********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method T95N Neutral 5 0.273 PhD-SNP: F[T]=12% F[N]=2% Nali=532 T95N Unclassified NA NA PANTHER: F[T]=NA F[N]=NA T95N Disease 1 0.567 SNPs&GO T96M Neutral 6 0.181 PhD-SNP: F[T]=21% F[M]=0% Nali=516 T96M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T96M Disease 1 0.531 SNPs&GO A97T Neutral 7 0.151 PhD-SNP: F[A]=19% F[T]=3% Nali=524 A97T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A97T Neutral 2 0.383 SNPs&GO T98I Neutral 8 0.123 PhD-SNP: F[T]=17% F[I]=3% Nali=544 T98I Unclassified NA NA PANTHER: F[T]=NA F[I]=NA T98I Neutral 0 0.484 SNPs&GO R99C Disease 4 0.682 PhD-SNP: F[R]=45% F[C]=0% Nali=587 R99C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R99C Disease 7 0.843 SNPs&GO P100L Neutral 0 0.478 PhD-SNP: F[P]=64% F[L]=0% Nali=560 P100L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P100L Disease 6 0.796 SNPs&GO R102L Disease 5 0.748 PhD-SNP: F[R]=50% F[L]=0% Nali=677 R102L Unclassified NA NA PANTHER: F[R]=NA F[L]=NA R102L Disease 7 0.844 SNPs&GO R102Q Disease 2 0.603 PhD-SNP: F[R]=50% F[Q]=1% Nali=677 R102Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R102Q Disease 5 0.772 SNPs&GO L105F Neutral 9 0.037 PhD-SNP: F[L]=12% F[F]=47% Nali=775 L105F Unclassified NA NA PANTHER: F[L]=NA F[F]=NA L105F Neutral 6 0.195 SNPs&GO K110R Neutral 8 0.101 PhD-SNP: F[K]=14% F[R]=6% Nali=965 K110R Unclassified NA NA PANTHER: F[K]=NA F[R]=NA K110R Neutral 2 0.384 SNPs&GO R114W Disease 8 0.920 PhD-SNP: F[R]=82% F[W]=1% Nali=1344 R114W Unclassified NA NA PANTHER: F[R]=NA F[W]=NA R114W Disease 10 0.986 SNPs&GO A116T Neutral 8 0.113 PhD-SNP: F[A]=15% F[T]=13% Nali=1361 A116T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A116T Neutral 4 0.299 SNPs&GO S119N Neutral 4 0.287 PhD-SNP: F[S]=12% F[N]=3% Nali=1399 S119N Unclassified NA NA PANTHER: F[S]=NA F[N]=NA S119N Disease 0 0.507 SNPs&GO I120V Neutral 4 0.277 PhD-SNP: F[I]=56% F[V]=13% Nali=1459 I120V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I120V Disease 3 0.642 SNPs&GO V121A Disease 1 0.566 PhD-SNP: F[V]=57% F[A]=2% Nali=1465 V121A Unclassified NA NA PANTHER: F[V]=NA F[A]=NA V121A Disease 5 0.755 SNPs&GO I128V Neutral 6 0.194 PhD-SNP: F[I]=16% F[V]=4% Nali=1592 I128V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I128V Neutral 2 0.397 SNPs&GO T133S Disease 0 0.523 PhD-SNP: F[T]=26% F[S]=2% Nali=1586 T133S Unclassified NA NA PANTHER: F[T]=NA F[S]=NA T133S Disease 5 0.771 SNPs&GO A136V Disease 3 0.660 PhD-SNP: F[A]=21% F[V]=7% Nali=1580 A136V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A136V Disease 8 0.889 SNPs&GO N137S Disease 0 0.509 PhD-SNP: F[N]=72% F[S]=24% Nali=1582 N137S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N137S Disease 8 0.891 SNPs&GO V139L Disease 3 0.646 PhD-SNP: F[V]=38% F[L]=12% Nali=1607 V139L Unclassified NA NA PANTHER: F[V]=NA F[L]=NA V139L Disease 8 0.880 SNPs&GO A140V Disease 2 0.591 PhD-SNP: F[A]=27% F[V]=9% Nali=1602 A140V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A140V Disease 7 0.870 SNPs&GO A142G Disease 1 0.575 PhD-SNP: F[A]=52% F[G]=15% Nali=1589 A142G Unclassified NA NA PANTHER: F[A]=NA F[G]=NA A142G Disease 8 0.907 SNPs&GO A142V Disease 6 0.820 PhD-SNP: F[A]=52% F[V]=2% Nali=1589 A142V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A142V Disease 9 0.954 SNPs&GO Y144C Disease 7 0.849 PhD-SNP: F[Y]=29% F[C]=0% Nali=1404 Y144C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y144C Disease 9 0.947 SNPs&GO S152T Neutral 6 0.181 PhD-SNP: F[S]=28% F[T]=11% Nali=1418 S152T Unclassified NA NA PANTHER: F[S]=NA F[T]=NA S152T Neutral 3 0.335 SNPs&GO N153D Neutral 5 0.234 PhD-SNP: F[N]=26% F[D]=6% Nali=1430 N153D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N153D Disease 1 0.568 SNPs&GO N153S Neutral 6 0.214 PhD-SNP: F[N]=26% F[S]=10% Nali=1430 N153S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N153S Neutral 1 0.455 SNPs&GO A154T Neutral 7 0.143 PhD-SNP: F[A]=18% F[T]=11% Nali=1405 A154T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A154T Neutral 3 0.350 SNPs&GO T155A Neutral 8 0.095 PhD-SNP: F[T]=20% F[A]=3% Nali=1309 T155A Unclassified NA NA PANTHER: F[T]=NA F[A]=NA T155A Neutral 4 0.281 SNPs&GO R161Q Neutral 4 0.284 PhD-SNP: F[R]=10% F[Q]=5% Nali=1557 R161Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R161Q Disease 2 0.587 SNPs&GO V162M Neutral 2 0.388 PhD-SNP: F[V]=23% F[M]=3% Nali=1643 V162M Unclassified NA NA PANTHER: F[V]=NA F[M]=NA V162M Disease 4 0.680 SNPs&GO F166L Disease 8 0.894 PhD-SNP: F[F]=89% F[L]=2% Nali=1691 F166L Unclassified NA NA PANTHER: F[F]=NA F[L]=NA F166L Disease 9 0.974 SNPs&GO L167F Disease 2 0.616 PhD-SNP: F[L]=13% F[F]=6% Nali=1690 L167F Unclassified NA NA PANTHER: F[L]=NA F[F]=NA L167F Disease 8 0.898 SNPs&GO T171M Disease 6 0.785 PhD-SNP: F[T]=48% F[M]=1% Nali=1711 T171M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T171M Disease 8 0.924 SNPs&GO V172A Neutral 3 0.336 PhD-SNP: F[V]=18% F[A]=8% Nali=1712 V172A Unclassified NA NA PANTHER: F[V]=NA F[A]=NA V172A Disease 2 0.583 SNPs&GO V172L Neutral 2 0.401 PhD-SNP: F[V]=18% F[L]=22% Nali=1712 V172L Unclassified NA NA PANTHER: F[V]=NA F[L]=NA V172L Disease 3 0.670 SNPs&GO E173G Disease 8 0.914 PhD-SNP: F[E]=98% F[G]=0% Nali=1713 E173G Unclassified NA NA PANTHER: F[E]=NA F[G]=NA E173G Disease 10 0.993 SNPs&GO A174P Disease 9 0.938 PhD-SNP: F[A]=16% F[P]=0% Nali=1713 A174P Unclassified NA NA PANTHER: F[A]=NA F[P]=NA A174P Disease 10 0.977 SNPs&GO A174V Disease 6 0.805 PhD-SNP: F[A]=16% F[V]=1% Nali=1713 A174V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A174V Disease 9 0.941 SNPs&GO I179T Disease 2 0.624 PhD-SNP: F[I]=31% F[T]=4% Nali=1715 I179T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I179T Disease 6 0.815 SNPs&GO I179V Neutral 7 0.148 PhD-SNP: F[I]=31% F[V]=29% Nali=1715 I179V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I179V Disease 0 0.509 SNPs&GO A180T Disease 8 0.896 PhD-SNP: F[A]=78% F[T]=1% Nali=1714 A180T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A180T Disease 10 0.979 SNPs&GO Y181C Disease 7 0.850 PhD-SNP: F[Y]=25% F[C]=1% Nali=1536 Y181C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y181C Disease 9 0.937 SNPs&GO Y181H Disease 4 0.696 PhD-SNP: F[Y]=25% F[H]=0% Nali=1536 Y181H Unclassified NA NA PANTHER: F[Y]=NA F[H]=NA Y181H Disease 7 0.868 SNPs&GO L183F Neutral 7 0.140 PhD-SNP: F[L]=29% F[F]=49% Nali=1450 L183F Unclassified NA NA PANTHER: F[L]=NA F[F]=NA L183F Disease 0 0.513 SNPs&GO P187S Disease 2 0.591 PhD-SNP: F[P]=35% F[S]=3% Nali=1236 P187S Unclassified NA NA PANTHER: F[P]=NA F[S]=NA P187S Disease 7 0.846 SNPs&GO N188D Neutral 2 0.387 PhD-SNP: F[N]=12% F[D]=3% Nali=1486 N188D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N188D Disease 6 0.790 SNPs&GO N188S Neutral 4 0.287 PhD-SNP: F[N]=12% F[S]=4% Nali=1486 N188S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N188S Disease 3 0.653 SNPs&GO R192C Disease 8 0.911 PhD-SNP: F[R]=50% F[C]=0% Nali=1719 R192C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R192C Disease 9 0.973 SNPs&GO R192H Disease 6 0.816 PhD-SNP: F[R]=50% F[H]=0% Nali=1719 R192H Unclassified NA NA PANTHER: F[R]=NA F[H]=NA R192H Disease 9 0.952 SNPs&GO G194A Neutral 2 0.389 PhD-SNP: F[G]=26% F[A]=17% Nali=1717 G194A Unclassified NA NA PANTHER: F[G]=NA F[A]=NA G194A Disease 1 0.555 SNPs&GO G194S Disease 1 0.531 PhD-SNP: F[G]=26% F[S]=10% Nali=1717 G194S Unclassified NA NA PANTHER: F[G]=NA F[S]=NA G194S Disease 4 0.717 SNPs&GO W195R Disease 9 0.956 PhD-SNP: F[W]=87% F[R]=0% Nali=1730 W195R Unclassified NA NA PANTHER: F[W]=NA F[R]=NA W195R Disease 10 0.992 SNPs&GO N196D Disease 8 0.878 PhD-SNP: F[N]=80% F[D]=1% Nali=1726 N196D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N196D Disease 10 0.980 SNPs&GO D199N Disease 9 0.941 PhD-SNP: F[D]=98% F[N]=0% Nali=1724 D199N Unclassified NA NA PANTHER: F[D]=NA F[N]=NA D199N Disease 10 0.994 SNPs&GO V204I Neutral 5 0.230 PhD-SNP: F[V]=23% F[I]=23% Nali=1698 V204I Unclassified NA NA PANTHER: F[V]=NA F[I]=NA V204I Neutral 2 0.425 SNPs&GO I211T Neutral 2 0.385 PhD-SNP: F[I]=21% F[T]=4% Nali=1520 I211T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I211T Disease 1 0.567 SNPs&GO Q214E Neutral 5 0.229 PhD-SNP: F[Q]=10% F[E]=10% Nali=916 Q214E Unclassified NA NA PANTHER: F[Q]=NA F[E]=NA Q214E Disease 1 0.560 SNPs&GO D219E Neutral 2 0.391 PhD-SNP: F[D]=34% F[E]=10% Nali=781 D219E Unclassified NA NA PANTHER: F[D]=NA F[E]=NA D219E Disease 3 0.626 SNPs&GO D219N Disease 1 0.530 PhD-SNP: F[D]=34% F[N]=4% Nali=781 D219N Unclassified NA NA PANTHER: F[D]=NA F[N]=NA D219N Disease 4 0.685 SNPs&GO A221G Neutral 4 0.311 PhD-SNP: F[A]=32% F[G]=10% Nali=962 A221G Unclassified NA NA PANTHER: F[A]=NA F[G]=NA A221G Disease 2 0.593 SNPs&GO A221T Neutral 1 0.464 PhD-SNP: F[A]=32% F[T]=2% Nali=962 A221T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A221T Disease 3 0.647 SNPs&GO N222D Neutral 1 0.470 PhD-SNP: F[N]=41% F[D]=1% Nali=939 N222D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N222D Disease 6 0.798 SNPs&GO A223G Neutral 4 0.297 PhD-SNP: F[A]=19% F[G]=4% Nali=949 A223G Neutral 4 0.297 PANTHER: F[A]=50% F[G]=4% A223G Disease 8 0.887 SNPs&GO A223T Neutral 5 0.225 PhD-SNP: F[A]=19% F[T]=10% Nali=949 A223T Neutral 5 0.268 PANTHER: F[A]=50% F[T]=4% A223T Disease 7 0.863 SNPs&GO G225R Disease 7 0.872 PhD-SNP: F[G]=59% F[R]=1% Nali=1034 G225R Disease 0 0.524 PANTHER: F[G]=64% F[R]=1% G225R Disease 10 0.983 SNPs&GO G225V Disease 7 0.829 PhD-SNP: F[G]=59% F[V]=1% Nali=1034 G225V Neutral 0 0.490 PANTHER: F[G]=64% F[V]=1% G225V Disease 9 0.972 SNPs&GO G226R Disease 6 0.783 PhD-SNP: F[G]=38% F[R]=1% Nali=828 G226R Disease 0 0.524 PANTHER: F[G]=64% F[R]=1% G226R Disease 10 0.975 SNPs&GO G228A Neutral 1 0.455 PhD-SNP: F[G]=29% F[A]=2% Nali=870 G228A Neutral 4 0.323 PANTHER: F[G]=66% F[A]=4% G228A Disease 8 0.890 SNPs&GO A229S Neutral 5 0.255 PhD-SNP: F[A]=11% F[S]=8% Nali=870 A229S Neutral 6 0.200 PANTHER: F[A]=49% F[S]=6% A229S Disease 6 0.799 SNPs&GO F231L Neutral 1 0.473 PhD-SNP: F[F]=38% F[L]=13% Nali=788 F231L Neutral 4 0.294 PANTHER: F[F]=60% F[L]=7% F231L Disease 9 0.927 SNPs&GO D232H Disease 1 0.543 PhD-SNP: F[D]=24% F[H]=0% Nali=1176 D232H Disease 10 0.985 PANTHER: F[D]=94% F[H]=0% D232H Disease 9 0.938 SNPs&GO D232Y Disease 6 0.782 PhD-SNP: F[D]=24% F[Y]=0% Nali=1176 D232Y Disease 10 0.991 PANTHER: F[D]=94% F[Y]=0% D232Y Disease 10 0.975 SNPs&GO A235V Neutral 4 0.301 PhD-SNP: F[A]=31% F[V]=22% Nali=1629 A235V Disease 6 0.809 PANTHER: F[A]=80% F[V]=1% A235V Disease 9 0.944 SNPs&GO R240C Disease 8 0.924 PhD-SNP: F[R]=93% F[C]=0% Nali=1746 R240C Disease 9 0.961 PANTHER: F[R]=84% F[C]=0% R240C Disease 10 0.979 SNPs&GO V241A Neutral 4 0.295 PhD-SNP: F[V]=49% F[A]=19% Nali=1746 V241A Disease 5 0.733 PANTHER: F[V]=73% F[A]=2% V241A Disease 8 0.906 SNPs&GO R243C Disease 8 0.900 PhD-SNP: F[R]=97% F[C]=0% Nali=1725 R243C Disease 9 0.961 PANTHER: F[R]=84% F[C]=0% R243C Disease 10 0.978 SNPs&GO P244S Disease 3 0.648 PhD-SNP: F[P]=54% F[S]=0% Nali=1724 P244S Disease 10 0.994 PANTHER: F[P]=98% F[S]=0% P244S Disease 9 0.956 SNPs&GO V248G Disease 1 0.548 PhD-SNP: F[V]=27% F[G]=0% Nali=1748 V248G Disease 7 0.869 PANTHER: F[V]=73% F[G]=0% V248G Disease 9 0.957 SNPs&GO V251I Neutral 8 0.076 PhD-SNP: F[V]=20% F[I]=17% Nali=1738 V251I Neutral 7 0.174 PANTHER: F[V]=52% F[I]=12% V251I Neutral 1 0.470 SNPs&GO Q255H Disease 1 0.563 PhD-SNP: F[Q]=17% F[H]=1% Nali=1752 Q255H Disease 1 0.563 PANTHER: F[Q]=51% F[H]=1% Q255H Disease 8 0.923 SNPs&GO I261T Neutral 0 0.494 PhD-SNP: F[I]=19% F[T]=0% Nali=1748 I261T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I261T Disease 4 0.705 SNPs&GO A264S Neutral 6 0.198 PhD-SNP: F[A]=33% F[S]=48% Nali=1754 A264S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A264S Neutral 0 0.490 SNPs&GO A264T Neutral 0 0.495 PhD-SNP: F[A]=33% F[T]=14% Nali=1754 A264T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A264T Disease 5 0.765 SNPs&GO A272T Neutral 4 0.287 PhD-SNP: F[A]=13% F[T]=5% Nali=1753 A272T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A272T Disease 2 0.575 SNPs&GO I279V Neutral 1 0.434 PhD-SNP: F[I]=22% F[V]=3% Nali=1753 I279V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I279V Disease 4 0.718 SNPs&GO A283T Disease 7 0.826 PhD-SNP: F[A]=58% F[T]=1% Nali=1758 A283T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A283T Disease 9 0.951 SNPs&GO I284V Disease 1 0.537 PhD-SNP: F[I]=65% F[V]=14% Nali=1758 I284V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I284V Disease 8 0.922 SNPs&GO I285L Disease 1 0.561 PhD-SNP: F[I]=36% F[L]=20% Nali=1759 I285L Unclassified NA NA PANTHER: F[I]=NA F[L]=NA I285L Disease 7 0.830 SNPs&GO L287F Disease 7 0.831 PhD-SNP: F[L]=29% F[F]=0% Nali=1756 L287F Unclassified NA NA PANTHER: F[L]=NA F[F]=NA L287F Disease 8 0.906 SNPs&GO L289I Disease 5 0.749 PhD-SNP: F[L]=68% F[I]=6% Nali=1757 L289I Unclassified NA NA PANTHER: F[L]=NA F[I]=NA L289I Disease 9 0.949 SNPs&GO M291I Disease 3 0.658 PhD-SNP: F[M]=23% F[I]=5% Nali=1477 M291I Unclassified NA NA PANTHER: F[M]=NA F[I]=NA M291I Disease 8 0.900 SNPs&GO T297P Disease 6 0.787 PhD-SNP: F[T]=23% F[P]=0% Nali=1267 T297P Unclassified NA NA PANTHER: F[T]=NA F[P]=NA T297P Disease 8 0.907 SNPs&GO N300D Neutral 3 0.353 PhD-SNP: F[N]=27% F[D]=14% Nali=1394 N300D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N300D Disease 4 0.710 SNPs&GO Q301E Neutral 7 0.142 PhD-SNP: F[Q]=10% F[E]=22% Nali=1389 Q301E Unclassified NA NA PANTHER: F[Q]=NA F[E]=NA Q301E Neutral 2 0.406 SNPs&GO I304L Neutral 6 0.198 PhD-SNP: F[I]=30% F[L]=12% Nali=1165 I304L Unclassified NA NA PANTHER: F[I]=NA F[L]=NA I304L Neutral 2 0.411 SNPs&GO I304V Neutral 8 0.106 PhD-SNP: F[I]=30% F[V]=11% Nali=1165 I304V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I304V Neutral 4 0.287 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. ** ** ** **********************************************************************************************