L. Fitzgerald, A. J. Mendez, K. J. Moore, L. P. Andersson, H. A. Panjeton, and M. W. Freeman, "ATP-binding cassette transporter A1 Contains an NH2-terminal signal anchor sequence that translocates the protein's first hydrophilic domain to the exoplasmic space," Journal of Biological Chemistry, vol. 276, no. 18, pp. 15137-15145, 2001.

[24] F. Scheffel, U. Demmer, E. Warkentin, A. Hulsmann, E. Schneider, and U. Ermler, "Structure of the ATPase subunit CysA of the putative sulfate ATP-binding cassette (ABC) transporter from Alicyclobacillus acidocaldarius," FEBS Letters, vol. 579, no. 13, pp. 2953-2958, 2005.

[25] C. L. Reyes and G. Chang, "Structure of the ABC transporter MsbA in complex with ADP.vanadate and lipopolysaccharide," Science, vol. 308, no. 5724, pp. 1028-1031, 2005.

[26] R. S. Kiss, N. Kavaslar, K. Okuhira et al., "Genetic etiology of isolated low HDL syndrome: incidence and heterogeneity of efflux defects," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 27, no. 5, pp. 1139-1145, 2007.

[27] K. Alrasadi, I. L. Ruel, M. Marcil, and J. Genest, "Functional mutations of the ABCA1 gene in subjects of French-Canadian descent with HDL deficiency," Atherosclerosis, vol. 188, no. 2, pp. 281-291, 2006.

[28] M. Mantaring, J. Rhyne, S. Ho Hong, and M. Miller, "Genotypic variation in ATP-binding cassette transporter-1 (ABCA1) as contributors to the high and low high-density lipoprotein-cholesterol (HDL-C) phenotype," Translational Research, vol. 149, no. 4, pp. 205-210, 2007

[29] T. L. Slatter, G. T. Jones, M. J. A. Williams, A. M. van Rij, and S. P. A. McCormick, "Novel rare mutations and promoter haplotypes in ABCA1 contribute to low-HDL-C levels," Clinical Genetics, vol. 73, no. 2, pp. 179-184, 2008.

[30] M. T. Chhabria, B. N. Suhagia, and S. B. Pathik, "HDL elevation and lipid lowering therapy: current scenario and future perspectives," Frontiers in Cardiovascular Drug Discovery, vol. 1, pp. 32-60, 2010.

[31] M. C. Probst, H. Thumann, C. Aslanidis et al., "Screening for functional sequence variations and mutations in ABCA1," Atherosclerosis, vol. 175, no. 2, pp. 269-279, 2004.

[32] C. Albrecht, K. Baynes, A. Sardini et al., "Two novel missense mutations in ABCA1 result in altered trafficking and cause severe autosomal recessive HDL deficiency," Biochimica et Biophysica Acta, vol. 1689, no. 1, pp. 47-57, 2004.

[33] M. Daimon, T. Kido, M. Baba et al., "Association of the ABCA1 gene polymorphisms with type 2 DM in a Japanese population," Biochemical and Biophysical Research Communications, vol. 329, no. 1, pp. 205-210, 2005.

[34] R. M. Lawn, D. P. Wade, M. R. Garvin et al., "The Tangier disease gene product ABC1 controls the cellular apolipoprotein-mediated lipid removal pathway," Journal of Clinical Investigation, vol. 104, no. 8, pp. R25-R31, 1999.

[35] A. von Eckardstein, C. Langer, T. Engel et al., "ATP binding cassette transporter ABCA1 modulates the secretion of apolipoprotein E from human monocyte-derived macrophages," The FASEB Journal, vol. 15, no. 9, pp. 1555-1561, 2001.

[36] M. R. Hayden, S. M. Clee, A. Brooks-Wilson, J. Genest Jr., A. Attie, and J. J. P. Kastelein, "Cholesterol efflux regulatory protein, Tangier disease and familial high density lipoprotein deficiency," Current Opinion in Lipidology, vol. 11, no. 2, pp. 117-122, 2000.

[37] M. Marcil, A. Brooks-Wilson, S. M. Clee et al., "Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux," The Lancet, vol. 354, no. 9187, pp. 1341-1346, 1999.

[38] H. H. Hobbs and D. J. Rader, "ABC1: connecting yellow tonsils, neuropathy, and very low HDL," The Journal of Clinical Investigation, vol. 104, no. 8, pp. 1015-1017, 1999.

[39] R. Frikke-Schmidt, B. G. Nordestgaard, G. B. Jensen, and A. Tybjaerg-Hansen, "Genetic variation in ABC transporter A1 contributes to HDL cholesterol in the general population," The Journal of Clinical Investigation, vol. 114, no. 9, pp. 1343-1353, 2004.

[40] M. Marcil, L. Yu, L. Krimbou et al., "Cellular cholesterol transport and efflux in fibroblasts are abnormal in subjects with familial HDL deficiency," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 19, no. 1, pp. 159-169, 1999.

[41] M. E. Brousseau, G. P. Eberhart, J. Dupuis et al., "Cellular cholesterol efflux in heterozygotes for Tangier disease is markedly reduced and correlates with high density lipoprotein cholesterol concentration and particle size," Journal of Lipid Research, vol. 41, no. 7, pp. 1125-1135, 2000.

[42] S. M. Clee, J. J. P. Kastelein, M. van Dam et al., "Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes," The Journal of Clinical Investigation, vol. 106, no. 10, pp. 1263-1270, 2000.

[43] N. F. Fitz, A. A. Cronican, M. Saleem et al., "Abca1 deficiency affects Alzheimer's disease-like phenotype in human ApoE4 but not in ApoE3-targeted replacement mice," Journal of Neuroscience, vol. 32, no. 38, pp. 13125-13136, 2012.

[44] E. J. Schaefer, L. A. Zech, D. E. Schwartz, and H. B. Brewer Jr., "Coronary heart disease prevalence and other clinical features in familial high-density lipoprotein deficiency (Tangier disease)," Annals of Internal Medicine, vol. 93, no. 2, pp. 261-266, 1980.

[45] B. Li, V. G. Krishnan, M. E. Mort et al., "Automated inference of molecular mechanisms of disease from amino acid substitutions," Bioinformatics, vol. 25, no. 21, pp. 2744-2750, 2009.

[46] I. A. Adzhubei, S. Schmidt, L. Peshkin et al., "A method and server for predicting damaging missense mutations," Nature Methods, vol. 7, no. 4, pp. 248-249, 2010.

[47] P. Cingolani, A. Platts, L. L. Wang et al., "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain [w.sup.1118]; iso-2; iso-3," Fly, vol. 6, no. 2, pp. 80-92, 2012.

[48] P. Kumar, S. Henikoff, and P. C. Ng, "Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm," Nature Protocols, vol. 4, no. 7, pp. 1073-1081, 2009.

[49] V. Ramensky, P. Bork, and S. Sunyaev, "Human non-synonymous SNPs: server and survey," Nucleic Acids Research, vol. 30, no. 17, pp. 3894-3900, 2002.

[50] S. Chun and J. C. Fay, "Identification of deleterious mutations within three human genomes," Genome Research, vol. 19, no. 9, pp. 1553-1561, 2009.

[51] J. C. Cohen, R. S. Kiss, A. Pertsemlidis, Y. L. Marcel, R. McPherson, and H. H. Hobbs, "Multiple rare alleles contribute to low plasma levels of HDL cholesterol," Science, vol. 305, no. 5685, pp. 869-872, 2004.

[52] R. M. Corbo and R. Scacchi, "Apolipoprotein E (APOE) allele distribution in the world. Is APOE*4 a "thrifty" allele?" Annals of Human Genetics, vol. 63, part 4, pp. 301-310, 1999.

[53] D. Weissglas-Volkov and P. Pajukanta, "Genetic causes of high and low serum HDL-cholesterol," Journal of Lipid Research, vol. 51, no. 8, pp. 2032-2057, 2010.

[54] R. R. Singaraja, H. Visscher, E. R. James et al., "Specific mutations in ABCA1 have discrete effects on ABCA1 function and lipid phenotypes both in vivo and in vitro," Circulation Research, vol. 99, no. 4, pp. 389-397, 2006.

[55] K. Nagao, M. Tomioka, and K. Ueda, "Function and regulation of ABCA1--membrane meso-domain organization and reorganization," The FEBS Journal, vol. 278, no. 18,pp. 3190-3203, 2011.

[56] M. L. Fitzgerald, A. L. Morris, J. S. Rhee, L. P. Andersson, A. J. Mendez, and M. W. Freeman, "Naturally occurring mutations in the largest extracellular loops of ABCA1 can disrupt its direct interaction with apolipoprotein A-I," The Journal of Biological Chemistry, vol. 277, no. 36, pp. 33178-33187, 2002.

[57] A. M. Vaughan, C. Tang, and J. F. Oram, "ABCA1 mutants reveal an interdependency between lipid export function, apoA-I binding activity, and Janus kinase 2 activation," Journal of Lipid Research, vol. 50, no. 2, pp. 285-292, 2009.

[58] R. Frikke-Schmidt, C. F. Sing, B. G. Nordestgaard, and A. Tybjaerg-Hansen, "Gender- and age-specific contributions of additional DNA sequence variation in the 5' regulatory region of the APOE gene to prediction of measures of lipid metabolism," Human Genetics, vol. 115, no. 4, pp. 331-345, 2004.

[59] R. Frikke-Schmidt, B. G. Nordestgaard, P. Schnohr, and A. Tybjaerg-Hansen, "Single nucleotide polymorphism in the low-density lipoprotein receptor is associated with a threefold risk ofstroke: a case-control and prospective study," European Heart Journal, vol. 25, no. 11, pp. 943-951, 2004.

[60] S. M. Clee, A. H. Zwinderman, J. C. Engert et al., "Common genetic variation in ABCA1 is associated with altered lipoprotein levels and a modified risk for coronary artery disease," Circulation, vol. 103, no. 9, pp. 1198-1205, 2001.

[61] M. V. Reddy, I. Iatan, D. Weissglas-Volkov et al., "Exome sequencing identifies 2 rare variants for low high-density lipoprotein cholesterol in an extended family," Circulation: Cardiovascular Genetics, vol. 5, no. 5, pp. 538-546, 2012.

[62] C. L. Wellington, Y. Yang, S. Zhou et al., "Truncation mutations in ABCA1 suppress normal upregulation of full-length ABCA1 by 9-cis-retinoic acid and 22-R-hydroxycholesterol," Journal of Lipid Research, vol. 43, no. 11, pp. 1939-1949, 2002.

[63] S. Wang, K. Gulshan, G. Brubaker, S. L. Hazen, and J. D. Smith, "ABCA1 mediates unfolding of apolipoprotein AI N terminus on the cell surface before lipidation and release of nascent high-density lipoprotein," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 33, no. 6, pp. 1197-1205, 2013.

[64] M. Denis, B. Haidar, M. Marcil, M. Bouvier, L. Krimbou, and J. Genest, "Characterization of oligomeric human ATP binding cassette transporter A1: potential implications for determining the structure of nascent high density lipoprotein particles," The Journal of Biological Chemistry, vol. 279, no. 40, pp. 41529-41536, 2004.

[65] S. Bertolini, L. Pisciotta, M. Seri et al., "A point mutation in ABC1 gene in a patient with severe premature coronary heart disease and mild clinical phenotype of Tangier disease," Atherosclerosis, vol. 154, no. 3, pp. 599-605, 2001.

[66] W. S. Kim, A. F. Hill, M. L. Fitzgerald, M. W. Freeman, G. Evin, and B. Garner, "Wild type and tangier disease ABCA1 mutants modulate cellular amyloid-[beta] production independent of cholesterol efflux activity," Journal of Alzheimer's Disease, vol. 27, no. 2, pp. 441-452, 2011.

[67] J. Wang, J. R. Burnett, S. Near et al., "Common and rare ABCA1 variants affecting plasma HDL cholesterol," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 20, no. 8, pp. 1983-1989, 2000.

[68] Y. Nishida, K. Hirano, K. Tsukamoto et al., "Expression and functional analyses of novel mutations of ATP-binding cassette transporter-1 in Japanese patients with high-density lipoprotein deficiency," Biochemical and Biophysical Research Communications, vol. 290, no. 2, pp. 713-721, 2002.

[69] N. Wang, D. Lan, M. Gerbod-Giannone et al., "ATP-binding cassette transporter A7 (ABCA7) binds apolipoprotein A-I and mediates cellular phospholipid but not cholesterol efflux," The Journal of Biological Chemistry, vol. 278, no. 44, pp. 42906-42912, 2003.

[70] S. Ho Hong, J. Rhyne, K. Zeller, and M. Miller, "Novel ABCA1 compound variant associated with HDL cholesterol deficiency," Biochimica et Biophysica Acta--Molecular Basis of Disease, vol. 1587, no. 1, pp. 60-64, 2002.

[71] M. Walter, S. Kerber, C. Fechtrup, U. Seedorf, G. Breithardt, and G. Assmann, "Characterization of atherosclerosis in a patient with familial high-density lipoprotein deficiency," Atherosclerosis, vol. 110, no. 2, pp. 203-208, 1994.

[72] R. P. Koldamova, I. M. Lefterov, M. Staufenbiel et al., "The liver X receptor ligaun T0901317 decreases amyloid [beta] production in vitro and in a mouse model of Alzheimer's disease," The Journal ofBiological Chemistry, vol. 280, no. 6, pp. 4079-4088, 2005.

[73] T. L. Slatter, M. J. A. Williams, R. Frikke-Schmidt, A. Tybjaerg-Hansen, I. M. Morison, and S. P. A. McCormick, "Promoter haplotype of a new ABCA1 mutant influences expression of familial hypoalphalipoproteinemia," Atherosclerosis, vol. 187, no. 2, pp. 393-400, 2006.

[74] R. J. Suetani, B. Sorrenson, J. D. A. Tyndall, M. J. A. Williams, and S. P. A. McCormick, "Homology modeling and functional testing of an ABCA1 mutation causing Tangier disease," Atherosclerosis, vol. 218, no. 2, pp. 404-410, 2011.

[75] L. Kelly, R. Karchin, and A. Sali, "Protein interactions and disease phenotypes in the ABC transporter superfamily," in Proceedings of the Pacific Symposium on Biocomputing, pp. 51-63, 2007.

[76] L. Pisciotta, L. Bocchi, C. Candini et al., "Severe HDL deficiency due to novel defects in the ABCA1 transporter," Journal of Internal Medicine, vol. 265, no. 3, pp. 359-372, 2009.

[77] T. Fasano, L. Bocchi, L. Pisciotta, S. Bertolini, and S. Calandra, "Denaturing high-performance liquid chromatography in the detection of ABCA1 gene mutations in familial HDL deficiency," Journal of Lipid Research, vol. 46, no. 4, pp. 817-822, 2005.

[78] M. E. Brousseau, E. J. Schaefer, J. Dupuis et al., "Novel mutations in the gene encoding ATP-binding cassette 1 in four tangier disease kindreds," Journal of Lipid Research, vol. 41, no. 3, pp. 433-441, 2000.

[79] W. Huang, K. Moriyama, T. Koga et al., "Novel mutations in ABCA1 gene in Japanese patients with Tangier disease and familial high density lipoprotein deficiency with coronary heart disease," Biochimica et Biophysica Acta, vol. 1537, no. 1, pp. 71-78, 2001.

[80] F. Quazi and R. S. Molday, "Differential phospholipid substrates and directional transport by ATP binding cassette proteins ABCA1, ABCA7, and ABCA4 and disease-causing mutants," The Journal of Biological Chemistry, vol. 288, no. 48, pp. 34414-34426, 2013.

[81] V. Kolovou, G. Kolovou, A. Marvaki et al., "ATP-binding-cassette transporter A1 gene polymorphisms and serum lipid levels in young Greek nurses," Lipids in Health and Disease, vol. 10, article 56, 2011.

[82] R. Frikke-Schmidt, B. G. Nordestgaard, G. B. Jensen, R. Steffensen, and A. Tybjaerg-Hansen, "Genetic variation in ABCA1 predicts ischemic heart disease in the general population," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 28, no. 1, pp. 180-186, 2008.

[83] A. Kitjaroentham, H. Hananantachai, A. Tungtrongchitr, S. Pooudong, and R. Tungtrongchitr, "R219K polymorphism of ATP binding cassette transporter A1 related with low HDL in overweight/obese Thai males," Archives of Medical Research, vol. 38, no. 8, pp. 834-838, 2007.

[84] A. Cenarro, M. Artieda, S. Castillo et al., "A common variant in the ABCA1 gene is associated with a lower risk for premature coronary heart disease in familial hypercholesterolaemia," Journal of Medical Genetics, vol. 40, no. 3, pp. 163-168, 2003.

[85] D. Tregouet, S. Ricard, V. Nicaud et al., "In-depth haplotype analysis of ABCA1 gene polymorphisms in relation to plasma ApoA1 levels and myocardial infarction," Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 24, no. 4, pp. 775-781, 2004.

[86] T. M. Morgan, H. M. Krumholz, R. P. Lifton, and J. A. Spertus, "Nonvalidation of reported genetic risk factors for acute coronary syndrome in a large-scale replication study," Journal of the American Medical Association, vol. 297, no. 14, pp. 1551-1561, 2007.

[87] Y. Li, K. Tang, K. Zhou et al., "Quantitative assessment of the effect of ABCA1 R219K polymorphism on the risk of coronary heart disease," Molecular Biology Reports, vol. 39, no. 2, pp. 1809-1813, 2012.

[88] V. Kolovou, A. Marvaki, A. Karakosta et al., "Association of gender, ABCA1 gene polymorphisms and lipid profile in Greek young nurses," Lipids in Health and Disease, vol. 11, article 62, 2012.

[89] Z. Xiao, J. Wang, W. Chen, P. Wang, and H. Zeng, "Association studies of several cholesterol-related genes (ABCA1, CETP and LIPC) with serum lipids and risk of Alzheimer's disease," Lipids in Health and Disease, vol. 11, article 163, 2012.

[90] F. Wavrant-De Vrieze, D. Compton, M. Womick et al., "ABCA1 polymorphisms and Alzheimer's disease," Neuroscience Letters, vol. 416, no. 2, pp. 180-183, 2007.

[91] E. B. Neufeld, J. A. Stonik, S. J. Demosky Jr. et al., "The ABCA1 transporter modulates late endocytic trafficking: insights from the correction of the genetic defect in Tangier disease," The Journal of Biological Chemistry, vol. 279, no. 15, pp. 15571-15578, 2004.

[92] E. J. Schaefer, C. B. Blum, R. I. Levy et al., "Metabolism of high density lipoprotein apolipoproteins in Tangier disease," The New England Journal of Medicine, vol. 299, no. 17, pp. 905-910, 1978.

[93] J. Huang, W. Huang, H. Li et al., "Relationship between the I883M polymorphism of ATP-binding cassette transporter 1 gene and cardiovascular disease," Shandong Medical Journal, vol. 9, 2009.

[94] A. Sandhofer, B. Iglseder, S. Kaser, E. More, B. Paulweber, and J. R. Patsch, "The influence of two variants in the adenosine triphosphate-binding cassette transporter 1 gene on plasma lipids and carotid atherosclerosis," Metabolism, vol. 57, no. 10, pp. 1398-1404, 2008.

[95] U. Hodoglugil, D. W. Williamson, Y. Huang, and R. W. Mahley, "Common polymorphisms of ATP binding cassette transporter A1, including a functional promoter polymorphism, associated with plasma high density lipoprotein cholesterol levels in Turks," Atherosclerosis, vol. 183, no. 2, pp. 199-212, 2005.

[96] M. K. Jensen, J. K. Pai, K. J. Mukamal, K. Overvad, and E. B. Rimm, "Common genetic variation in the ATP-binding cassette transporter A1, plasma lipids, and risk of coronary heart disease," Atherosclerosis, vol. 195, no. 1, pp. e172-e180, 2007

[97] I. Porchay-Balderelli, F. Pean, N. Emery et al., "Relationships between common polymorphisms of adenosine triphosphate-binding cassette transporter A1 and high-density lipoprotein cholesterol and coronary heart disease in a population with type 2 diabetes mellitus," Metabolism: Clinical and Experimental, vol. 58, no. 1, pp. 74-79, 2009.

[98] M. E. Brousseau, M. Bodzioch, E. J. Schaefer et al., "Common variants in the gene encoding ATP-binding cassette transporter 1 in men with low HDL cholesterol levels and coronary heart disease," Atherosclerosis, vol. 154, no. 3, pp. 607-611, 2001.

[99] T. Harada, Y. Imai, T. Nojiri et al., "A common Ile 823 Met variant of ATP-binding cassette transporter A1 gene (ABCA1) alters high density lipoprotein cholesterol level in Japanese population," Atherosclerosis, vol. 169, no. 1, pp. 105-112, 2003.

[100] E. J. Schaefer, D. W. Anderson, L. A. Zech et al., "Metabolism of high density lipoprotein subfractions and constituents in Tangier disease following the infusion of high density lipoproteins," Journal of Lipid Research, vol. 22, no. 2, pp. 217-228, 1981.

[101] M. T. Villarreal-Molina, C. A. Aguilar-Salinas, M. Rodriguez-Cruz et al., "The ATP-binding cassette transporter A1 R230C variant affects HDL cholesterol levels and BMI in the Mexican population: association with obesity and obesity-related comorbidities," Diabetes, vol. 56, no. 7, pp. 1881-1887, 2007.

[102] C. A. Aguilar-Salinas, S. Canizales-Quinteros, R. Rojas-Martinez et al., "The non-synonymous Arg230Cys variant (R230C) of the ATP-binding cassette transporter A1 is associated with low HDL cholesterol concentrations in Mexican adults: a population based nation wide study," Atherosclerosis, vol. 216, no. 1, pp. 146-150, 2011.

[103] B. Sorrenson, R. J. Suetani, M. J. A. Williams et al., "Functional rescue of mutant ABCA1 proteins by sodium 4-phenylbutyrate," Journal of Lipid Research, vol. 54, no. 1, pp. 55-62, 2013.

[104] S. H. Hong, J. Rhyne, K. Zeller, and M. Miller, "ABCAlAlabama: a novel variant associated with HDL deficiency and premature coronary artery disease," Atherosclerosis, vol. 164, no. 2, pp. 245-250, 2002.

[105] S. Bungert, L. L. Molday, and R. S. Molday, "Membrane topology of the ATP binding cassette transporter ABCR and its relationship to ABC1 and related ABCA transporters: identification of N-linked glycosylation sites," The Journal of Biological Chemistry, vol. 276, no. 26, pp. 23539-23546, 2001.

Francisco R. Marin-Martin (1), Cristina Soler-Rivas (1), Roberto Martin-Hernandez (2), and Arantxa Rodriguez-Casado (2,3)

(1) Department of Production and Characterization of New Foods, Institute of Food Science Research (CIAL), UAM-CSIC, Campus de Cantoblanco, 28049 Madrid, Spain

(2) IMDEA Food Institute, Campus de Cantoblanco, 28049 Madrid, Spain

(3) Nutritional Genomics of the Cardiovascular Disease and Obesity, IMDEA Food Institute, Carretera Cantoblanco 8, 28049 Madrid, Spain

Correspondence should be addressed to Arantxa Rodriguez-Casado; arantxa.rodriguez@imdea.org

Received 30 April 2014; Revised 7 July 2014; Accepted 24 July 2014; Published 19 August 2014

Academic Editor: Akihiro Inazu

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                X          X
    surface area
  Phi-psi dihedral angles           X
  Normalized accessible             X
    surface area
  Change in accessible              X
    surface propensity
  Change in residue side            X
    chain volume
  Region of the phi-psi map         X
    (Ramachandran map)
  Normalized B-factor               X          X
  Ligand contacts                   X
  Interchain contacts               X
  Functional site contacts          X
  Molecular Recognition                        X
    Fragments (MoRFs)

TABLE 2: Functional effects of nsSNPs for ABCA1 gene (UniProt:
095477) predicted by PolyPhen2 and MutPred. A score > 0.5 means
that the mutation is classified as damaging by the algorithms. In
addition, MutPred algorithm formulates hypotheses about
structural and functional impact of the mutation; the most
statistically significant hypothesis is reported in this table.
The MAP column includes Minor Allele Frequency. The deviation
column represents how close the two predicted scores are; a value
of 0 corresponding to identical values.

Mutation   pph2_prob    Polyphen     RFscore       Mutpred
                          class                  hypothesis

A1010V       0,104       neutral      0,816        Loss of
                                               ubiquitination
                                                  at K1009

A1046D       0,999     deleterious    0,938     Loss of MoRF
                                                   binding

A1182T       0,001       neutral      0,425     Loss of sheet

A1407T       0,119       neutral      0,277     Gain of helix

A1631V       0,401       neutral      0,321     Loss of sheet

A1670T       0,997     deleterious    0,566        Gain of
                                                glycosylation
                                                  at A1670

A1756T       0,81      deleterious    0,418        Gain of
                                                glycosylation
                                                  at A1756

A2028V       0,146       neutral      0,564        Gain of
                                               methylation at
                                                    K2023

A255T          0         neutral      0,755     Loss of helix

A343V        0,001       neutral      0,227        Loss of
                                                  disorder

A391S        0,318       neutral      0,34         Gain of
                                                  disorder

A594T        0,02        neutral      0,406        Loss of
                                                  catalytic
                                               residue at A594

A697T        0,416       neutral      0,508     Gain of sheet

A746G          1       deleterious    0,608        Loss of
                                                  stability

A779T        0,411       neutral      0,468     Loss of helix

A795S        0,07        neutral      0,494     Loss of helix

A937V        0,991     deleterious    0,921        Loss of
                                                  disorder

C1477F         1       deleterious    0,496        Loss of
                                                  catalytic
                                                 residue at
                                                    C1477

C1477R         1       deleterious    0,852        Gain of
                                               methylation at
                                                    C1477

C1660R       0,954     deleterious    0,917        Gain of
                                               methylation at
                                                    C1660

CSS          0,005       neutral      0,48         Gain of
                                                  disorder

C887F        0,002       neutral      0,604        Gain of
                                               phosphorylation
                                                   at S884

D1018G       0,992     deleterious    0,535        Loss of
                                                  catalytic
                                                 residue at
                                                    D1018

D1099N         1       deleterious    0,906     Gain of sheet

D1099Y         1       deleterious    0,946        Loss of
                                                  disorder

D1263E       0,003       neutral      0,214     Gain of helix

D1289N       0,339       neutral      0,573     Gain of sheet

D1553E       0,001       neutral      0,273     Loss of helix

D1706N         1       deleterious    0,611     Loss of helix

D2243E       0,078       neutral      0,491        Gain of
                                                  relative
                                                   solvent
                                                accessibility

D434E        0,005       neutral      0,413        Gain of
                                                  disorder

D441N          0         neutral      0,348     Loss of helix

D444E          0         neutral      0,338     Loss of helix

D446E          0         neutral      0,301     Loss of helix

D457E        0,001       neutral      0,566     Loss of helix

D462G        0,071       neutral      0,555        Loss of
                                                  catalytic
                                               residue at D462

D581E        0,38        neutral      0,346     Loss of helix

D677E        0,158       neutral      0,846     Loss of loop

D831N        0,999     deleterious    0,589     Gain of helix

D917N         0,1        neutral      0,577     Gain of MoRF
                                                   binding

E1005K       0,026       neutral      0,542     Gain of MoRF
                                                   binding

E1172D       0,003       neutral      0,253     Loss of sheet

E1172G       0,003       neutral      0,281     Loss of sheet

E1253K       0,048       neutral      0,453        Gain of
                                               ubiquitination
                                                  at E1253

E1916A       0,027       neutral      0,34      Gain of MoRF
                                                   binding

E226G        0,019       neutral      0,47         Loss of
                                                  stability

E284K        0,206       neutral      0,842        Gain of
                                               methylation at
                                                    E284

E815G        0,072       neutral      0,361        Loss of
                                                  disorder

E868K        0,051       neutral      0,69         Gain of
                                               methylation at
                                                    E868

F1285L       0,001       neutral      0,235     Loss of loop

F1573S       0,065       neutral      0,532        Gain of
                                                  disorder

F2009S       0,811     deleterious    0,932        Gain of
                                                  disorder

F2082V       0,266       neutral      0,442     Gain of MoRF
                                                   binding

F2163S       0,939     deleterious    0,727     Loss of sheet

F346L          0         neutral      0,239        Gain of
                                                  disorder

F426L        0,94      deleterious    0,549     Gain of helix

F632C        0,998     deleterious    0,694        Loss of
                                                  stability

F950S        0,995     deleterious    0,664        Gain of
                                                  disorder

G1049R         1       deleterious    0,638     Gain of MoRF
                                                   binding

G1216V       0,951     deleterious    0,844        Loss of
                                               ubiquitination
                                                  at K1214

G1321A       0,936     deleterious    0,715        Gain of
                                                  catalytic
                                                 residue at
                                                    G1321

G156V        0,017       neutral      0,389     Loss of helix

G2147E       0,49        neutral      0,397        Loss of
                                                  catalytic
                                                 residue at
                                                    S2148

G315W        0,997     deleterious    0,526        Loss of
                                                  disorder

G616V        0,998     deleterious    0,444        Loss of
                                                  disorder

G788W          1       deleterious    0,664        Loss of
                                                  catalytic
                                               residue at P784

G851R        0,998     deleterious    0,71         Gain of
                                                  catalytic
                                               residue at G851

H263D          0         neutral      0,399     Loss of helix

H551D        0,613     deleterious    0,468     Gain of sheet

I1084V       0,241       neutral      0,511     Gain of MoRF
                                                   binding

I1239V       0,078       neutral      0,376        Loss of
                                                  catalytic
                                                 residue at
                                                    L1244

I1517R       0,962     deleterious    0,917        Gain of
                                                  catalytic
                                                 residue at
                                                    11517

I1555T       0,439       neutral      0,484        Loss of
                                                  stability

I1911T       0,006       neutral      0,437        Loss of
                                                  stability

I35V         0,066       neutral      0,31      Loss of helix

I546V          0         neutral      0,31      Gain of MoRF
                                                   binding

I560T        0,829     deleterious    0,496        Loss of
                                                  stability

I649F        0,97      deleterious    0,669        Loss of
                                                  catalytic
                                               residue at 1649

1659V        0,034       neutral      0,405        Loss of
                                               methylation at
                                                    K663

I883M        0,002       neutral      0,296        Gain of
                                                  disorder

K1250R       0,118       neutral      0,377        Foss of
                                               methylation at
                                                    K1250

K1587R       0,034       neutral      0,377     Gain of helix

K166R          0         neutral      0,251        Foss of
                                               ubiquitination
                                                   at K166

K1761T       0,038       neutral      0,545        Foss of
                                               methylation at
                                                    K1761

K1974R       0,158       neutral      0,679        Foss of
                                               ubiquitination
                                                  at K1974

K2040E       0,243       neutral      0,459     Foss of MoRF
                                                   binding

K401Q        0,007       neutral      0,322        Foss of
                                               ubiquitination
                                                   at K401


K613E        0,002       neutral      0,428        Foss of
                                               ubiquitination
                                                   at K613

K776N        0,985     deleterious    0,568        Foss of
                                               methylation at
                                                    K776

L1041V       0,999     deleterious    0,625        Foss of
                                               ubiquitination
                                                  at K1040

L1379F       0,987     deleterious    0,866        Foss of
                                                  catalytic
                                                 residue at
                                                    F1379

L1408F       0,443       neutral      0,418        Foss of
                                                  stability

F1648P       0,961     deleterious    0,749        Foss of
                                                  stability

F184S        0,007       neutral      0,576     Foss of sheet

F184W        0,928     deleterious    0,54      Gain of helix

F2032M       0,897     deleterious    0,688        Gain of
                                               methylation at
                                                    K2036

F2168P       0,984     deleterious    0,693        Gain of
                                                  disorder

F2187Q       0,995     deleterious    0,698        Gain of
                                                  disorder

M1012I       0,008       neutral      0,595        Foss of
                                                  catalytic
                                                 residue at
                                                    V1008

M1091T       0,98      deleterious    0,955        Gain of
                                                  disorder

M233V          0         neutral      0,417        Foss of
                                                  stability

M415F        0,002       neutral      0,423        Gain of
                                                  relative
                                                   solvent
                                                accessibility

M674F        0,534     deleterious    0,599        Foss of
                                                  catalytic
                                               residue at M674

N1185K       0,01        neutral      0,583     Gain of MoRF
                                                   binding

N1185S       0,002       neutral      0,358     Gain of helix

N1406K       0,006       neutral      0,408        Gain of
                                               ubiquitination
                                                  at N1406

N1611D       0,968     deleterious    0,921     Foss of MoRF
                                                   binding

N1800H       0,758     deleterious    0,826        Foss of
                                                  stability

N1800S       0,241       neutral      0,84         Foss of
                                                  stability

N2119Y       0,96      deleterious    0,727     Foss of MoRF
                                                   binding

N820S        0,001       neutral      0,348        Foss of
                                                  catalytic
                                               residue at N820

N935H        0,996     deleterious    0,966        Gain of
                                                  disorder

N935S        0,831     deleterious    0,969        Gain of
                                                  disorder

P1065S       0,998     deleterious    0,906     Gain of MoRF
                                                   binding

P1475S         1       deleterious    0,235        Gain of
                                               phosphorylation
                                                  at P1475

P1878T       0,019       neutral      0,482     Gain of helix

P2150F       0,068       neutral      0,826        Foss of
                                                  disorder

P248A          0         neutral      0,207     Foss of helix

P250F          0         neutral      0,244        Foss of
                                                glycosylation
                                                   at P250

P641L          1       deleterious    0,603     Gain of MoRF
                                                   binding

P855S        0,97      deleterious    0,59         Loss of
                                                  catalytic
                                               residue at W856

P85L         0,394       neutral      0,618        Loss of
                                                  disorder

Q1279K       0,032       neutral      0,715     Gain of MoRF
                                                   binding

Q188K        0,001       neutral      0,543        Gain of
                                               ubiquitination
                                                   at Q188

Q205E        0,01        neutral      0,255     Loss of loop

Q205R          0         neutral      0,279     Gain of helix

Q2196H       0,011       neutral      0,798     Loss of MoRF
                                                   binding

Q2210H       0,984     deleterious    0,388        Gain of
                                                  catalytic
                                                 residue at
                                                    D2214

Q597R          1       deleterious    0,71      Gain of MoRF
                                                   binding

Q849R        0,689     deleterious    0,662        Gain of
                                               methylation at
                                                    Q849

R104C        0,985     deleterious    0,589     Loss of MoRF
                                                   binding

R1068C         1       deleterious    0,962     Loss of MoRF
                                                   binding

R1068H         1       deleterious    0,972     Loss of MoRF
                                                   binding

R1082C         1       deleterious    0,694     Loss of MoRF
                                                   binding

R1195Q       0,044       neutral      0,364     Loss of loop

R1195W       0,952     deleterious    0,589        Gain of
                                                  catalytic
                                                 residue at
                                                    A1194

R126H          0         neutral      0,467     Loss of MoRF
                                                   binding

R1273L       0,007       neutral      0,35      Loss of loop

R1283C       0,001       neutral      0,449        Gain of
                                               ubiquitination
                                                  at K1278

R1341T       0,016       neutral      0,604        Loss of
                                               methylation at
                                                    R1341

R1344W       0,993     deleterious    0,64         Loss of
                                               methylation at
                                                    K1345

R1417H       0,837     deleterious    0,457        Loss of
                                               phosphorylation
                                                  at T1416

R1615P       0,947     deleterious    0,895        Loss of
                                               methylation at
                                                    R1615

R1615Q       0,187       neutral      0,679     Gain of helix

R1680Q       0,997     deleterious    0,807        Gain of
                                               ubiquitination
                                                  at K1683

R1680W         1       deleterious    0,911        Loss of
                                                  disorder

R1839H       0,006       neutral      0,48         Loss of
                                               phosphorylation
                                                  at S1842

R1851Q       0,015       neutral      0,897        Gain of
                                                  catalytic
                                                 residue at
                                                    R1851

R1897W       0,009       neutral      0,408       Probably
                                                  damaging

R1901S       0,091       neutral      0,81         Gain of
                                               phosphorylation
                                                  at R1901

R1925Q       0,006       neutral      0,69      Loss of MoRF
                                                   binding

R2004K       0,911     deleterious    0,699        Gain of
                                               ubiquitination
                                                  at R2004

R2030Q       0,032       neutral      0,442     Loss of MoRF
                                                   binding

R2081W       0,998     deleterious    0,936     Loss of MoRF
                                                   binding

R2173Q       0,008       neutral      0,382     Gain of sheet

R2189G       0,142       neutral      0,443     Loss of MoRF
                                                   binding

R219K          0         neutral      0,41         Gain of
                                               ubiquitination
                                                   at R219

R230C          0         neutral      0,68      Loss of MoRF
                                                   binding

R306G        0,04        neutral      0,463     Loss of helix

R306H        0,899     deleterious    0,431     Loss of helix

R369H        0,937     deleterious    0,433     Loss of MoRF
                                                   binding

R437Q        0,088       neutral      0,48      Loss of helix

R437W        0,991     deleterious    0,562        Gain of
                                                  catalytic
                                               residue at L435

R443K          0         neutral      0,44         Loss of
                                                  stability

R496W        0,209       neutral      0,576     Loss of loop

R500H        0,013       neutral      0,519     Loss of helix

R587W          1       deleterious    0,688        Loss of
                                                  disorder

R638Q        0,957     deleterious    0,664        Loss of
                                               methylation at
                                                    R638

R638W        0,999     deleterious    0,671        Loss of
                                               methylation at
                                                    R638

R666Q          1       deleterious    0,437        Gain of
                                               ubiquitination
                                                   at K668

R666W          1       deleterious    0,56         Gain of
                                                  catalytic
                                               residue at R666

R672Q        0,832     deleterious    0,501     Loss of MoRF
                                                   binding

R965C        0,302       neutral      0,608        Loss of
                                                  disorder

R999C        0,127       neutral      0,766    Loss of solvent
                                                accessibility

R999L        0,208       neutral      0,748    Loss of solvent
                                                accessibility

S107A        0,002       neutral      0,342     Gain of helix

S1141Y       0,805     deleterious    0,306        Loss of
                                               phosphorylation
                                                  at S1141

S1157N       0,022       neutral      0,355     Gain of sheet

S116N        0,196       neutral      0,241        Loss of
                                               phosphorylation
                                                   at S116

S1181F       0,042       neutral      0,542        Loss of
                                                  disorder

S1255R       0,027       neutral      0,326        Loss of
                                                glicosilation
                                                  at S1255

S1280R       0,009       neutral      0,351     Gain of sheet

S1376G       0,007       neutral      0,407        Gain of
                                               methylation at
                                                    K1373

S139G          0         neutral      0,284     Gain of helix

S1506L       0,996     deleterious    0,733     Loss of helix

S1536F       0,998     deleterious    0,594        Loss of
                                                  disorder

S1731C       0,893     deleterious    0,526     Loss of helix

S212T        0,028       neutral      0,375     Gain of helix

S2182F       0,578     deleterious    0,498        Loss of
                                                  disorder

S2186F       0,862     deleterious    0,458        Loss of
                                                  disorder

S442R        0,001       neutral      0,449     Loss of helix

S713G          1       deleterious    0,576        Loss of
                                                  stability

S780N        0,996     deleterious    0,559        Loss of
                                                  stability

T1175M       0,432       neutral      0,331     Loss of sheet

T1242M       0,993     deleterious    0,62         Loss of
                                                  catalytic
                                                 residue at
                                                    T1242

T1399M       0,003       neutral      0,279        Loss of
                                                glycosylation
                                                  at T1399

T1401I       0,003       neutral      0,368        Loss of
                                                glycosylation
                                                  at T1401

T1427M       0,005       neutral      0,352        Gain of
                                                  catalytic
                                                 residue at
                                                    T1427

T2073A       0,852     deleterious    0,657        Loss of
                                               phosphorylation
                                                  at T2073

T459P        0,03        neutral      0,534     Gain of helix

T515A        0,04        neutral      0,449     Gain of helix

T774P        0,003       neutral      0,61         Gain of
                                               methylation at
                                                    K776

T929I        0,946     deleterious    0,889        Loss of
                                                  disorder

T940M          1       deleterious    0,844        Loss of
                                               methylation at
                                                    K939

V1054I       0,951     deleterious    0,51         Loss of
                                               ubiquitination
                                                  at K1052

V1096I         0         neutral      0,467     Gain of helix

V1158I       0,065       neutral      0,226     Loss of sheet

V1674I       0,053       neutral      0,376        Loss of
                                                  catalytic
                                                 residue at
                                                    V1674

V1704D       0,752     deleterious    0,876     Loss of helix

V1806M       0,98      deleterious    0,417        Gain of
                                               ubiquitination
                                                  at K1804

V1858M       0,305       neutral      0,472        Loss of
                                                  catalytic
                                                 residue at
                                                    V1858

V2035M       0,042       neutral      0,38         Loss of
                                               methylation at
                                                    K2036

V2244I       0,002       neutral      0,386     Gain of sheet

V304M        0,823     deleterious    0,387        Gain of
                                                  disorder

V380I        0,001       neutral      0,353        Gain of
                                               methylation at
                                                    K376

V399A        0,071       neutral      0,563        Gain of
                                                  disorder

V408G        0,101       neutral      0,431        Loss of
                                                  stability

V481L        0,001       neutral      0,374     Gain of sheet

V589I        0,004       neutral      0,334        Gain of
                                                  catalytic
                                               residue at V589

V654G        0,433       neutral      0,438        Loss of
                                                  stability

V702A        0,002       neutral      0,408        Loss of
                                                  stability

V724M        0,833     deleterious    0,462        Loss of
                                                  catalytic
                                               residue at V724

V771M        0,034       neutral      0,421        Loss of
                                               ubiquitination
                                                   at K776

V825I        0,001       neutral      0,401        Loss of
                                                  catalytic
                                               residue at V825

W1699C         1       deleterious    0,915        Gain of
                                                  catalytic
                                                 residue at
                                                    L1700

W590L        0,841     deleterious    0,888     Loss of helix

W590S        0,889     deleterious    0,857        Gain of
                                                  disorder

W840R        0,998     deleterious    0,923        Gain of
                                               methylation at
                                                    W840

Y1921H       0,986     deleterious    0,752        Gain of
                                                  disorder

Y2178H       0,982     deleterious    0,826        Gain of
                                                  disorder

Y2206D       0,992     deleterious    0,878     Gain of sheet

Y482C        0,03        neutral      0,826     Gain of loop

Y835H        0,967     deleterious    0,653        Loss of
                                                  stability

Mutation      MAF       Deviation

A1010V         NA       0,50346003

A1046D         NA       0,04313351

A1182T     0,00045914   0,29981328

A1407T     0,00045914   0,11172287

A1631V         NA       0,05656854

A1670T         NA       0,30476302

A1756T         NA       0,27718586

A2028V         0        0,29557064

A255T          NA       0,53386562

A343V          NA       0,15980613

A391S          NA       0,01555635

A594T          NA       0,27294322

A697T      0,00045914   0,06505382

A746G      0,00045914   0,27718586

A779T          NA       0,04030509

A795S          NA       0,29981328

A937V          NA       0,04949748

C1477F         NA       0,35638182

C1477R         NA       0,10465181

C1660R         NA       0,02616295

CSS            NA       0,33587572

C887F      0,00137741   0,42567828

D1018G         NA       0,3231478

D1099N         NA       0,06646804

D1099Y         NA       0,03818377

D1263E         NA       0,14919953

D1289N         NA       0,16546299

D1553E         NA       0,19233304

D1706N         NA       0,27506454

D2243E     0,00459137   0,2920351

D434E          NA       0,28849957

D441N          NA       0,24607316

D444E          NA       0,23900209

D446E          NA       0,21283914

D457E          NA       0,39951533

D462G          NA       0,34223968

D581E          NA       0,02404163

D677E          NA       0,48648947

D831N          NA       0,28991378

D917N          NA       0,33728994

E1005K         NA       0,3648671

E1172D     0,0509642    0,1767767

E1172G     0,00091827   0,19657569

E1253K         NA       0,28637825

E1916A     0,00183655   0,22132442

E226G          NA       0,31890516

E284K          NA       0,44971991

E815G          NA       0,20435386

E868K      0,00275482   0,45184123

F1285L         NA       0,16546299

F1573S         NA       0,33021887

F2009S         NA       0,08555992

F2082V         NA       0,12445079

F2163S         NA       0,14990664

F346L          NA       0,16899852

F426L      0,00045914   0,27647875

F632C      0,00045914   0,21496046

F950S          NA       0,23405235

G1049R         NA       0,25597266

G1216V         NA       0,07566043

G1321A         NA       0,15627061

G156V          NA       0,26304372

G2147E         NA       0,06576093

G315W          NA       0,33304729

G616V          NA       0,39173716

G788W          NA       0,23758788

G851R          NA       0,20364675

H263D          NA       0,28213561

H551D          NA       0,10253048

I1084V         NA       0,19091883

I1239V         NA       0,21071782

I1517R         NA       0,03181981

I1555T         NA       0,03181981

I1911T     0,00045914   0,30476302

I35V       0,00045914   0,17253406

I546V          NA       0,2192031

I560T          NA       0,23546656

I649F          NA       0,21283914

1659V          NA       0,26233662

I883M       0,365473    0,20788939

K1250R     0,00045914   0,18314066

K1587R      0,410927    0,24253763

K166R          NA       0,1774838

K1761T     0,00045914   0,35850314

K1974R         NA       0,36840263

K2040E     0,00045914   0,15273507

K401Q          NA       0,22273864

K613E      0,00045914   0,30122749

K776N      0,00183655   0,29486353

L1041V     0,00137741   0,26445794

L1379F         NA       0,08555992

L1408F     0,00045914   0,01767767

F1648P         NA       0,14990664

F184S      0,00045914   0,40234376

F184W      0,00045914   0,27435743

F2032M         NA       0,14778532

F2168P         NA       0,20576807

F2187Q     0,00045914   0,21001071

M1012I         NA       0,41507168

M1091T         NA       0,01767767

M233V          NA       0,29486353

M415F          NA       0,29769196

M674F      0,00045914   0,04596194

N1185K         NA       0,40517219

N1185S         NA       0,25173001

N1406K         NA       0,28425693

N1611D         NA       0,03323402

N1800H         NA       0,04808326

N1800S         NA       0,42355696

N2119Y         NA       0,16475588

N820S          NA       0,24536605

N935H          NA       0,02121321

N935S          NA       0,09758074

P1065S         NA       0,06505382

P1475S         NA       0,54093669

P1878T         NA       0,32739044

P2150F         NA       0,53598694

P248A          NA       0,1463711

P250F          NA       0,17253406

P641L          NA       0,28072139

P855S          NA       0,26870058

P85L       0,00045914   0,15839192

Q1279K         NA       0,48295393

Q188K          0        0,38325188

Q205E          NA       0,17324116

Q205R          NA       0,19728279

Q2196H         NA       0,55649304

Q2210H         NA       0,42143564

Q597R          NA       0,20506097

Q849R          NA       0,01909188

R104C          NA       0,28001429

R1068C         NA       0,02687006

R1068H         NA       0,01979899

R1082C         NA       0,21637468

R1195Q         NA       0,22627417

R1195W         NA       0,25667976

R126H          NA       0,33021887

R1273L         NA       0,24253763

R1283C         NA       0,31678384

R1341T    [less than
          or equal to]
              0,001     0,41577879

R1344W     0,00045914   0,24960869

R1417H     0,00183655   0,26870058

R1615P    [less than
          or equal to]
              0,001     0,03676955

R1615Q         NA       0,34789654

R1680Q         NA       0,13435029

R1680W         NA       0,06293251

R1839H     0,00045914   0,33516861

R1851Q         NA       0,62366818

R1897W         NA       0,28213561

R1901S         NA       0,50840978

R1925Q     0,00229568   0,48366104

R2004K         NA       0,14990664

R2030Q         NA       0,28991378

R2081W         NA       0,04384062

R2173Q         NA       0,26445794

R2189G         NA       0,21283914

R219K       0,419192    0,28991378

R230C      0,00734619   0,48083261

R306G     [less than
          or equal to]
            0,001       0,29910617

R306H          NA       0,33092597

R369H          NA       0,35638182

R437Q          NA       0,27718586

R437W          NA       0,30334881

R443K      0,00045914   0,31112698

R496W          NA       0,25950819

R500H          NA       0,35779603

R587W          NA       0,22061732

R638Q          NA       0,20718229

R638W      0,00045914   0,23193102

R666Q          NA       0,39810112

R666W          NA       0,31112698

R672Q          NA       0,23405235

R965C     [less than
          or equal to]
              0,001     0,21637468

R999C          NA       0,45184123

R999L          NA       0,38183766

S107A          NA       0,24041631

S1141Y         NA       0,35284628

S1157N     0,00045914   0,23546656

S116N          NA       0,03181981

S1181F     0,00045914   0,35355339

S1255R     0,00183655   0,21142493

S1280R     0,00045914   0,24183052

S1376G    [less than
          or equal to]
             0,001      0,28284271

S139G          NA       0,20081833

S1506L         NA       0,18596908

S1536F         NA       0,28567114

S1731C    [less than
          or equal to]
             0,001      0,2595081

S212T      0,00459137   0,24536605

S2182F         NA       0,05656854

S2186F         NA       0,28567114

S442R          NA       0,31678384

S713G          NA       0,29981328

S780N          NA       0,30900566

T1175M     0,00091827   0,07141779

T1242M         NA       0,26375083

T1399M         NA       0,19516147

T1401I         NA       0,25809398

T1427M     0,00091827   0,24536605

T2073A     [less than
          or equal to]
              0,001     0,13788582

T459P       [less than
          or equal to]
              0,001     0,35638182

T515A          NA       0,28920667

T774P      0,00183655   0,42921382

T929I          NA       0,04030509

T940M          NA       0,11030866

V1054I         NA       0,31183409

V1096I         NA       0,33021887

V1158I         NA       0,11384419

V1674I     0,00137741   0,22839549

V1704D         NA       0,08768124

V1806M         NA       0,39810112

V1858M         NA       0,11808683

V2035M         NA       0,23900209

V2244I         NA        0,271529

V304M          NA       0,30829856

V380I          NA       0,24890159

V399A      0,00183655   0,34789654

V408G          NA       0,23334524

V481L      0,00045914   0,26375083

V589I      0,00091827   0,23334524

V654G          NA       0,00353553

V702A          NA       0,28708535

V724M      0,00045914   0,26233662

V771M      0,0606061    0,27365032

V825I       0,128099    0,28284271

W1699C         NA       0,06010408

W590L     [less than
          or equal to]
             0,001      0,03323402

W590S     [less than
          or equal to]
             0,001      0,02262742

W840R          NA       0,05303301

Y1921H         NA       0,16546299

Y2178H         NA       0,11030866

Y2206D         NA       0,08061017

Y482C          NA       0,56285691

Y835H          NA       0,22203153
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Article Details
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Title Annotation:Research Article; single nucleotide polymorphisms; ATP-binding cassette transporter
Author:Marin-Martin, Francisco R.; Soler-Rivas, Cristina; Martin-Hernandez, Roberto; Rodriguez-Casado, Aran
Publication:Cholesterol
Article Type:Report
Geographic Code:4EUSP
Date:Jan 1, 2014
Words:12906
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