********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method P467L Neutral 4 0.280 PhD-SNP: F[P]=48% F[L]=5% Nali=616 P467L Disease 3 0.629 PANTHER: F[P]=71% F[L]=1% P467L Disease 8 0.903 SNPs&GO S469I Neutral 4 0.324 PhD-SNP: F[S]=36% F[I]=2% Nali=607 S469I Disease 1 0.565 PANTHER: F[S]=51% F[I]=1% S469I Disease 8 0.915 SNPs&GO S469N Neutral 7 0.138 PhD-SNP: F[S]=36% F[N]=7% Nali=607 S469N Neutral 1 0.433 PANTHER: F[S]=51% F[N]=2% S469N Disease 6 0.797 SNPs&GO E470D Neutral 8 0.087 PhD-SNP: F[E]=29% F[D]=13% Nali=600 E470D Neutral 6 0.214 PANTHER: F[E]=39% F[D]=7% E470D Neutral 1 0.458 SNPs&GO T471I Neutral 6 0.208 PhD-SNP: F[T]=26% F[I]=3% Nali=614 T471I Neutral 4 0.315 PANTHER: F[T]=26% F[I]=2% T471I Disease 4 0.676 SNPs&GO T471N Neutral 7 0.148 PhD-SNP: F[T]=26% F[N]=7% Nali=614 T471N Neutral 8 0.114 PANTHER: F[T]=26% F[N]=10% T471N Neutral 2 0.420 SNPs&GO E472K Neutral 4 0.304 PhD-SNP: F[E]=33% F[K]=8% Nali=627 E472K Neutral 4 0.310 PANTHER: F[E]=48% F[K]=4% E472K Disease 7 0.828 SNPs&GO V474F Neutral 2 0.402 PhD-SNP: F[V]=29% F[F]=4% Nali=591 V474F Neutral 1 0.474 PANTHER: F[V]=47% F[F]=2% V474F Disease 9 0.929 SNPs&GO V474I Neutral 9 0.072 PhD-SNP: F[V]=29% F[I]=12% Nali=591 V474I Neutral 7 0.169 PANTHER: F[V]=47% F[I]=11% V474I Disease 1 0.575 SNPs&GO V474L Neutral 7 0.149 PhD-SNP: F[V]=29% F[L]=11% Nali=591 V474L Neutral 6 0.223 PANTHER: F[V]=47% F[L]=7% V474L Disease 6 0.793 SNPs&GO N475H Neutral 5 0.263 PhD-SNP: F[N]=29% F[H]=3% Nali=593 N475H Disease 2 0.612 PANTHER: F[N]=54% F[H]=1% N475H Disease 8 0.889 SNPs&GO E477K Neutral 4 0.302 PhD-SNP: F[E]=37% F[K]=8% Nali=598 E477K Neutral 5 0.251 PANTHER: F[E]=36% F[K]=5% E477K Disease 6 0.819 SNPs&GO N478I Neutral 4 0.289 PhD-SNP: F[N]=28% F[I]=3% Nali=562 N478I Disease 1 0.546 PANTHER: F[N]=43% F[I]=1% N478I Disease 8 0.902 SNPs&GO V479M Neutral 7 0.163 PhD-SNP: F[V]=23% F[M]=3% Nali=533 V479M Neutral 2 0.405 PANTHER: F[V]=34% F[M]=2% V479M Disease 5 0.750 SNPs&GO A480G Neutral 7 0.136 PhD-SNP: F[A]=21% F[G]=4% Nali=531 A480G Neutral 4 0.281 PANTHER: F[A]=34% F[G]=4% A480G Disease 4 0.681 SNPs&GO A480T Neutral 7 0.170 PhD-SNP: F[A]=21% F[T]=4% Nali=531 A480T Neutral 5 0.233 PANTHER: F[A]=34% F[T]=5% A480T Disease 5 0.744 SNPs&GO G481A Neutral 5 0.254 PhD-SNP: F[G]=28% F[A]=6% Nali=534 G481A Neutral 8 0.091 PANTHER: F[G]=33% F[A]=18% G481A Disease 1 0.552 SNPs&GO G481E Neutral 2 0.405 PhD-SNP: F[G]=28% F[E]=11% Nali=534 G481E Neutral 4 0.301 PANTHER: F[G]=33% F[E]=3% G481E Disease 8 0.900 SNPs&GO G481R Neutral 1 0.427 PhD-SNP: F[G]=28% F[R]=2% Nali=534 G481R Neutral 2 0.376 PANTHER: F[G]=33% F[R]=2% G481R Disease 8 0.881 SNPs&GO G482D Neutral 0 0.488 PhD-SNP: F[G]=30% F[D]=6% Nali=549 G482D Neutral 1 0.471 PANTHER: F[G]=57% F[D]=2% G482D Disease 9 0.934 SNPs&GO G482S Neutral 3 0.344 PhD-SNP: F[G]=30% F[S]=8% Nali=549 G482S Neutral 4 0.314 PANTHER: F[G]=57% F[S]=5% G482S Disease 7 0.828 SNPs&GO E485D Neutral 5 0.251 PhD-SNP: F[E]=34% F[D]=10% Nali=579 E485D Neutral 6 0.215 PANTHER: F[E]=46% F[D]=8% E485D Disease 6 0.794 SNPs&GO E485K Disease 2 0.578 PhD-SNP: F[E]=34% F[K]=6% Nali=579 E485K Neutral 4 0.286 PANTHER: F[E]=46% F[K]=5% E485K Disease 9 0.939 SNPs&GO G486R Disease 1 0.559 PhD-SNP: F[G]=27% F[R]=1% Nali=576 G486R Disease 1 0.562 PANTHER: F[G]=58% F[R]=1% G486R Disease 9 0.951 SNPs&GO E487A Neutral 2 0.394 PhD-SNP: F[E]=33% F[A]=4% Nali=610 E487A Neutral 2 0.418 PANTHER: F[E]=57% F[A]=3% E487A Disease 8 0.906 SNPs&GO N488S Neutral 6 0.201 PhD-SNP: F[N]=23% F[S]=11% Nali=627 N488S Neutral 6 0.179 PANTHER: F[N]=28% F[S]=6% N488S Disease 3 0.627 SNPs&GO C489R Disease 7 0.850 PhD-SNP: F[C]=49% F[R]=1% Nali=624 C489R Disease 1 0.560 PANTHER: F[C]=51% F[R]=1% C489R Disease 10 0.987 SNPs&GO G490E Disease 1 0.573 PhD-SNP: F[G]=29% F[E]=4% Nali=636 G490E Neutral 2 0.382 PANTHER: F[G]=35% F[E]=2% G490E Disease 9 0.943 SNPs&GO G490R Neutral 0 0.477 PhD-SNP: F[G]=29% F[R]=5% Nali=636 G490R Neutral 2 0.414 PANTHER: F[G]=35% F[R]=2% G490R Disease 8 0.915 SNPs&GO G490V Neutral 1 0.470 PhD-SNP: F[G]=29% F[V]=5% Nali=636 G490V Neutral 4 0.289 PANTHER: F[G]=35% F[V]=4% G490V Disease 7 0.844 SNPs&GO A491G Neutral 5 0.247 PhD-SNP: F[A]=24% F[G]=5% Nali=653 A491G Neutral 4 0.288 PANTHER: F[A]=38% F[G]=4% A491G Disease 6 0.820 SNPs&GO R492M Disease 0 0.500 PhD-SNP: F[R]=40% F[M]=6% Nali=667 R492M Disease 3 0.637 PANTHER: F[R]=48% F[M]=1% R492M Disease 9 0.942 SNPs&GO R492S Disease 3 0.644 PhD-SNP: F[R]=40% F[S]=3% Nali=667 R492S Neutral 3 0.341 PANTHER: F[R]=48% F[S]=4% R492S Disease 9 0.946 SNPs&GO L493M Neutral 4 0.290 PhD-SNP: F[L]=38% F[M]=4% Nali=682 L493M Neutral 7 0.153 PANTHER: F[L]=44% F[M]=12% L493M Disease 2 0.588 SNPs&GO H495Q Neutral 6 0.197 PhD-SNP: F[H]=18% F[Q]=9% Nali=685 H495Q Neutral 6 0.223 PANTHER: F[H]=26% F[Q]=4% H495Q Disease 4 0.704 SNPs&GO R496Q Neutral 0 0.496 PhD-SNP: F[R]=30% F[Q]=4% Nali=708 R496Q Neutral 1 0.439 PANTHER: F[R]=60% F[Q]=3% R496Q Disease 9 0.932 SNPs&GO R496W Disease 5 0.745 PhD-SNP: F[R]=30% F[W]=2% Nali=708 R496W Disease 7 0.854 PANTHER: F[R]=60% F[W]=0% R496W Disease 10 0.977 SNPs&GO K499T Neutral 6 0.222 PhD-SNP: F[K]=33% F[T]=6% Nali=786 K499T Disease 6 0.797 PANTHER: F[K]=75% F[T]=1% K499T Disease 8 0.913 SNPs&GO K501E Neutral 3 0.354 PhD-SNP: F[K]=31% F[E]=10% Nali=772 K501E Neutral 2 0.415 PANTHER: F[K]=58% F[E]=3% K501E Disease 8 0.920 SNPs&GO W506G Disease 1 0.536 PhD-SNP: F[W]=42% F[G]=2% Nali=787 W506G Neutral 4 0.324 PANTHER: F[W]=28% F[G]=2% W506G Disease 6 0.823 SNPs&GO R507C Disease 5 0.745 PhD-SNP: F[R]=43% F[C]=1% Nali=801 R507C Disease 7 0.834 PANTHER: F[R]=63% F[C]=0% R507C Disease 9 0.963 SNPs&GO R507H Neutral 1 0.450 PhD-SNP: F[R]=43% F[H]=1% Nali=801 R507H Disease 3 0.655 PANTHER: F[R]=63% F[H]=1% R507H Disease 8 0.923 SNPs&GO R508Q Neutral 4 0.289 PhD-SNP: F[R]=32% F[Q]=9% Nali=776 R508Q Neutral 0 0.486 PANTHER: F[R]=63% F[Q]=3% R508Q Disease 7 0.835 SNPs&GO R508W Disease 4 0.682 PhD-SNP: F[R]=32% F[W]=2% Nali=776 R508W Disease 8 0.876 PANTHER: F[R]=63% F[W]=0% R508W Disease 9 0.964 SNPs&GO N510S Neutral 9 0.075 PhD-SNP: F[N]=35% F[S]=10% Nali=838 N510S Disease 6 0.809 PANTHER: F[N]=82% F[S]=1% N510S Disease 5 0.735 SNPs&GO R511Q Neutral 2 0.379 PhD-SNP: F[R]=44% F[Q]=6% Nali=802 R511Q Neutral 0 0.486 PANTHER: F[R]=63% F[Q]=3% R511Q Disease 7 0.841 SNPs&GO R511W Disease 5 0.733 PhD-SNP: F[R]=44% F[W]=2% Nali=802 R511W Disease 8 0.876 PANTHER: F[R]=63% F[W]=0% R511W Disease 9 0.967 SNPs&GO R514G Disease 5 0.769 PhD-SNP: F[R]=75% F[G]=1% Nali=1059 R514G Disease 9 0.974 PANTHER: F[R]=95% F[G]=0% R514G Disease 9 0.970 SNPs&GO K516N Neutral 6 0.217 PhD-SNP: F[K]=28% F[N]=3% Nali=1082 K516N Neutral 1 0.454 PANTHER: F[K]=55% F[N]=2% K516N Disease 4 0.721 SNPs&GO R518C Disease 7 0.859 PhD-SNP: F[R]=31% F[C]=0% Nali=1102 R518C Disease 7 0.834 PANTHER: F[R]=63% F[C]=0% R518C Disease 9 0.974 SNPs&GO R518H Neutral 3 0.357 PhD-SNP: F[R]=31% F[H]=13% Nali=1102 R518H Disease 3 0.655 PANTHER: F[R]=63% F[H]=1% R518H Disease 8 0.901 SNPs&GO A519T Neutral 7 0.149 PhD-SNP: F[A]=12% F[T]=7% Nali=1116 A519T Neutral 2 0.401 PANTHER: F[A]=60% F[T]=4% A519T Disease 5 0.767 SNPs&GO A519V Neutral 6 0.197 PhD-SNP: F[A]=12% F[V]=4% Nali=1116 A519V Neutral 1 0.444 PANTHER: F[A]=60% F[V]=3% A519V Disease 5 0.773 SNPs&GO A520S Neutral 3 0.347 PhD-SNP: F[A]=13% F[S]=1% Nali=1184 A520S Neutral 3 0.336 PANTHER: F[A]=60% F[S]=5% A520S Disease 7 0.829 SNPs&GO A520T Neutral 5 0.252 PhD-SNP: F[A]=13% F[T]=2% Nali=1184 A520T Neutral 2 0.401 PANTHER: F[A]=60% F[T]=4% A520T Disease 6 0.824 SNPs&GO V521A Disease 5 0.741 PhD-SNP: F[V]=68% F[A]=1% Nali=1319 V521A Disease 9 0.936 PANTHER: F[V]=88% F[A]=1% V521A Disease 9 0.955 SNPs&GO K522R Neutral 4 0.280 PhD-SNP: F[K]=26% F[R]=2% Nali=1325 K522R Disease 8 0.919 PANTHER: F[K]=93% F[R]=1% K522R Disease 8 0.875 SNPs&GO N524T Neutral 5 0.266 PhD-SNP: F[N]=11% F[T]=4% Nali=1336 N524T Neutral 1 0.442 PANTHER: F[N]=54% F[T]=2% N524T Disease 6 0.796 SNPs&GO F526S Disease 9 0.934 PhD-SNP: F[F]=87% F[S]=0% Nali=1391 F526S Disease 2 0.621 PANTHER: F[F]=61% F[S]=1% F526S Disease 9 0.972 SNPs&GO W528G Disease 2 0.614 PhD-SNP: F[W]=23% F[G]=1% Nali=1390 W528G Disease 10 0.980 PANTHER: F[W]=97% F[G]=0% W528G Disease 9 0.944 SNPs&GO W528R Disease 3 0.640 PhD-SNP: F[W]=23% F[R]=9% Nali=1390 W528R Disease 10 0.989 PANTHER: F[W]=97% F[R]=0% W528R Disease 9 0.930 SNPs&GO V530G Disease 7 0.863 PhD-SNP: F[V]=30% F[G]=0% Nali=1521 V530G Disease 2 0.606 PANTHER: F[V]=55% F[G]=1% V530G Disease 10 0.976 SNPs&GO V530L Disease 6 0.814 PhD-SNP: F[V]=30% F[L]=1% Nali=1521 V530L Neutral 5 0.267 PANTHER: F[V]=55% F[L]=7% V530L Disease 9 0.951 SNPs&GO I531S Disease 6 0.805 PhD-SNP: F[I]=26% F[S]=0% Nali=1523 I531S Disease 2 0.579 PANTHER: F[I]=52% F[S]=1% I531S Disease 9 0.957 SNPs&GO I531V Neutral 4 0.310 PhD-SNP: F[I]=26% F[V]=6% Nali=1523 I531V Neutral 7 0.170 PANTHER: F[I]=52% F[V]=14% I531V Disease 1 0.568 SNPs&GO V534M Disease 5 0.767 PhD-SNP: F[V]=20% F[M]=0% Nali=1579 V534M Disease 9 0.967 PANTHER: F[V]=88% F[M]=0% V534M Disease 10 0.978 SNPs&GO F535I Disease 1 0.525 PhD-SNP: F[F]=21% F[I]=9% Nali=1578 F535I Neutral 1 0.459 PANTHER: F[F]=61% F[I]=3% F535I Disease 8 0.922 SNPs&GO N537D Disease 7 0.854 PhD-SNP: F[N]=79% F[D]=1% Nali=1590 N537D Disease 10 0.987 PANTHER: F[N]=97% F[D]=0% N537D Disease 9 0.961 SNPs&GO N537Y Disease 9 0.936 PhD-SNP: F[N]=79% F[Y]=0% Nali=1590 N537Y Disease 10 0.996 PANTHER: F[N]=97% F[Y]=0% N537Y Disease 9 0.972 SNPs&GO T538M Disease 0 0.521 PhD-SNP: F[T]=50% F[M]=11% Nali=1593 T538M Disease 10 0.997 PANTHER: F[T]=96% F[M]=0% T538M Disease 9 0.938 SNPs&GO T540A Neutral 6 0.178 PhD-SNP: F[T]=32% F[A]=16% Nali=1590 T540A Neutral 4 0.298 PANTHER: F[T]=55% F[A]=6% T540A Disease 6 0.796 SNPs&GO I541T Neutral 0 0.476 PhD-SNP: F[I]=13% F[T]=1% Nali=1586 I541T Neutral 0 0.492 PANTHER: F[I]=52% F[T]=2% I541T Disease 9 0.929 SNPs&GO A542S Disease 3 0.637 PhD-SNP: F[A]=60% F[S]=8% Nali=1593 A542S Neutral 4 0.297 PANTHER: F[A]=57% F[S]=6% A542S Disease 9 0.936 SNPs&GO E544A Disease 3 0.656 PhD-SNP: F[E]=72% F[A]=0% Nali=1589 E544A Disease 7 0.841 PANTHER: F[E]=82% F[A]=1% E544A Disease 9 0.941 SNPs&GO N547S Neutral 6 0.211 PhD-SNP: F[N]=18% F[S]=3% Nali=1562 N547S Neutral 6 0.204 PANTHER: F[N]=28% F[S]=5% N547S Disease 2 0.623 SNPs&GO N550H Neutral 8 0.121 PhD-SNP: F[N]=5% F[H]=4% Nali=1573 N550H Neutral 8 0.076 PANTHER: F[N]=10% F[H]=16% N550H Neutral 5 0.239 SNPs&GO N550K Neutral 8 0.082 PhD-SNP: F[N]=5% F[K]=16% Nali=1573 N550K Neutral 8 0.075 PANTHER: F[N]=10% F[K]=7% N550K Neutral 1 0.435 SNPs&GO N550S Neutral 8 0.113 PhD-SNP: F[N]=5% F[S]=4% Nali=1573 N550S Neutral 8 0.094 PANTHER: F[N]=10% F[S]=5% N550S Neutral 3 0.359 SNPs&GO T553A Neutral 6 0.179 PhD-SNP: F[T]=30% F[A]=2% Nali=1585 T553A Neutral 4 0.292 PANTHER: F[T]=55% F[A]=6% T553A Disease 5 0.752 SNPs&GO E554K Neutral 3 0.365 PhD-SNP: F[E]=18% F[K]=4% Nali=1579 E554K Neutral 6 0.217 PANTHER: F[E]=34% F[K]=5% E554K Disease 6 0.823 SNPs&GO V555A Neutral 5 0.248 PhD-SNP: F[V]=28% F[A]=18% Nali=1590 V555A Neutral 3 0.350 PANTHER: F[V]=53% F[A]=4% V555A Disease 7 0.834 SNPs&GO V555I Neutral 7 0.144 PhD-SNP: F[V]=28% F[I]=21% Nali=1590 V555I Neutral 6 0.178 PANTHER: F[V]=53% F[I]=12% V555I Disease 4 0.685 SNPs&GO T558M Neutral 2 0.376 PhD-SNP: F[T]=7% F[M]=1% Nali=1609 T558M Neutral 4 0.302 PANTHER: F[T]=26% F[M]=2% T558M Disease 6 0.802 SNPs&GO A559T Neutral 1 0.430 PhD-SNP: F[A]=26% F[T]=6% Nali=1614 A559T Neutral 2 0.384 PANTHER: F[A]=59% F[T]=4% A559T Disease 8 0.904 SNPs&GO A562T Neutral 0 0.493 PhD-SNP: F[A]=7% F[T]=1% Nali=1629 A562T Neutral 5 0.236 PANTHER: F[A]=33% F[T]=5% A562T Disease 8 0.887 SNPs&GO A565T Neutral 0 0.485 PhD-SNP: F[A]=19% F[T]=4% Nali=1643 A565T Neutral 2 0.384 PANTHER: F[A]=59% F[T]=4% A565T Disease 8 0.913 SNPs&GO L566P Disease 9 0.935 PhD-SNP: F[L]=27% F[P]=0% Nali=1647 L566P Disease 5 0.760 PANTHER: F[L]=62% F[P]=0% L566P Disease 10 0.988 SNPs&GO T568M Disease 5 0.734 PhD-SNP: F[T]=35% F[M]=3% Nali=1646 T568M Disease 3 0.668 PANTHER: F[T]=55% F[M]=1% T568M Disease 9 0.962 SNPs&GO L572I Neutral 4 0.299 PhD-SNP: F[L]=34% F[I]=15% Nali=1637 L572I Neutral 4 0.290 PANTHER: F[L]=62% F[I]=7% L572I Disease 5 0.771 SNPs&GO K574N Disease 7 0.863 PhD-SNP: F[K]=95% F[N]=0% Nali=1642 K574N Disease 10 0.992 PANTHER: F[K]=96% F[N]=0% K574N Disease 9 0.939 SNPs&GO K574R Disease 6 0.802 PhD-SNP: F[K]=95% F[R]=3% Nali=1642 K574R Disease 9 0.973 PANTHER: F[K]=96% F[R]=0% K574R Disease 9 0.942 SNPs&GO M575L Neutral 0 0.479 PhD-SNP: F[M]=20% F[L]=28% Nali=1634 M575L Neutral 7 0.164 PANTHER: F[M]=48% F[L]=13% M575L Disease 7 0.859 SNPs&GO M575T Disease 4 0.691 PhD-SNP: F[M]=20% F[T]=0% Nali=1634 M575T Neutral 1 0.466 PANTHER: F[M]=48% F[T]=2% M575T Disease 9 0.951 SNPs&GO Y576C Disease 7 0.875 PhD-SNP: F[Y]=17% F[C]=0% Nali=1623 Y576C Disease 9 0.958 PANTHER: F[Y]=82% F[C]=0% Y576C Disease 10 0.978 SNPs&GO S577G Neutral 0 0.495 PhD-SNP: F[S]=12% F[G]=11% Nali=1620 S577G Neutral 2 0.392 PANTHER: F[S]=56% F[G]=3% S577G Disease 9 0.946 SNPs&GO A582D Disease 5 0.747 PhD-SNP: F[A]=14% F[D]=2% Nali=1568 A582D Unclassified NA NA PANTHER: F[A]=NA F[D]=NA A582D Disease 8 0.924 SNPs&GO A582T Neutral 3 0.343 PhD-SNP: F[A]=14% F[T]=4% Nali=1568 A582T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A582T Disease 3 0.668 SNPs&GO V585L Neutral 0 0.477 PhD-SNP: F[V]=8% F[L]=1% Nali=1660 V585L Neutral 5 0.256 PANTHER: F[V]=54% F[L]=7% V585L Disease 8 0.879 SNPs&GO V585M Neutral 4 0.303 PhD-SNP: F[V]=8% F[M]=2% Nali=1660 V585M Disease 0 0.521 PANTHER: F[V]=54% F[M]=2% V585M Disease 8 0.898 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. ** ** ** **********************************************************************************************