********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method I304T Neutral 2 0.398 PhD-SNP: F[I]=30% F[T]=5% Nali=1165 I304T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I304T Disease 1 0.530 SNPs&GO A305T Neutral 8 0.084 PhD-SNP: F[A]=8% F[T]=10% Nali=1265 A305T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A305T Neutral 5 0.270 SNPs&GO P308L Neutral 6 0.217 PhD-SNP: F[P]=26% F[L]=6% Nali=1174 P308L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P308L Neutral 0 0.479 SNPs&GO A309T Neutral 7 0.148 PhD-SNP: F[A]=16% F[T]=6% Nali=1266 A309T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A309T Neutral 2 0.418 SNPs&GO E310A Neutral 6 0.222 PhD-SNP: F[E]=33% F[A]=3% Nali=1260 E310A Unclassified NA NA PANTHER: F[E]=NA F[A]=NA E310A Neutral 2 0.408 SNPs&GO D312E Neutral 5 0.264 PhD-SNP: F[D]=38% F[E]=11% Nali=1215 D312E Unclassified NA NA PANTHER: F[D]=NA F[E]=NA D312E Disease 1 0.559 SNPs&GO P313A Neutral 8 0.122 PhD-SNP: F[P]=36% F[A]=9% Nali=1167 P313A Unclassified NA NA PANTHER: F[P]=NA F[A]=NA P313A Neutral 5 0.252 SNPs&GO P313H Neutral 3 0.332 PhD-SNP: F[P]=36% F[H]=1% Nali=1167 P313H Unclassified NA NA PANTHER: F[P]=NA F[H]=NA P313H Disease 0 0.520 SNPs&GO S314F Neutral 7 0.164 PhD-SNP: F[S]=19% F[F]=6% Nali=1200 S314F Unclassified NA NA PANTHER: F[S]=NA F[F]=NA S314F Neutral 3 0.329 SNPs&GO P315L Neutral 7 0.145 PhD-SNP: F[P]=31% F[L]=14% Nali=1160 P315L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P315L Neutral 3 0.369 SNPs&GO A317E Neutral 5 0.255 PhD-SNP: F[A]=20% F[E]=4% Nali=1175 A317E Unclassified NA NA PANTHER: F[A]=NA F[E]=NA A317E Disease 3 0.640 SNPs&GO A317T Neutral 7 0.151 PhD-SNP: F[A]=20% F[T]=3% Nali=1175 A317T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A317T Neutral 2 0.424 SNPs&GO A317V Neutral 7 0.135 PhD-SNP: F[A]=20% F[V]=4% Nali=1175 A317V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A317V Neutral 1 0.437 SNPs&GO L318P Neutral 1 0.465 PhD-SNP: F[L]=22% F[P]=3% Nali=1088 L318P Unclassified NA NA PANTHER: F[L]=NA F[P]=NA L318P Disease 4 0.717 SNPs&GO E319V Neutral 6 0.221 PhD-SNP: F[E]=24% F[V]=3% Nali=1097 E319V Unclassified NA NA PANTHER: F[E]=NA F[V]=NA E319V Disease 0 0.508 SNPs&GO T320M Neutral 8 0.117 PhD-SNP: F[T]=20% F[M]=1% Nali=1175 T320M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T320M Neutral 1 0.447 SNPs&GO G321D Neutral 4 0.302 PhD-SNP: F[G]=39% F[D]=18% Nali=1202 G321D Unclassified NA NA PANTHER: F[G]=NA F[D]=NA G321D Disease 2 0.605 SNPs&GO H322D Neutral 5 0.264 PhD-SNP: F[H]=13% F[D]=3% Nali=1194 H322D Unclassified NA NA PANTHER: F[H]=NA F[D]=NA H322D Disease 3 0.659 SNPs&GO H322Y Neutral 5 0.233 PhD-SNP: F[H]=13% F[Y]=4% Nali=1194 H322Y Unclassified NA NA PANTHER: F[H]=NA F[Y]=NA H322Y Disease 2 0.578 SNPs&GO G323R Disease 1 0.549 PhD-SNP: F[G]=46% F[R]=1% Nali=1223 G323R Unclassified NA NA PANTHER: F[G]=NA F[R]=NA G323R Disease 7 0.839 SNPs&GO R324Q Disease 0 0.516 PhD-SNP: F[R]=36% F[Q]=2% Nali=1118 R324Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R324Q Disease 4 0.689 SNPs&GO R324W Disease 3 0.665 PhD-SNP: F[R]=36% F[W]=1% Nali=1118 R324W Unclassified NA NA PANTHER: F[R]=NA F[W]=NA R324W Disease 6 0.812 SNPs&GO Q325K Neutral 4 0.281 PhD-SNP: F[Q]=23% F[K]=6% Nali=1208 Q325K Unclassified NA NA PANTHER: F[Q]=NA F[K]=NA Q325K Disease 3 0.626 SNPs&GO Q325R Neutral 7 0.157 PhD-SNP: F[Q]=23% F[R]=5% Nali=1208 Q325R Unclassified NA NA PANTHER: F[Q]=NA F[R]=NA Q325R Disease 0 0.524 SNPs&GO G329S Disease 0 0.515 PhD-SNP: F[G]=43% F[S]=5% Nali=1240 G329S Neutral 6 0.204 PANTHER: F[G]=29% F[S]=5% G329S Disease 7 0.855 SNPs&GO T330M Neutral 7 0.168 PhD-SNP: F[T]=29% F[M]=4% Nali=1232 T330M Disease 4 0.675 PANTHER: F[T]=55% F[M]=1% T330M Disease 8 0.899 SNPs&GO V331M Neutral 6 0.206 PhD-SNP: F[V]=24% F[M]=3% Nali=1171 V331M Neutral 3 0.333 PANTHER: F[V]=28% F[M]=2% V331M Disease 6 0.782 SNPs&GO P334H Neutral 6 0.207 PhD-SNP: F[P]=18% F[H]=1% Nali=1165 P334H Neutral 2 0.416 PANTHER: F[P]=25% F[H]=1% P334H Disease 4 0.716 SNPs&GO W336C Disease 9 0.930 PhD-SNP: F[W]=60% F[C]=0% Nali=1376 W336C Disease 10 0.994 PANTHER: F[W]=96% F[C]=0% W336C Disease 10 0.986 SNPs&GO D337E Neutral 6 0.204 PhD-SNP: F[D]=12% F[E]=16% Nali=1315 D337E Neutral 8 0.092 PANTHER: F[D]=37% F[E]=19% D337E Disease 3 0.648 SNPs&GO D337H Neutral 3 0.350 PhD-SNP: F[D]=12% F[H]=3% Nali=1315 D337H Neutral 1 0.446 PANTHER: F[D]=37% F[H]=1% D337H Disease 8 0.877 SNPs&GO G342S Disease 6 0.793 PhD-SNP: F[G]=67% F[S]=3% Nali=953 G342S Disease 10 0.976 PANTHER: F[G]=97% F[S]=0% G342S Disease 9 0.964 SNPs&GO T344I Disease 1 0.563 PhD-SNP: F[T]=38% F[I]=14% Nali=1394 T344I Disease 10 0.981 PANTHER: F[T]=92% F[I]=0% T344I Disease 9 0.972 SNPs&GO F351Y Neutral 2 0.415 PhD-SNP: F[F]=14% F[Y]=8% Nali=1715 F351Y Neutral 4 0.294 PANTHER: F[F]=61% F[Y]=7% F351Y Disease 7 0.835 SNPs&GO M353V Disease 2 0.586 PhD-SNP: F[M]=24% F[V]=5% Nali=1718 M353V Disease 4 0.711 PANTHER: F[M]=75% F[V]=2% M353V Disease 9 0.967 SNPs&GO T355M Disease 3 0.632 PhD-SNP: F[T]=35% F[M]=1% Nali=1718 T355M Disease 10 0.990 PANTHER: F[T]=92% F[M]=0% T355M Disease 9 0.963 SNPs&GO I360V Neutral 4 0.284 PhD-SNP: F[I]=25% F[V]=4% Nali=1722 I360V Neutral 7 0.166 PANTHER: F[I]=52% F[V]=14% I360V Disease 2 0.581 SNPs&GO T366M Neutral 5 0.273 PhD-SNP: F[T]=21% F[M]=9% Nali=1718 T366M Disease 10 0.990 PANTHER: F[T]=92% F[M]=0% T366M Disease 9 0.946 SNPs&GO D367N Neutral 1 0.438 PhD-SNP: F[D]=33% F[N]=14% Nali=1720 D367N Neutral 1 0.441 PANTHER: F[D]=64% F[N]=3% D367N Disease 8 0.879 SNPs&GO V368M Disease 3 0.655 PhD-SNP: F[V]=33% F[M]=1% Nali=1705 V368M Disease 1 0.528 PANTHER: F[V]=55% F[M]=2% V368M Disease 9 0.933 SNPs&GO V376I Neutral 5 0.267 PhD-SNP: F[V]=20% F[I]=8% Nali=1565 V376I Unclassified NA NA PANTHER: F[V]=NA F[I]=NA V376I Neutral 2 0.422 SNPs&GO G377A Disease 6 0.779 PhD-SNP: F[G]=57% F[A]=6% Nali=1591 G377A Disease 9 0.969 PANTHER: F[G]=96% F[A]=0% G377A Disease 8 0.901 SNPs&GO R378G Neutral 2 0.417 PhD-SNP: F[R]=6% F[G]=1% Nali=1532 R378G Neutral 6 0.223 PANTHER: F[R]=11% F[G]=1% R378G Disease 3 0.665 SNPs&GO R378M Neutral 5 0.272 PhD-SNP: F[R]=6% F[M]=1% Nali=1532 R378M Neutral 5 0.245 PANTHER: F[R]=11% F[M]=1% R378M Disease 0 0.500 SNPs&GO W380G Disease 4 0.696 PhD-SNP: F[W]=29% F[G]=2% Nali=1484 W380G Neutral 5 0.229 PANTHER: F[W]=7% F[G]=1% W380G Disease 7 0.831 SNPs&GO W380S Disease 5 0.752 PhD-SNP: F[W]=29% F[S]=3% Nali=1484 W380S Neutral 7 0.146 PANTHER: F[W]=7% F[S]=2% W380S Disease 7 0.832 SNPs&GO P381S Neutral 0 0.487 PhD-SNP: F[P]=23% F[S]=4% Nali=1385 P381S Disease 1 0.554 PANTHER: F[P]=74% F[S]=2% P381S Disease 8 0.885 SNPs&GO P381T Neutral 1 0.427 PhD-SNP: F[P]=23% F[T]=2% Nali=1385 P381T Disease 2 0.618 PANTHER: F[P]=74% F[T]=1% P381T Disease 7 0.861 SNPs&GO Y384C Disease 9 0.931 PhD-SNP: F[Y]=69% F[C]=0% Nali=1584 Y384C Disease 10 0.991 PANTHER: F[Y]=92% F[C]=0% Y384C Disease 9 0.954 SNPs&GO T387R Disease 6 0.822 PhD-SNP: F[T]=8% F[R]=0% Nali=1560 T387R Neutral 6 0.208 PANTHER: F[T]=13% F[R]=2% T387R Disease 7 0.862 SNPs&GO I389V Neutral 2 0.410 PhD-SNP: F[I]=64% F[V]=12% Nali=1563 I389V Neutral 8 0.092 PANTHER: F[I]=23% F[V]=43% I389V Neutral 6 0.200 SNPs&GO I391L Neutral 3 0.373 PhD-SNP: F[I]=31% F[L]=25% Nali=1563 I391L Neutral 9 0.057 PANTHER: F[I]=15% F[L]=15% I391L Disease 1 0.556 SNPs&GO G392V Disease 7 0.873 PhD-SNP: F[G]=71% F[V]=7% Nali=1563 G392V Disease 10 0.989 PANTHER: F[G]=96% F[V]=0% G392V Disease 9 0.925 SNPs&GO F394L Disease 5 0.764 PhD-SNP: F[F]=74% F[L]=10% Nali=1545 F394L Disease 9 0.941 PANTHER: F[F]=93% F[L]=0% F394L Disease 8 0.916 SNPs&GO V396I Neutral 2 0.425 PhD-SNP: F[V]=31% F[I]=6% Nali=1530 V396I Neutral 6 0.200 PANTHER: F[V]=55% F[I]=11% V396I Disease 6 0.783 SNPs&GO G402R Disease 7 0.868 PhD-SNP: F[G]=45% F[R]=0% Nali=1538 G402R Disease 10 0.988 PANTHER: F[G]=96% F[R]=0% G402R Disease 9 0.957 SNPs&GO G402S Disease 4 0.712 PhD-SNP: F[G]=45% F[S]=3% Nali=1538 G402S Disease 10 0.975 PANTHER: F[G]=96% F[S]=0% G402S Disease 9 0.928 SNPs&GO K410R Neutral 3 0.329 PhD-SNP: F[K]=29% F[R]=2% Nali=1377 K410R Unclassified NA NA PANTHER: F[K]=NA F[R]=NA K410R Disease 2 0.578 SNPs&GO R412M Disease 1 0.546 PhD-SNP: F[R]=31% F[M]=0% Nali=1299 R412M Unclassified NA NA PANTHER: F[R]=NA F[M]=NA R412M Disease 5 0.734 SNPs&GO A415V Neutral 5 0.225 PhD-SNP: F[A]=29% F[V]=12% Nali=1161 A415V Neutral 1 0.444 PANTHER: F[A]=60% F[V]=3% A415V Disease 8 0.879 SNPs&GO K416N Neutral 4 0.292 PhD-SNP: F[K]=21% F[N]=3% Nali=1092 K416N Disease 0 0.501 PANTHER: F[K]=58% F[N]=2% K416N Disease 8 0.915 SNPs&GO A417T Neutral 6 0.207 PhD-SNP: F[A]=20% F[T]=2% Nali=1053 A417T Neutral 2 0.401 PANTHER: F[A]=60% F[T]=4% A417T Disease 7 0.836 SNPs&GO R418P Disease 6 0.801 PhD-SNP: F[R]=33% F[P]=0% Nali=1049 R418P Disease 10 0.984 PANTHER: F[R]=95% F[P]=0% R418P Disease 10 0.981 SNPs&GO R418W Disease 3 0.672 PhD-SNP: F[R]=33% F[W]=0% Nali=1049 R418W Disease 10 0.995 PANTHER: F[R]=95% F[W]=0% R418W Disease 9 0.968 SNPs&GO G419A Neutral 8 0.124 PhD-SNP: F[G]=24% F[A]=5% Nali=1043 G419A Disease 7 0.847 PANTHER: F[G]=91% F[A]=1% G419A Disease 6 0.816 SNPs&GO G419R Neutral 5 0.251 PhD-SNP: F[G]=24% F[R]=7% Nali=1043 G419R Disease 9 0.943 PANTHER: F[G]=91% F[R]=0% G419R Disease 8 0.880 SNPs&GO Q422R Neutral 3 0.354 PhD-SNP: F[Q]=31% F[R]=3% Nali=1046 Q422R Disease 6 0.801 PANTHER: F[Q]=81% F[R]=1% Q422R Disease 9 0.960 SNPs&GO R425L Disease 4 0.683 PhD-SNP: F[R]=45% F[L]=4% Nali=1091 R425L Disease 8 0.892 PANTHER: F[R]=84% F[L]=0% R425L Disease 10 0.981 SNPs&GO R425Q Disease 1 0.534 PhD-SNP: F[R]=45% F[Q]=3% Nali=1091 R425Q Disease 7 0.843 PANTHER: F[R]=84% F[Q]=1% R425Q Disease 9 0.970 SNPs&GO D433N Disease 0 0.522 PhD-SNP: F[D]=37% F[N]=2% Nali=838 D433N Disease 6 0.814 PANTHER: F[D]=84% F[N]=1% D433N Disease 9 0.968 SNPs&GO L434I Neutral 4 0.290 PhD-SNP: F[L]=48% F[I]=4% Nali=838 L434I Disease 3 0.652 PANTHER: F[L]=80% F[I]=4% L434I Disease 8 0.906 SNPs&GO G436A Neutral 3 0.327 PhD-SNP: F[G]=47% F[A]=10% Nali=765 G436A Disease 7 0.847 PANTHER: F[G]=91% F[A]=1% G436A Disease 9 0.926 SNPs&GO L438R Disease 4 0.675 PhD-SNP: F[L]=46% F[R]=7% Nali=714 L438R Disease 4 0.689 PANTHER: F[L]=63% F[R]=1% L438R Disease 9 0.968 SNPs&GO Q443E Neutral 0 0.481 PhD-SNP: F[Q]=35% F[E]=5% Nali=646 Q443E Neutral 2 0.375 PANTHER: F[Q]=55% F[E]=4% Q443E Disease 9 0.944 SNPs&GO A444T Disease 1 0.548 PhD-SNP: F[A]=53% F[T]=2% Nali=643 A444T Neutral 2 0.401 PANTHER: F[A]=60% F[T]=4% A444T Disease 9 0.945 SNPs&GO E445K Disease 2 0.579 PhD-SNP: F[E]=54% F[K]=3% Nali=630 E445K Disease 9 0.972 PANTHER: F[E]=94% F[K]=0% E445K Disease 10 0.984 SNPs&GO E445Q Neutral 4 0.285 PhD-SNP: F[E]=54% F[Q]=6% Nali=630 E445Q Disease 9 0.975 PANTHER: F[E]=94% F[Q]=0% E445Q Disease 9 0.958 SNPs&GO D446G Neutral 0 0.499 PhD-SNP: F[D]=32% F[G]=2% Nali=642 D446G Disease 0 0.522 PANTHER: F[D]=64% F[G]=2% D446G Disease 9 0.962 SNPs&GO D448A Neutral 0 0.496 PhD-SNP: F[D]=40% F[A]=6% Nali=640 D448A Disease 0 0.508 PANTHER: F[D]=64% F[A]=2% D448A Disease 9 0.946 SNPs&GO D448N Neutral 0 0.480 PhD-SNP: F[D]=40% F[N]=2% Nali=640 D448N Neutral 1 0.452 PANTHER: F[D]=64% F[N]=3% D448N Disease 9 0.958 SNPs&GO D448Y Disease 4 0.692 PhD-SNP: F[D]=40% F[Y]=0% Nali=640 D448Y Disease 6 0.783 PANTHER: F[D]=64% F[Y]=0% D448Y Disease 10 0.980 SNPs&GO E450A Neutral 5 0.240 PhD-SNP: F[E]=38% F[A]=7% Nali=591 E450A Neutral 1 0.466 PANTHER: F[E]=60% F[A]=3% E450A Disease 8 0.889 SNPs&GO E450D Neutral 7 0.169 PhD-SNP: F[E]=38% F[D]=10% Nali=591 E450D Neutral 3 0.326 PANTHER: F[E]=60% F[D]=6% E450D Disease 7 0.859 SNPs&GO E450Q Neutral 7 0.152 PhD-SNP: F[E]=38% F[Q]=9% Nali=591 E450Q Neutral 0 0.485 PANTHER: F[E]=60% F[Q]=2% E450Q Disease 8 0.882 SNPs&GO D453Y Neutral 1 0.465 PhD-SNP: F[D]=29% F[Y]=0% Nali=614 D453Y Disease 5 0.748 PANTHER: F[D]=62% F[Y]=0% D453Y Disease 9 0.963 SNPs&GO E454K Neutral 5 0.265 PhD-SNP: F[E]=33% F[K]=13% Nali=617 E454K Neutral 2 0.425 PANTHER: F[E]=60% F[K]=3% E454K Disease 9 0.932 SNPs&GO M456I Neutral 6 0.222 PhD-SNP: F[M]=21% F[I]=6% Nali=585 M456I Neutral 7 0.137 PANTHER: F[M]=29% F[I]=9% M456I Disease 5 0.738 SNPs&GO M456L Neutral 7 0.139 PhD-SNP: F[M]=21% F[L]=20% Nali=585 M456L Neutral 9 0.056 PANTHER: F[M]=29% F[L]=28% M456L Neutral 1 0.461 SNPs&GO M456R Neutral 2 0.415 PhD-SNP: F[M]=21% F[R]=4% Nali=585 M456R Neutral 0 0.476 PANTHER: F[M]=29% F[R]=1% M456R Disease 9 0.929 SNPs&GO M456T Neutral 3 0.336 PhD-SNP: F[M]=21% F[T]=6% Nali=585 M456T Neutral 3 0.345 PANTHER: F[M]=29% F[T]=2% M456T Disease 8 0.893 SNPs&GO M456V Neutral 5 0.242 PhD-SNP: F[M]=21% F[V]=4% Nali=585 M456V Neutral 7 0.153 PANTHER: F[M]=29% F[V]=8% M456V Disease 4 0.692 SNPs&GO P461A Neutral 5 0.232 PhD-SNP: F[P]=42% F[A]=7% Nali=616 P461A Neutral 1 0.464 PANTHER: F[P]=71% F[A]=3% P461A Disease 8 0.889 SNPs&GO P461R Neutral 2 0.376 PhD-SNP: F[P]=42% F[R]=10% Nali=616 P461R Disease 3 0.650 PANTHER: F[P]=71% F[R]=1% P461R Disease 9 0.954 SNPs&GO P461T Neutral 3 0.363 PhD-SNP: F[P]=42% F[T]=4% Nali=616 P461T Disease 1 0.571 PANTHER: F[P]=71% F[T]=2% P461T Disease 9 0.928 SNPs&GO R462G Neutral 1 0.426 PhD-SNP: F[R]=40% F[G]=2% Nali=639 R462G Disease 1 0.547 PANTHER: F[R]=60% F[G]=1% R462G Disease 9 0.954 SNPs&GO R462Q Neutral 3 0.344 PhD-SNP: F[R]=40% F[Q]=5% Nali=639 R462Q Neutral 1 0.439 PANTHER: F[R]=60% F[Q]=3% R462Q Disease 8 0.915 SNPs&GO M466T Neutral 5 0.236 PhD-SNP: F[M]=20% F[T]=4% Nali=615 M466T Neutral 4 0.318 PANTHER: F[M]=37% F[T]=3% M466T Disease 7 0.840 SNPs&GO M466V Neutral 7 0.128 PhD-SNP: F[M]=20% F[V]=7% Nali=615 M466V Neutral 6 0.188 PANTHER: F[M]=37% F[V]=7% M466V Disease 2 0.592 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. ** ** ** **********************************************************************************************