ABCA1 p.Glu284Lys
| Predicted by SNAP2: | A: N (72%), C: N (57%), D: N (61%), F: N (57%), G: N (57%), H: N (53%), I: N (61%), K: N (57%), L: N (66%), M: N (53%), N: N (66%), P: D (71%), Q: N (72%), R: D (53%), S: N (72%), T: N (72%), V: N (72%), W: D (71%), Y: N (61%), |
| Predicted by PROVEAN: | A: N, C: N, D: N, F: N, G: N, H: N, I: N, K: N, L: N, M: N, N: N, P: N, Q: N, R: N, S: N, T: N, V: N, W: N, Y: N, |
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[hide] Accurate prediction of the functional significance... PLoS Genet. 2005 Dec;1(6):e83. Epub 2005 Dec 30. Brunham LR, Singaraja RR, Pape TD, Kejariwal A, Thomas PD, Hayden MR
Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.
PLoS Genet. 2005 Dec;1(6):e83. Epub 2005 Dec 30., [PMID:16429166]
Abstract [show]
The human genome contains an estimated 100,000 to 300,000 DNA variants that alter an amino acid in an encoded protein. However, our ability to predict which of these variants are functionally significant is limited. We used a bioinformatics approach to define the functional significance of genetic variation in the ABCA1 gene, a cholesterol transporter crucial for the metabolism of high density lipoprotein cholesterol. To predict the functional consequence of each coding single nucleotide polymorphism and mutation in this gene, we calculated a substitution position-specific evolutionary conservation score for each variant, which considers site-specific variation among evolutionarily related proteins. To test the bioinformatics predictions experimentally, we evaluated the biochemical consequence of these sequence variants by examining the ability of cell lines stably transfected with the ABCA1 alleles to elicit cholesterol efflux. Our bioinformatics approach correctly predicted the functional impact of greater than 94% of the naturally occurring variants we assessed. The bioinformatics predictions were significantly correlated with the degree of functional impairment of ABCA1 mutations (r2 = 0.62, p = 0.0008). These results have allowed us to define the impact of genetic variation on ABCA1 function and to suggest that the in silico evolutionary approach we used may be a useful tool in general for predicting the effects of DNA variation on gene function. In addition, our data suggest that considering patterns of positive selection, along with patterns of negative selection such as evolutionary conservation, may improve our ability to predict the functional effects of amino acid variation.
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No. Sentence Comment
48 This SNP has been reported to be associated with decreased HDL cholesterol and increased severity of atherosclerosis in Table 1. subPSEC Scores and Probability of Functional Impairment (Pdeleterious) for ABCA1 Mutations and SNPs Mutations SNPs Variant SubPSEC Pdeleterious Variant subPSEC Pdeleterious P85L À4.62 0.83 R219K À0.57 0.08 H160F À2.79 0.45 V399A À2.26 0.32 R230C À4.27 0.78 V771M À2.86 0.46 A255T À1.81 0.23 T774P À1.99 0.27 E284K À2.34 0.34 K776N À3.53 0.63 Y482C À4.21 0.77 V825I À1.06 0.13 R587W À6.04 0.95 I883M À1.38 0.17 W590S À5.19 0.9 E1172D À1.96 0.26 W590L À4.48 0.82 R1587K À0.58 0.08 Q597R À7.15 0.98 S1731C À4.21 0.77 T929I À4.29 0.78 N935H À8.54 1 N935S À7.53 0.99 A937V À6.6 0.97 A1046D À7.52 0.99 M1091T À3.56 0.64 D1099Y À6.09 0.96 D1289N À2.48 0.37 L1379F À3.81 0.69 C1477R À5.44 0.92 S1506L À5.17 0.9 N1611D À5.69 0.94 R1680W À6.02 0.95 V1704D À3.21 0.55 N1800H À4.23 0.77 R1901S À5.06 0.89 F2009S À2.73 0.43 R2081W À8.08 0.99 P2150L À2.88 0.47 Q2196H À2.74 0.43 DOI: 10.1371/journal.pgen.0010083.t001 PLoS Genetics | www.plosgenetics.org December 2005 | Volume 1 | Issue 6 | e83 0740 Accurate Prediction of ABCA1 Variants Synopsis A major goal of human genetics research is to understand how genetic variation leads to differences in the function of genes.
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ABCA1 p.Glu284Lys 16429166:48:437
status: NEWX
ABCA1 p.Glu284Lys 16429166:48:477
status: NEW[hide] Familial HDL deficiency due to ABCA1 gene mutation... Atherosclerosis. 2004 Feb;172(2):309-20. Pisciotta L, Hamilton-Craig I, Tarugi P, Bellocchio A, Fasano T, Alessandrini P, Bon GB, Siepi D, Mannarino E, Cattin L, Averna M, Cefalu AB, Cantafora A, Calandra S, Bertolini S
Familial HDL deficiency due to ABCA1 gene mutations with or without other genetic lipoprotein disorders.
Atherosclerosis. 2004 Feb;172(2):309-20., [PMID:15019541]
Abstract [show]
Mutations in ABCA1 have been shown to be the cause of Tangier disease (TD) and some forms of familial hypoalphalipoproteinemia (HA), two genetic disorders characterized by low plasma HDL levels. Here we report six subjects with low HDL, carrying seven ABCA1 mutations, six of which are previously unreported. Two mutations (R557X and H160FsX173) were predicted to generate short truncated proteins; two mutations (E284K and Y482C) were located in the first extracellular loop and two (R1901S and Q2196H) in the C-terminal cytoplasmic domain of ABCA1. Two subjects found to be compound heterozygotes for ABCA1 mutations did not have overt clinical manifestations of TD. Three subjects, all with premature coronary artery disease (pCAD), had a combination of genetic defects. Besides being heterozygotes for ABCA1 mutations, two of them were also carriers of the R3500Q substitution in apolipoprotein B and the third was a carrier of N291S substitution in lipoprotein lipase. By extending family studies we identified 17 heterozygotes for ABCA1 mutations. Plasma HDL-C and Apo A-I values in these subjects were 38.3 and 36.9% lower than in unaffected family members and similar to the values found in heterozygotes for Apo A-I gene mutations which prevent Apo A-I synthesis. This survey underlines the allelic heterogeneity of ABCA1 mutations and suggests that: (i) TD subjects, if asymptomatic, may be overlooked and (ii) there may be a selection bias in genotyping towards carriers of ABCA1 mutations who have pCAD possibly related to a combination of genetic and environmental cardiovascular risk factors.
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2 Two mutations (R557X and H160FsX173) were predicted to generate short truncated proteins; two mutations (E284K and Y482C) were located in the first extracellular loop and two (R1901S and Q2196H) in the C-terminal cytoplasmic domain of ABCA1.
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ABCA1 p.Glu284Lys 15019541:2:105
status: NEW61 The proband of Family 1 was a carrier of an ABCA1 mutation (E284K) and an Apo B mutation (R3500Q).
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ABCA1 p.Glu284Lys 15019541:61:60
status: NEW118 Transition c.850 G > A in exon 9 (E284K) A 181 bp fragment of exon 9 was amplified using a forward mismatched primer: 5 -AAG CTG GAG TGA CAT GCG ATC G-3 and a canonic reverse primer: 5 -GTC TCC AAA GAG GGC TTT GTA G-3 .
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ABCA1 p.Glu284Lys 15019541:118:34
status: NEW140 The sequence of ABCA1 gene revealed an heterozygous transition c.850 G > A (E284K) in exon 9 (Fig. 3).
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ABCA1 p.Glu284Lys 15019541:140:76
status: NEW164 II.2 W/W 43 M 28.0 5.10 3.70 0.96 0.80 104 98 ε3ε4 III.3 M2/W 9 M - 3.00 1.94 0.75 0.70 92 52 ε3ε4 Family 4 II.1 M4/W 62 M 23.3 4.45 2.71 0.72 2.21 102 92 ε3ε3 +++ Family 5 II.1a M5/W 59 M 36.7 7.16 6.02 0.52 1.71 81 133 ε3ε4 +++ III.1a W/W 33 F 21.8 7.52 5.02 1.99 1.13 162 112 ε4ε4 III.2 M5/W 31 F 22.8 4.68 3.28 0.85 1.18 92 82 ε3ε4 III.3 M5/W 31 F 24.4 4.00 2.74 0.90 0.78 97 72 ε3ε4 Family 6 I.2 M6/W 53 F 40.2 4.76 3.00 1.16 1.31 104 81 ε3ε3 II.1 W/W 41 M 27.5 6.54 4.35 1.19 2.20 141 148 ε3ε4 II.2 M6/W 39 M 26.2 3.57 2.44 0.77 0.77 93 71 ε3ε4 II.3 M6/W 37 F 21.3 4.44 2.63 0.76 2.30 85 89 ε3ε4 II.4 M7/W 37 M 18.8 3.67 2.43 1.00 0.50 89 57 ε3ε3 III.1 M6/M7 16 F 25.4 3.33 2.45 0.18 1.55 12 102 ε3ε3 III.2 M7/W 10 F 14.2 2.66 1.34 0.98 0.76 103 38 ε3ε3 W, ABCA1 wild-type allele; M, ABCA1 mutant allele: M1 (E284K); M2 (N1800H); M3 (Y482C); M4 (Q2196H); M5 (R557X); M6 (H160FsX173); M7 (R1901S); ND: not determined.
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ABCA1 p.Glu284Lys 15019541:164:955
status: NEWX
ABCA1 p.Glu284Lys 15019541:164:983
status: NEW200 of our series (Families 2 and 3), we are tempted to suggest that N1800H might be a recurrent mutation.
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ABCA1 p.Glu284Lys 15019541:200:216
status: NEW201 The novel mutations we identified included: (a) one non-sense (R557X) and one frameshift (H160FsX173) mutation, both predicted to encode short peptides presumably devoid of any function; (b) four missense mutations (E284K, Y482C, R1901S and Q2196H) resulting in non-homologous amino acid substitutions.
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ABCA1 p.Glu284Lys 15019541:201:216
status: NEW204 The E284K and the Y482C are located in the first extracellular loop of ABCA1, where they may interfere with the binding to Apo A-I and/or the membrane release of phospholipids, as it has been demonstrated for other mutations (R587W and Q597R) located in the same extracellular domain [40,41].
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ABCA1 p.Glu284Lys 15019541:204:4
status: NEW203 The E284K and the Y482C are located in the first extracellular loop of ABCA1, where they may interfere with the binding to Apo A-I and/or the membrane release of phospholipids, as it has been demonstrated for other mutations (R587W and Q597R) located in the same extracellular domain [40,41].
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ABCA1 p.Glu284Lys 15019541:203:4
status: NEW