Research Article

A Comprehensive In Silico Analysis of the Functional and Structural Impact of Nonsynonymous SNPs in the ABCA1 Transporter Gene

Table 2

Functional effects of nsSNPs for ABCA1 gene (UniProt: O95477) 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.

Mutationpph2_probPolyphen classRFscoreMutpred hypothesisMAFDeviation

A1010V0,104neutral0,816Loss of ubiquitination at K1009NA0,50346003
A1046D0,999deleterious0,938Loss of MoRF bindingNA0,04313351
A1182T0,001neutral0,425Loss of sheet0,000459140,29981328
A1407T0,119neutral0,277Gain of helix0,000459140,11172287
A1631V0,401neutral0,321Loss of sheetNA0,05656854
A1670T0,997deleterious0,566Gain of glycosylation at A1670NA0,30476302
A1756T0,81deleterious0,418Gain of glycosylation at A1756NA0,27718586
A2028V0,146neutral0,564Gain of methylation at K202300,29557064
A255T0neutral0,755Loss of helixNA0,53386562
A343V0,001neutral0,227Loss of disorderNA0,15980613
A391S0,318neutral0,34Gain of disorderNA0,01555635
A594T0,02neutral0,406Loss of catalytic residue at A594NA0,27294322
A697T0,416neutral0,508Gain of sheet0,000459140,06505382
A746G1deleterious0,608Loss of stability0,000459140,27718586
A779T0,411neutral0,468Loss of helixNA0,04030509
A795S0,07neutral0,494Loss of helixNA0,29981328
A937V0,991deleterious0,921Loss of disorderNA0,04949748
C1477F1deleterious0,496Loss of catalytic residue at C1477NA0,35638182
C1477R1deleterious0,852Gain of methylation at C1477NA0,10465181
C1660R0,954deleterious0,917Gain of methylation at C1660NA0,02616295
C3S0,005neutral0,48Gain of disorderNA0,33587572
C887F0,002neutral0,604Gain of phosphorylation at S8840,001377410,42567828
D1018G0,992deleterious0,535Loss of catalytic residue at D1018NA0,3231478
D1099N1deleterious0,906Gain of sheetNA0,06646804
D1099Y1deleterious0,946Loss of disorderNA0,03818377
D1263E0,003neutral0,214Gain of helixNA0,14919953
D1289N0,339neutral0,573Gain of sheetNA0,16546299
D1553E0,001neutral0,273Loss of helixNA0,19233304
D1706N1deleterious0,611Loss of helixNA0,27506454
D2243E0,078neutral0,491Gain of relative solvent accessibility0,004591370,2920351
D434E0,005neutral0,413Gain of disorderNA0,28849957
D441N0neutral0,348Loss of helixNA0,24607316
D444E0neutral0,338Loss of helix NA0,23900209
D446E0neutral0,301Loss of helixNA0,21283914
D457E0,001neutral0,566Loss of helixNA0,39951533
D462G0,071neutral0,555Loss of catalytic residue at D462NA0,34223968
D581E0,38neutral0,346Loss of helixNA0,02404163
D677E0,158neutral0,846Loss of loopNA0,48648947
D831N0,999deleterious0,589Gain of helixNA0,28991378
D917N0,1neutral0,577Gain of MoRF bindingNA0,33728994
E1005K0,026neutral0,542Gain of MoRF bindingNA0,3648671
E1172D0,003neutral0,253Loss of sheet0,05096420,1767767
E1172G0,003neutral0,281Loss of sheet0,000918270,19657569
E1253K0,048neutral0,453Gain of ubiquitination at E1253NA0,28637825
E1916A0,027neutral0,34Gain of MoRF binding0,001836550,22132442
E226G0,019neutral0,47Loss of stabilityNA0,31890516
E284K0,206neutral0,842Gain of methylation at E284NA0,44971991
E815G0,072neutral0,361Loss of disorderNA0,20435386
E868K0,051neutral0,69Gain of methylation at E8680,002754820,45184123
F1285L0,001neutral0,235Loss of loopNA0,16546299
F1573S0,065neutral0,532Gain of disorder NA0,33021887
F2009S0,811deleterious0,932Gain of disorderNA0,08555992
F2082V0,266neutral0,442Gain of MoRF bindingNA0,12445079
F2163S0,939deleterious0,727Loss of sheetNA0,14990664
F346L0neutral0,239Gain of disorderNA0,16899852
F426L0,94deleterious0,549Gain of helix0,000459140,27647875
F632C0,998deleterious0,694Loss of stability0,000459140,21496046
F950S0,995deleterious0,664Gain of disorderNA0,23405235
G1049R1deleterious0,638Gain of MoRF bindingNA0,25597266
G1216V0,951deleterious0,844Loss of ubiquitination at K1214NA0,07566043
G1321A0,936deleterious0,715Gain of catalytic residue at G1321NA0,15627061
G156V0,017neutral0,389Loss of helixNA0,26304372
G2147E0,49neutral0,397Loss of catalytic residue at S2148NA0,06576093
G315W0,997deleterious0,526Loss of disorderNA0,33304729
G616V0,998deleterious0,444Loss of disorderNA0,39173716
G788W1deleterious0,664Loss of catalytic residue at P784NA0,23758788
G851R0,998deleterious0,71Gain of catalytic residue at G851NA0,20364675
H263D0neutral0,399Loss of helixNA0,28213561
H551D0,613deleterious0,468Gain of sheetNA0,10253048
I1084V0,241neutral0,511Gain of MoRF bindingNA0,19091883
I1239V0,078neutral0,376Loss of catalytic residue at L1244NA0,21071782
I1517R0,962deleterious0,917Gain of catalytic residue at I1517NA0,03181981
I1555T0,439neutral0,484Loss of stabilityNA0,03181981
I1911T0,006neutral0,437Loss of stability0,000459140,30476302
I35V0,066neutral0,31Loss of helix0,000459140,17253406
I546V0neutral0,31Gain of MoRF bindingNA0,2192031
I560T0,829deleterious0,496Loss of stabilityNA0,23546656
I649F0,97deleterious0,669Loss of catalytic residue at I649NA0,21283914
I659V0,034neutral0,405Loss of methylation at K663NA0,26233662
I883M0,002neutral0,296Gain of disorder0,3654730,20788939
K1250R0,118neutral0,377Loss of methylation at K12500,000459140,18314066
K1587R0,034neutral0,377Gain of helix0,4109270,24253763
K166R0neutral0,251Loss of ubiquitination at K166NA0,1774838
K1761T0,038neutral0,545Loss of methylation at K17610,000459140,35850314
K1974R0,158neutral0,679Loss of ubiquitination at K1974NA0,36840263
K2040E0,243neutral0,459Loss of MoRF binding0,000459140,15273507
K401Q0,007neutral0,322Loss of ubiquitination at K401NA0,22273864
K613E0,002neutral0,428Loss of ubiquitination at K6130,000459140,30122749
K776N0,985deleterious0,568Loss of methylation at K7760,001836550,29486353
L1041V0,999deleterious0,625Loss of ubiquitination at K10400,001377410,26445794
L1379F0,987deleterious0,866Loss of catalytic residue at L1379NA0,08555992
L1408F0,443neutral0,418Loss of stability0,000459140,01767767
L1648P0,961deleterious0,749Loss of stabilityNA0,14990664
L184S0,007neutral0,576Loss of sheet0,000459140,40234376
L184W0,928deleterious0,54Gain of helix0,000459140,27435743
L2032M0,897deleterious0,688Gain of methylation at K2036NA0,14778532
L2168P0,984deleterious0,693Gain of disorderNA0,20576807
L2187Q0,995deleterious0,698Gain of disorder0,000459140,21001071
M1012I0,008neutral0,595Loss of catalytic residue at V1008NA0,41507168
M1091T0,98deleterious0,955Gain of disorderNA0,01767767
M233V0neutral0,417Loss of stabilityNA0,29486353
M415L0,002neutral0,423Gain of relative solvent accessibilityNA0,29769196
M674L0,534deleterious0,599Loss of catalytic residue at M6740,000459140,04596194
N1185K0,01neutral0,583Gain of MoRF bindingNA0,40517219
N1185S0,002neutral0,358Gain of helixNA0,25173001
N1406K0,006neutral0,408Gain of ubiquitination at N1406NA0,28425693
N1611D0,968deleterious0,921Loss of MoRF bindingNA0,03323402
N1800H0,758deleterious0,826Loss of stabilityNA0,04808326
N1800S0,241neutral0,84Loss of stabilityNA0,42355696
N2119Y0,96deleterious0,727Loss of MoRF bindingNA0,16475588
N820S0,001neutral0,348Loss of catalytic residue at N820NA0,24536605
N935H0,996deleterious0,966Gain of disorderNA0,02121321
N935S0,831deleterious0,969Gain of disorderNA0,09758074
P1065S0,998deleterious0,906Gain of MoRF bindingNA0,06505382
P1475S1deleterious0,235Gain of phosphorylation at P1475NA0,54093669
P1878T0,019neutral0,482Gain of helixNA0,32739044
P2150L0,068neutral0,826Loss of disorderNA0,53598694
P248A0neutral0,207Loss of helixNA0,1463711
P250L0neutral0,244Loss of glycosylation at P250NA0,17253406
P641L1deleterious0,603Gain of MoRF bindingNA0,28072139
P855S0,97deleterious0,59Loss of catalytic residue at W856NA0,26870058
P85L0,394neutral0,618Loss of disorder0,000459140,15839192
Q1279K0,032neutral0,715Gain of MoRF bindingNA0,48295393
Q188K0,001neutral0,543Gain of ubiquitination at Q18800,38325188
Q205E0,01neutral0,255Loss of loopNA0,17324116
Q205R0neutral0,279Gain of helixNA0,19728279
Q2196H0,011neutral0,798Loss of MoRF bindingNA0,55649304
Q2210H0,984deleterious0,388Gain of catalytic residue at D2214NA0,42143564
Q597R1deleterious0,71Gain of MoRF bindingNA0,20506097
Q849R0,689deleterious0,662Gain of methylation at Q849NA0,01909188
R104C0,985deleterious0,589Loss of MoRF bindingNA0,28001429
R1068C1deleterious0,962Loss of MoRF bindingNA0,02687006
R1068H1deleterious0,972Loss of MoRF bindingNA0,01979899
R1082C1deleterious0,694Loss of MoRF bindingNA0,21637468
R1195Q0,044neutral0,364Loss of loopNA0,22627417
R1195W0,952deleterious0,589Gain of catalytic residue at A1194NA0,25667976
R126H0neutral0,467Loss of MoRF bindingNA0,33021887
R1273L0,007neutral0,35Loss of loopNA0,24253763
R1283C0,001neutral0,449Gain of ubiquitination at K1278NA0,31678384
R1341T0,016neutral0,604Loss of methylation at R13410,0010,41577879
R1344W0,993deleterious0,64Loss of methylation at K13450,000459140,24960869
R1417H0,837deleterious0,457Loss of phosphorylation at T14160,001836550,26870058
R1615P0,947deleterious0,895Loss of methylation at R16150,0010,03676955
R1615Q0,187neutral0,679Gain of helixNA0,34789654
R1680Q0,997deleterious0,807Gain of ubiquitination at K1683NA0,13435029
R1680W1deleterious0,911Loss of disorderNA0,06293251
R1839H0,006neutral0,48Loss of phosphorylation at S18420,000459140,33516861
R1851Q0,015neutral0,897Gain of catalytic residue at R1851NA0,62366818
R1897W0,009neutral0,408Probably damagingNA0,28213561
R1901S0,091neutral0,81Gain of phosphorylation at R1901NA0,50840978
R1925Q0,006neutral0,69Loss of MoRF binding0,002295680,48366104
R2004K0,911deleterious0,699Gain of ubiquitination at R2004NA0,14990664
R2030Q0,032neutral0,442Loss of MoRF bindingNA0,28991378
R2081W0,998deleterious0,936Loss of MoRF bindingNA0,04384062
R2173Q0,008neutral0,382Gain of sheetNA0,26445794
R2189G0,142neutral0,443Loss of MoRF bindingNA0,21283914
R219K0neutral0,41Gain of ubiquitination at R2190,4191920,28991378
R230C0neutral0,68Loss of MoRF binding0,007346190,48083261
R306G0,04neutral0,463Loss of helix0,0010,29910617
R306H0,899deleterious0,431Loss of helixNA0,33092597
R369H0,937deleterious0,433Loss of MoRF bindingNA0,35638182
R437Q0,088neutral0,48Loss of helixNA0,27718586
R437W0,991deleterious0,562Gain of catalytic residue at L435NA0,30334881
R443K0neutral0,44Loss of stability0,000459140,31112698
R496W0,209neutral0,576Loss of loopNA0,25950819
R500H0,013neutral0,519Loss of helixNA0,35779603
R587W1deleterious0,688Loss of disorderNA0,22061732
R638Q0,957deleterious0,664Loss of methylation at R638NA0,20718229
R638W0,999deleterious0,671Loss of methylation at R6380,000459140,23193102
R666Q1deleterious0,437Gain of ubiquitination at K668NA0,39810112
R666W1deleterious0,56Gain of catalytic residue at R666NA0,31112698
R672Q0,832deleterious0,501Loss of MoRF bindingNA0,23405235
R965C0,302neutral0,608Loss of disorder0,0010,21637468
R999C0,127neutral0,766Loss of solvent accessibilityNA0,45184123
R999L0,208neutral0,748Loss of solvent accessibilityNA0,38183766
S107A0,002neutral0,342Gain of helixNA0,24041631
S1141Y0,805deleterious0,306Loss of phosphorylation at S1141NA0,35284628
S1157N0,022neutral0,355Gain of sheet0,000459140,23546656
S116N0,196neutral0,241Loss of phosphorylation at S116NA0,03181981
S1181F0,042neutral0,542Loss of disorder0,000459140,35355339
S1255R0,027neutral0,326Loss of glicosilation at S12550,001836550,21142493
S1280R0,009neutral0,351Gain of sheet0,000459140,24183052
S1376G0,007neutral0,407Gain of methylation at K13730,0010,28284271
S139G0neutral0,284Gain of helixNA0,20081833
S1506L0,996deleterious0,733Loss of helixNA0,18596908
S1536F0,998deleterious0,594Loss of disorderNA0,28567114
S1731C0,893deleterious0,526Loss of helix0,0010,25950819
S212T0,028neutral0,375Gain of helix0,004591370,24536605
S2182F0,578deleterious0,498Loss of disorderNA0,05656854
S2186F0,862deleterious0,458Loss of disorderNA0,28567114
S442R0,001neutral0,449Loss of helixNA0,31678384
S713G1deleterious0,576Loss of stabilityNA0,29981328
S780N0,996deleterious0,559Loss of stabilityNA0,30900566
T1175M0,432neutral0,331Loss of sheet0,000918270,07141779
T1242M0,993deleterious0,62Loss of catalytic residue at T1242NA0,26375083
T1399M0,003neutral0,279Loss of glycosylation at T1399NA0,19516147
T1401I0,003neutral0,368Loss of glycosylation at T1401NA0,25809398
T1427M0,005neutral0,352Gain of catalytic residue at T14270,000918270,24536605
T2073A0,852deleterious0,657Loss of phosphorylation at T20730,0010,13788582
T459P0,03neutral0,534Gain of helix0,0010,35638182
T515A0,04neutral0,449Gain of helixNA0,28920667
T774P0,003neutral0,61Gain of methylation at K7760,001836550,42921382
T929I0,946deleterious0,889Loss of disorderNA0,04030509
T940M1deleterious0,844Loss of methylation at K939NA0,11030866
V1054I0,951deleterious0,51Loss of ubiquitination at K1052NA0,31183409
V1096I0neutral0,467Gain of helixNA0,33021887
V1158I0,065neutral0,226Loss of sheetNA0,11384419
V1674I0,053neutral0,376Loss of catalytic residue at V16740,001377410,22839549
V1704D0,752deleterious0,876Loss of helixNA0,08768124
V1806M0,98deleterious0,417Gain of ubiquitination at K1804NA0,39810112
V1858M0,305neutral0,472Loss of catalytic residue at V1858NA0,11808683
V2035M0,042neutral0,38Loss of methylation at K2036NA0,23900209
V2244I0,002neutral0,386Gain of sheetNA0,271529
V304M0,823deleterious0,387Gain of disorderNA0,30829856
V380I0,001neutral0,353Gain of methylation at K376NA0,24890159
V399A0,071neutral0,563Gain of disorder0,001836550,34789654
V408G0,101neutral0,431Loss of stabilityNA0,23334524
V481L0,001neutral0,374Gain of sheet0,000459140,26375083
V589I0,004neutral0,334Gain of catalytic residue at V5890,000918270,23334524
V654G0,433neutral0,438Loss of stabilityNA0,00353553
V702A0,002neutral0,408Loss of stabilityNA0,28708535
V724M0,833deleterious0,462Loss of catalytic residue at V7240,000459140,26233662
V771M0,034neutral0,421Loss of ubiquitination at K7760,06060610,27365032
V825I0,001neutral0,401Loss of catalytic residue at V8250,1280990,28284271
W1699C1deleterious0,915Gain of catalytic residue at L1700NA0,06010408
W590L0,841deleterious0,888Loss of helix0,0010,03323402
W590S0,889deleterious0,857Gain of disorder0,0010,02262742
W840R0,998deleterious0,923Gain of methylation at W840NA0,05303301
Y1921H0,986deleterious0,752Gain of disorderNA0,16546299
Y2178H0,982deleterious0,826Gain of disorderNA0,11030866
Y2206D0,992deleterious0,878Gain of sheetNA0,08061017
Y482C0,03neutral0,826Gain of loopNA0,56285691
Y835H0,967deleterious0,653Loss of stabilityNA0,22203153