********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** WARNING: Incorrect mutation X13537_SPLICE WARNING: Incorrect mutation R1787QFS*36 WARNING: Incorrect mutation E10431* WARNING: Incorrect mutation G10932* WARNING: Incorrect mutation E8107* Sequence File: fileseq.seq Mutation Prediction RI Probability Method E372D Disease 1 0.563 PhD-SNP: F[E]=100% F[D]=0% Nali=3 E372D Unclassified NA NA PANTHER: F[E]=NA F[D]=NA E372D Neutral 4 0.280 SNPs&GO T623K Neutral 2 0.402 PhD-SNP: F[T]=100% F[K]=0% Nali=3 T623K Unclassified NA NA PANTHER: F[T]=NA F[K]=NA T623K Neutral 7 0.128 SNPs&GO A1359S Neutral 4 0.297 PhD-SNP: F[A]=75% F[S]=0% Nali=3 A1359S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A1359S Neutral 9 0.068 SNPs&GO V1589I Neutral 6 0.212 PhD-SNP: F[V]=100% F[I]=0% Nali=3 V1589I Unclassified NA NA PANTHER: F[V]=NA F[I]=NA V1589I Neutral 9 0.063 SNPs&GO F2090C Neutral 2 0.421 PhD-SNP: F[F]=100% F[C]=0% Nali=3 F2090C Unclassified NA NA PANTHER: F[F]=NA F[C]=NA F2090C Neutral 9 0.069 SNPs&GO A2118V Neutral 8 0.115 PhD-SNP: F[A]=50% F[V]=0% Nali=3 A2118V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A2118V Neutral 10 0.024 SNPs&GO A2125S Neutral 0 0.497 PhD-SNP: F[A]=100% F[S]=0% Nali=3 A2125S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A2125S Neutral 7 0.141 SNPs&GO L2531H Neutral 1 0.434 PhD-SNP: F[L]=100% F[H]=0% Nali=3 L2531H Unclassified NA NA PANTHER: F[L]=NA F[H]=NA L2531H Neutral 8 0.084 SNPs&GO D2646Y Disease 3 0.633 PhD-SNP: F[D]=100% F[Y]=0% Nali=3 D2646Y Unclassified NA NA PANTHER: F[D]=NA F[Y]=NA D2646Y Neutral 8 0.124 SNPs&GO M2786I Neutral 3 0.348 PhD-SNP: F[M]=100% F[I]=0% Nali=3 M2786I Unclassified NA NA PANTHER: F[M]=NA F[I]=NA M2786I Neutral 7 0.170 SNPs&GO T3574K Neutral 6 0.189 PhD-SNP: F[T]=100% F[K]=0% Nali=4 T3574K Unclassified NA NA PANTHER: F[T]=NA F[K]=NA T3574K Neutral 9 0.069 SNPs&GO M3613I Neutral 2 0.397 PhD-SNP: F[M]=100% F[I]=0% Nali=4 M3613I Unclassified NA NA PANTHER: F[M]=NA F[I]=NA M3613I Neutral 7 0.150 SNPs&GO A3670S Neutral 2 0.412 PhD-SNP: F[A]=100% F[S]=0% Nali=4 A3670S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A3670S Neutral 8 0.114 SNPs&GO D3737H Disease 4 0.676 PhD-SNP: F[D]=100% F[H]=0% Nali=3 D3737H Unclassified NA NA PANTHER: F[D]=NA F[H]=NA D3737H Neutral 7 0.164 SNPs&GO A3757T Neutral 4 0.280 PhD-SNP: F[A]=100% F[T]=0% Nali=3 A3757T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A3757T Neutral 9 0.042 SNPs&GO T4145I Neutral 8 0.092 PhD-SNP: F[T]=50% F[I]=0% Nali=7 T4145I Unclassified NA NA PANTHER: F[T]=NA F[I]=NA T4145I Neutral 9 0.028 SNPs&GO A4482V Neutral 9 0.044 PhD-SNP: F[A]=50% F[V]=40% Nali=9 A4482V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A4482V Neutral 10 0.007 SNPs&GO T5571I Neutral 8 0.075 PhD-SNP: F[T]=29% F[I]=0% Nali=6 T5571I Unclassified NA NA PANTHER: F[T]=NA F[I]=NA T5571I Neutral 9 0.046 SNPs&GO R5610Q Neutral 2 0.412 PhD-SNP: F[R]=50% F[Q]=0% Nali=5 R5610Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R5610Q Neutral 7 0.159 SNPs&GO A5705V Neutral 4 0.305 PhD-SNP: F[A]=50% F[V]=0% Nali=5 A5705V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A5705V Neutral 7 0.130 SNPs&GO L5942I Neutral 5 0.232 PhD-SNP: F[L]=86% F[I]=0% Nali=6 L5942I Unclassified NA NA PANTHER: F[L]=NA F[I]=NA L5942I Neutral 9 0.075 SNPs&GO A6519V Neutral 9 0.046 PhD-SNP: F[A]=83% F[V]=17% Nali=5 A6519V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A6519V Neutral 10 0.008 SNPs&GO T6542A Neutral 7 0.170 PhD-SNP: F[T]=100% F[A]=0% Nali=5 T6542A Unclassified NA NA PANTHER: F[T]=NA F[A]=NA T6542A Neutral 9 0.070 SNPs&GO V6559M Neutral 2 0.379 PhD-SNP: F[V]=86% F[M]=0% Nali=6 V6559M Unclassified NA NA PANTHER: F[V]=NA F[M]=NA V6559M Neutral 9 0.069 SNPs&GO D6754G Neutral 6 0.199 PhD-SNP: F[D]=78% F[G]=11% Nali=8 D6754G Unclassified NA NA PANTHER: F[D]=NA F[G]=NA D6754G Neutral 9 0.037 SNPs&GO T7136M Neutral 7 0.158 PhD-SNP: F[T]=43% F[M]=0% Nali=6 T7136M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T7136M Neutral 9 0.063 SNPs&GO A7507V Neutral 5 0.254 PhD-SNP: F[A]=29% F[V]=0% Nali=6 A7507V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A7507V Neutral 8 0.089 SNPs&GO P7714S Neutral 7 0.163 PhD-SNP: F[P]=86% F[S]=14% Nali=6 P7714S Unclassified NA NA PANTHER: F[P]=NA F[S]=NA P7714S Neutral 9 0.038 SNPs&GO T8126I Neutral 6 0.221 PhD-SNP: F[T]=88% F[I]=0% Nali=7 T8126I Unclassified NA NA PANTHER: F[T]=NA F[I]=NA T8126I Neutral 9 0.069 SNPs&GO M8138V Neutral 8 0.099 PhD-SNP: F[M]=25% F[V]=0% Nali=7 M8138V Unclassified NA NA PANTHER: F[M]=NA F[V]=NA M8138V Neutral 9 0.040 SNPs&GO I8166V Neutral 9 0.050 PhD-SNP: F[I]=50% F[V]=13% Nali=7 I8166V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I8166V Neutral 10 0.021 SNPs&GO Q8171H Neutral 8 0.082 PhD-SNP: F[Q]=75% F[H]=25% Nali=7 Q8171H Unclassified NA NA PANTHER: F[Q]=NA F[H]=NA Q8171H Neutral 10 0.019 SNPs&GO R8310M Neutral 8 0.080 PhD-SNP: F[R]=25% F[M]=25% Nali=7 R8310M Unclassified NA NA PANTHER: F[R]=NA F[M]=NA R8310M Neutral 9 0.031 SNPs&GO I8773V Neutral 8 0.108 PhD-SNP: F[I]=29% F[V]=0% Nali=6 I8773V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I8773V Neutral 9 0.037 SNPs&GO T9052I Neutral 8 0.107 PhD-SNP: F[T]=60% F[I]=0% Nali=4 T9052I Unclassified NA NA PANTHER: F[T]=NA F[I]=NA T9052I Neutral 9 0.042 SNPs&GO T9109S Neutral 7 0.128 PhD-SNP: F[T]=60% F[S]=0% Nali=4 T9109S Unclassified NA NA PANTHER: F[T]=NA F[S]=NA T9109S Neutral 9 0.043 SNPs&GO T9507M Neutral 5 0.244 PhD-SNP: F[T]=78% F[M]=0% Nali=8 T9507M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T9507M Neutral 8 0.092 SNPs&GO E9530Q Neutral 6 0.176 PhD-SNP: F[E]=38% F[Q]=0% Nali=7 E9530Q Unclassified NA NA PANTHER: F[E]=NA F[Q]=NA E9530Q Neutral 9 0.045 SNPs&GO T9655A Neutral 6 0.186 PhD-SNP: F[T]=100% F[A]=0% Nali=7 T9655A Unclassified NA NA PANTHER: F[T]=NA F[A]=NA T9655A Neutral 8 0.089 SNPs&GO S9962Y Neutral 7 0.163 PhD-SNP: F[S]=50% F[Y]=0% Nali=5 S9962Y Unclassified NA NA PANTHER: F[S]=NA F[Y]=NA S9962Y Neutral 9 0.042 SNPs&GO A9978S Neutral 5 0.246 PhD-SNP: F[A]=40% F[S]=0% Nali=4 A9978S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A9978S Neutral 8 0.084 SNPs&GO M10102I Neutral 8 0.078 PhD-SNP: F[M]=29% F[I]=14% Nali=6 M10102I Unclassified NA NA PANTHER: F[M]=NA F[I]=NA M10102I Neutral 10 0.025 SNPs&GO R10400K Neutral 4 0.309 PhD-SNP: F[R]=100% F[K]=0% Nali=2 R10400K Unclassified NA NA PANTHER: F[R]=NA F[K]=NA R10400K Neutral 7 0.167 SNPs&GO P10448L Neutral 1 0.440 PhD-SNP: F[P]=100% F[L]=0% Nali=2 P10448L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P10448L Neutral 8 0.105 SNPs&GO P10687L Neutral 6 0.209 PhD-SNP: F[P]=67% F[L]=0% Nali=5 P10687L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P10687L Neutral 9 0.060 SNPs&GO L11118I Neutral 9 0.037 PhD-SNP: F[L]=38% F[I]=0% Nali=7 L11118I Unclassified NA NA PANTHER: F[L]=NA F[I]=NA L11118I Neutral 10 0.017 SNPs&GO F11222L Neutral 8 0.083 PhD-SNP: F[F]=43% F[L]=0% Nali=6 F11222L Unclassified NA NA PANTHER: F[F]=NA F[L]=NA F11222L Neutral 10 0.024 SNPs&GO T11280A Neutral 8 0.083 PhD-SNP: F[T]=57% F[A]=0% Nali=6 T11280A Unclassified NA NA PANTHER: F[T]=NA F[A]=NA T11280A Neutral 9 0.040 SNPs&GO F11509C Neutral 1 0.463 PhD-SNP: F[F]=50% F[C]=0% Nali=5 F11509C Unclassified NA NA PANTHER: F[F]=NA F[C]=NA F11509C Neutral 7 0.129 SNPs&GO T11770A Neutral 7 0.154 PhD-SNP: F[T]=100% F[A]=0% Nali=5 T11770A Unclassified NA NA PANTHER: F[T]=NA F[A]=NA T11770A Neutral 9 0.066 SNPs&GO L11826I Neutral 7 0.157 PhD-SNP: F[L]=50% F[I]=0% Nali=5 L11826I Unclassified NA NA PANTHER: F[L]=NA F[I]=NA L11826I Neutral 8 0.080 SNPs&GO S11868F Neutral 5 0.264 PhD-SNP: F[S]=100% F[F]=0% Nali=5 S11868F Unclassified NA NA PANTHER: F[S]=NA F[F]=NA S11868F Neutral 8 0.077 SNPs&GO R12038C Disease 3 0.666 PhD-SNP: F[R]=38% F[C]=0% Nali=15 R12038C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R12038C Neutral 4 0.297 SNPs&GO R12249C Neutral 5 0.234 PhD-SNP: F[R]=18% F[C]=1% Nali=109 R12249C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R12249C Neutral 7 0.148 SNPs&GO R12305C Neutral 0 0.487 PhD-SNP: F[R]=41% F[C]=0% Nali=116 R12305C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R12305C Neutral 7 0.172 SNPs&GO E12713K Neutral 4 0.301 PhD-SNP: F[E]=27% F[K]=1% Nali=139 E12713K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E12713K Neutral 7 0.139 SNPs&GO G12720D Disease 0 0.511 PhD-SNP: F[G]=78% F[D]=9% Nali=143 G12720D Unclassified NA NA PANTHER: F[G]=NA F[D]=NA G12720D Neutral 6 0.216 SNPs&GO G13230R Neutral 0 0.495 PhD-SNP: F[G]=75% F[R]=10% Nali=141 G13230R Unclassified NA NA PANTHER: F[G]=NA F[R]=NA G13230R Neutral 6 0.182 SNPs&GO T13448I Neutral 7 0.143 PhD-SNP: F[T]=65% F[I]=2% Nali=90 T13448I Neutral 2 0.412 PANTHER: F[T]=41% F[I]=2% T13448I Neutral 8 0.086 SNPs&GO T13473I Neutral 7 0.140 PhD-SNP: F[T]=40% F[I]=0% Nali=82 T13473I Neutral 3 0.348 PANTHER: F[T]=34% F[I]=2% T13473I Neutral 9 0.066 SNPs&GO A13543V Neutral 7 0.150 PhD-SNP: F[A]=37% F[V]=2% Nali=142 A13543V Neutral 4 0.315 PANTHER: F[A]=52% F[V]=4% A13543V Neutral 8 0.093 SNPs&GO L13639F Disease 0 0.521 PhD-SNP: F[L]=75% F[F]=4% Nali=133 L13639F Neutral 3 0.353 PANTHER: F[L]=56% F[F]=3% L13639F Neutral 6 0.183 SNPs&GO G13681D Disease 4 0.708 PhD-SNP: F[G]=76% F[D]=2% Nali=131 G13681D Disease 0 0.511 PANTHER: F[G]=68% F[D]=2% G13681D Neutral 0 0.486 SNPs&GO A13785T Neutral 9 0.060 PhD-SNP: F[A]=35% F[T]=21% Nali=84 A13785T Neutral 4 0.289 PANTHER: F[A]=52% F[T]=4% A13785T Neutral 9 0.045 SNPs&GO Q14018H Neutral 5 0.228 PhD-SNP: F[Q]=33% F[H]=3% Nali=122 Q14018H Neutral 0 0.484 PANTHER: F[Q]=46% F[H]=1% Q14018H Neutral 5 0.225 SNPs&GO R14199W Neutral 5 0.236 PhD-SNP: F[R]=14% F[W]=0% Nali=58 R14199W Disease 5 0.750 PANTHER: F[R]=50% F[W]=0% R14199W Neutral 5 0.261 SNPs&GO L14227M Neutral 7 0.173 PhD-SNP: F[L]=20% F[M]=3% Nali=65 L14227M Neutral 4 0.289 PANTHER: F[L]=52% F[M]=4% L14227M Neutral 9 0.042 SNPs&GO T14425I Neutral 3 0.350 PhD-SNP: F[T]=72% F[I]=6% Nali=68 T14425I Neutral 4 0.278 PANTHER: F[T]=43% F[I]=3% T14425I Neutral 8 0.118 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. ** ** ** **********************************************************************************************