********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** WARNING: Incorrect mutation L959V WARNING: Incorrect mutation H960R WARNING: Incorrect mutation K961R WARNING: Incorrect mutation K961N WARNING: Incorrect mutation G962D WARNING: Incorrect mutation S963C WARNING: Incorrect mutation R966W WARNING: Incorrect mutation R966Q WARNING: Incorrect mutation V976A WARNING: Incorrect mutation V979M WARNING: Incorrect mutation G985V WARNING: Incorrect mutation I986V WARNING: Incorrect mutation S989G WARNING: Incorrect mutation N992S WARNING: Incorrect mutation V993L WARNING: Incorrect mutation V994M WARNING: Incorrect mutation R998Q WARNING: Incorrect mutation R1001Q WARNING: Incorrect mutation P1005S WARNING: Incorrect mutation I1009V WARNING: Incorrect mutation C1021R WARNING: Incorrect mutation C1021G WARNING: Incorrect mutation A1025T WARNING: Incorrect mutation G1030R WARNING: Incorrect mutation V1033M WARNING: Incorrect mutation T1036A WARNING: Incorrect mutation T1036S WARNING: Incorrect mutation G1047R WARNING: Incorrect mutation G1047A WARNING: Incorrect mutation K1054R WARNING: Incorrect mutation C1058Y WARNING: Incorrect mutation D1060N WARNING: Incorrect mutation S1061G WARNING: Incorrect mutation S1062F WARNING: Incorrect mutation Q1064K WARNING: Incorrect mutation A1067T WARNING: Incorrect mutation A1067V WARNING: Incorrect mutation E1068Q WARNING: Incorrect mutation N1072K WARNING: Incorrect mutation I1074V WARNING: Incorrect mutation T1075M WARNING: Incorrect mutation K1077R WARNING: Incorrect mutation D1078E WARNING: Incorrect mutation G1079R WARNING: Incorrect mutation V1081F WARNING: Incorrect mutation V1081A WARNING: Incorrect mutation D1082N WARNING: Incorrect mutation D1082A WARNING: Incorrect mutation D1082G WARNING: Incorrect mutation P1084A WARNING: Incorrect mutation I1085N WARNING: Incorrect mutation Q1087H WARNING: Incorrect mutation P1088T WARNING: Incorrect mutation P1088A WARNING: Incorrect mutation P1088S WARNING: Incorrect mutation P1088H WARNING: Incorrect mutation R1089C WARNING: Incorrect mutation S1090R WARNING: Incorrect mutation W1091C WARNING: Incorrect mutation S1094N WARNING: Incorrect mutation K1095R WARNING: Incorrect mutation D1099N WARNING: Incorrect mutation N1100S WARNING: Incorrect mutation A1103G WARNING: Incorrect mutation A1104G WARNING: Incorrect mutation A1104V WARNING: Incorrect mutation M1106I WARNING: Incorrect mutation T1110A WARNING: Incorrect mutation T1110I WARNING: Incorrect mutation V1111I WARNING: Incorrect mutation V1111F WARNING: Incorrect mutation T1113P WARNING: Incorrect mutation T1113I WARNING: Incorrect mutation F1114S WARNING: Incorrect mutation E1115K WARNING: Incorrect mutation E1115G WARNING: Incorrect mutation G1116E WARNING: Incorrect mutation G1116A WARNING: Incorrect mutation Y1122S WARNING: Incorrect mutation R1123S WARNING: Incorrect mutation R1123G WARNING: Incorrect mutation R1123C WARNING: Incorrect mutation R1123H WARNING: Incorrect mutation I1125V WARNING: Incorrect mutation D1126N WARNING: Incorrect mutation T1129M WARNING: Incorrect mutation D1131N WARNING: Incorrect mutation K1132E WARNING: Incorrect mutation G1133S WARNING: Incorrect mutation G1133D WARNING: Incorrect mutation I1135V WARNING: Incorrect mutation I1135M WARNING: Incorrect mutation R1139H WARNING: Incorrect mutation V1140E WARNING: Incorrect mutation I1142L WARNING: Incorrect mutation I1144V WARNING: Incorrect mutation I1147V WARNING: Incorrect mutation I1148T WARNING: Incorrect mutation I1152F WARNING: Incorrect mutation I1153V WARNING: Incorrect mutation A1154T WARNING: Incorrect mutation A1154S WARNING: Incorrect mutation A1154V WARNING: Incorrect mutation M1158K WARNING: Incorrect mutation V1162M WARNING: Incorrect mutation V1162L WARNING: Incorrect mutation I1166T WARNING: Incorrect mutation V1167I WARNING: Incorrect mutation V1167A WARNING: Incorrect mutation T1168N WARNING: Incorrect mutation Q1170R WARNING: Incorrect mutation K1178N WARNING: Incorrect mutation K1184N WARNING: Incorrect mutation V1190M WARNING: Incorrect mutation V1190L WARNING: Incorrect mutation V1190G WARNING: Incorrect mutation A1193T WARNING: Incorrect mutation A1193V WARNING: Incorrect mutation A1196T WARNING: Incorrect mutation R1197W WARNING: Incorrect mutation R1197Q WARNING: Incorrect mutation R1200Q WARNING: Incorrect mutation I1203V WARNING: Incorrect mutation I1203T WARNING: Incorrect mutation K1205E WARNING: Incorrect mutation K1205R WARNING: Incorrect mutation K1205N WARNING: Incorrect mutation Q1209K WARNING: Incorrect mutation Q1209R WARNING: Incorrect mutation Q1209H WARNING: Incorrect mutation Y1210H WARNING: Incorrect mutation K1211E WARNING: Incorrect mutation Y1214H WARNING: Incorrect mutation V1215M WARNING: Incorrect mutation V1215L WARNING: Incorrect mutation V1216I WARNING: Incorrect mutation N1217T WARNING: Incorrect mutation F1221L WARNING: Incorrect mutation F1226S WARNING: Incorrect mutation F1226L WARNING: Incorrect mutation F1226L WARNING: Incorrect mutation V1227I WARNING: Incorrect mutation V1227L WARNING: Incorrect mutation L1231F WARNING: Incorrect mutation I1234V WARNING: Incorrect mutation I1234F WARNING: Incorrect mutation I1234N WARNING: Incorrect mutation I1234T WARNING: Incorrect mutation C1235F WARNING: Incorrect mutation A1237V WARNING: Incorrect mutation M1238V WARNING: Incorrect mutation Y1241S WARNING: Incorrect mutation G1242S WARNING: Incorrect mutation S1244N WARNING: Incorrect mutation F1247L WARNING: Incorrect mutation A1250T WARNING: Incorrect mutation A1250S WARNING: Incorrect mutation M1251T WARNING: Incorrect mutation M1251I WARNING: Incorrect mutation L1254V WARNING: Incorrect mutation N1255S WARNING: Incorrect mutation L1257F WARNING: Incorrect mutation V1264M Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method N898S Neutral 2 0.399 PhD-SNP: F[N]=20% F[S]=2% Nali=1124 N898S Neutral 2 0.388 PANTHER: F[N]=56% F[S]=4% N898S Disease 7 0.846 SNPs&GO D899N Neutral 4 0.281 PhD-SNP: F[D]=6% F[N]=9% Nali=1125 D899N Neutral 6 0.215 PANTHER: F[D]=33% F[N]=5% D899N Disease 6 0.810 SNPs&GO T900M Neutral 5 0.265 PhD-SNP: F[T]=7% F[M]=0% Nali=1128 T900M Neutral 1 0.463 PANTHER: F[T]=29% F[M]=1% T900M Disease 7 0.835 SNPs&GO I901M Neutral 6 0.186 PhD-SNP: F[I]=11% F[M]=5% Nali=1109 I901M Neutral 1 0.452 PANTHER: F[I]=51% F[M]=2% I901M Disease 7 0.845 SNPs&GO I901V Neutral 7 0.156 PhD-SNP: F[I]=11% F[V]=4% Nali=1109 I901V Neutral 7 0.160 PANTHER: F[I]=51% F[V]=14% I901V Disease 1 0.537 SNPs&GO L912I Disease 0 0.515 PhD-SNP: F[L]=55% F[I]=7% Nali=1136 L912I Neutral 4 0.285 PANTHER: F[L]=61% F[I]=7% L912I Disease 7 0.844 SNPs&GO S913G Disease 4 0.709 PhD-SNP: F[S]=49% F[G]=1% Nali=1142 S913G Disease 9 0.936 PANTHER: F[S]=91% F[G]=1% S913G Disease 9 0.972 SNPs&GO S913N Neutral 5 0.226 PhD-SNP: F[S]=49% F[N]=44% Nali=1142 S913N Disease 9 0.968 PANTHER: F[S]=91% F[N]=0% S913N Disease 9 0.937 SNPs&GO I915V Neutral 7 0.158 PhD-SNP: F[I]=43% F[V]=17% Nali=1144 I915V Neutral 7 0.143 PANTHER: F[I]=49% F[V]=14% I915V Disease 0 0.521 SNPs&GO S916F Disease 1 0.570 PhD-SNP: F[S]=17% F[F]=8% Nali=1147 S916F Disease 3 0.634 PANTHER: F[S]=53% F[F]=1% S916F Disease 9 0.969 SNPs&GO A919V Neutral 3 0.372 PhD-SNP: F[A]=25% F[V]=4% Nali=1131 A919V Disease 9 0.964 PANTHER: F[A]=92% F[V]=0% A919V Disease 9 0.961 SNPs&GO P922A Neutral 3 0.365 PhD-SNP: F[P]=67% F[A]=1% Nali=893 P922A Disease 10 0.978 PANTHER: F[P]=97% F[A]=0% P922A Disease 9 0.937 SNPs&GO F936C Disease 6 0.810 PhD-SNP: F[F]=44% F[C]=1% Nali=533 F936C Unclassified NA NA PANTHER: F[F]=NA F[C]=NA F936C Disease 8 0.903 SNPs&GO F936L Neutral 1 0.441 PhD-SNP: F[F]=44% F[L]=15% Nali=533 F936L Unclassified NA NA PANTHER: F[F]=NA F[L]=NA F936L Disease 3 0.672 SNPs&GO F936S Disease 3 0.660 PhD-SNP: F[F]=44% F[S]=3% Nali=533 F936S Unclassified NA NA PANTHER: F[F]=NA F[S]=NA F936S Disease 7 0.856 SNPs&GO I938T Disease 0 0.503 PhD-SNP: F[I]=43% F[T]=4% Nali=507 I938T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I938T Disease 5 0.750 SNPs&GO V939A Neutral 6 0.198 PhD-SNP: F[V]=23% F[A]=7% Nali=545 V939A Unclassified NA NA PANTHER: F[V]=NA F[A]=NA V939A Neutral 2 0.383 SNPs&GO T942A Neutral 5 0.249 PhD-SNP: F[T]=22% F[A]=9% Nali=566 T942A Unclassified NA NA PANTHER: F[T]=NA F[A]=NA T942A Disease 0 0.515 SNPs&GO T942S Neutral 5 0.264 PhD-SNP: F[T]=22% F[S]=12% Nali=566 T942S Unclassified NA NA PANTHER: F[T]=NA F[S]=NA T942S Disease 0 0.517 SNPs&GO I943V Neutral 6 0.218 PhD-SNP: F[I]=39% F[V]=15% Nali=557 I943V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I943V Disease 2 0.576 SNPs&GO F944C Disease 6 0.796 PhD-SNP: F[F]=45% F[C]=1% Nali=502 F944C Unclassified NA NA PANTHER: F[F]=NA F[C]=NA F944C Disease 7 0.874 SNPs&GO F944L Disease 2 0.623 PhD-SNP: F[F]=45% F[L]=8% Nali=502 F944L Unclassified NA NA PANTHER: F[F]=NA F[L]=NA F944L Disease 5 0.754 SNPs&GO I946T Neutral 1 0.465 PhD-SNP: F[I]=31% F[T]=2% Nali=562 I946T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I946T Disease 3 0.634 SNPs&GO S983T Neutral 4 0.297 PhD-SNP: F[S]=28% F[T]=18% Nali=1305 S983T Neutral 3 0.325 PANTHER: F[S]=53% F[T]=4% S983T Disease 7 0.864 SNPs&GO F984S Disease 7 0.838 PhD-SNP: F[F]=30% F[S]=0% Nali=1337 F984S Disease 8 0.907 PANTHER: F[F]=82% F[S]=0% F984S Disease 10 0.986 SNPs&GO I991V Neutral 7 0.167 PhD-SNP: F[I]=27% F[V]=15% Nali=1405 I991V Neutral 7 0.143 PANTHER: F[I]=49% F[V]=14% I991V Disease 0 0.510 SNPs&GO V1022M Disease 2 0.622 PhD-SNP: F[V]=52% F[M]=0% Nali=1423 V1022M Disease 9 0.967 PANTHER: F[V]=89% F[M]=0% V1022M Disease 9 0.945 SNPs&GO R1027Q Disease 7 0.853 PhD-SNP: F[R]=58% F[Q]=0% Nali=1421 R1027Q Disease 7 0.850 PANTHER: F[R]=85% F[Q]=1% R1027Q Disease 10 0.979 SNPs&GO R1027W Disease 9 0.931 PhD-SNP: F[R]=58% F[W]=0% Nali=1421 R1027W Disease 9 0.974 PANTHER: F[R]=85% F[W]=0% R1027W Disease 10 0.985 SNPs&GO F1043L Neutral 5 0.234 PhD-SNP: F[F]=14% F[L]=18% Nali=1428 F1043L Neutral 4 0.287 PANTHER: F[F]=60% F[L]=7% F1043L Disease 6 0.813 SNPs&GO I1046V Neutral 7 0.162 PhD-SNP: F[I]=30% F[V]=17% Nali=1430 I1046V Neutral 7 0.160 PANTHER: F[I]=51% F[V]=14% I1046V Neutral 2 0.409 SNPs&GO T1057I Neutral 1 0.447 PhD-SNP: F[T]=8% F[I]=7% Nali=1426 T1057I Neutral 3 0.373 PANTHER: F[T]=33% F[I]=2% T1057I Disease 7 0.867 SNPs&GO V1101I Neutral 8 0.095 PhD-SNP: F[V]=23% F[I]=8% Nali=950 V1101I Unclassified NA NA PANTHER: F[V]=NA F[I]=NA V1101I Neutral 5 0.235 SNPs&GO I1249F Disease 7 0.869 PhD-SNP: F[I]=81% F[F]=0% Nali=1201 I1249F Disease 10 0.987 PANTHER: F[I]=94% F[F]=0% I1249F Disease 9 0.956 SNPs&GO N1252S Disease 6 0.785 PhD-SNP: F[N]=89% F[S]=4% Nali=1202 N1252S Disease 10 0.989 PANTHER: F[N]=97% F[S]=0% N1252S Disease 8 0.922 SNPs&GO N1252Y Disease 8 0.923 PhD-SNP: F[N]=89% F[Y]=0% Nali=1202 N1252Y Disease 10 0.996 PANTHER: F[N]=97% F[Y]=0% N1252Y Disease 9 0.959 SNPs&GO Mutation: WT+POS+NEW WT: Residue in wild-type protein POS: Residue position NEW: New residue after mutation Prediction: Neutral: Neutral variation Disease: Disease associated variation RI: Reliability Index Probability: Disease probability (if >0.5 mutation is predicted Disease) Method: SVM type and data PANTHER: Output of the PANTHER algorithm PhD-SNP: SVM input is the sequence and profile at the mutated position SNPs&GO: SVM input is all the input in PhD-SNP, PANTHER and GO term features F[X]: Frequency of residue X in the sequence profile Nali: Number of aligned sequences in the mutated site ********************************************************************************************** ** ** ** Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. (2009). Functional ** ** annotations improve the predictive score of human disease-related mutations in ** ** proteins. Human Mutation. 30:1237-1244. ** ** ** ** Capriotti E, Altman RB. (2011). Improving the prediction of disease-related vari- ** ** ants using protein three-dimensional structure. BMC Bioinformatics. 12 (Sup.4) S3. ** ** ** **********************************************************************************************