********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** WARNING: Incorrect mutation P1755R WARNING: Incorrect mutation P1755L WARNING: Incorrect mutation S1757N WARNING: Incorrect mutation S1757I WARNING: Incorrect mutation S1759L WARNING: Incorrect mutation T1761N WARNING: Incorrect mutation N1764H WARNING: Incorrect mutation N1766S WARNING: Incorrect mutation I1767V WARNING: Incorrect mutation N1768D WARNING: Incorrect mutation A1770T WARNING: Incorrect mutation A1770D WARNING: Incorrect mutation A1770G WARNING: Incorrect mutation N1772D WARNING: Incorrect mutation T1773P WARNING: Incorrect mutation A1774T WARNING: Incorrect mutation A1774S WARNING: Incorrect mutation A1774V WARNING: Incorrect mutation G1776S WARNING: Incorrect mutation R1777C WARNING: Incorrect mutation R1777H WARNING: Incorrect mutation R1780C WARNING: Incorrect mutation R1780H WARNING: Incorrect mutation R1780L WARNING: Incorrect mutation A1782T WARNING: Incorrect mutation A1782P WARNING: Incorrect mutation G1783S WARNING: Incorrect mutation G1783C WARNING: Incorrect mutation Y1784C WARNING: Incorrect mutation P1785S WARNING: Incorrect mutation P1785L WARNING: Incorrect mutation S1786G WARNING: Incorrect mutation S1786N WARNING: Incorrect mutation T1787M WARNING: Incorrect mutation V1788I WARNING: Incorrect mutation V1788A WARNING: Incorrect mutation S1789T WARNING: Incorrect mutation V1791A WARNING: Incorrect mutation V1791G WARNING: Incorrect mutation E1792K WARNING: Incorrect mutation E1792G WARNING: Incorrect mutation H1794Y WARNING: Incorrect mutation H1794Q WARNING: Incorrect mutation G1795R WARNING: Incorrect mutation G1795E WARNING: Incorrect mutation P1796T WARNING: Incorrect mutation P1796S WARNING: Incorrect mutation P1796H WARNING: Incorrect mutation P1796L WARNING: Incorrect mutation P1797A WARNING: Incorrect mutation P1797S WARNING: Incorrect mutation P1797H WARNING: Incorrect mutation P1797L WARNING: Incorrect mutation P1800T WARNING: Incorrect mutation P1800S WARNING: Incorrect mutation P1800L WARNING: Incorrect mutation I1802V WARNING: Incorrect mutation I1802N WARNING: Incorrect mutation I1802T WARNING: Incorrect mutation I1802S WARNING: Incorrect mutation R1803G WARNING: Incorrect mutation R1803W WARNING: Incorrect mutation R1803Q WARNING: Incorrect mutation R1803P WARNING: Incorrect mutation V1804M WARNING: Incorrect mutation V1804L WARNING: Incorrect mutation V1804A WARNING: Incorrect mutation Q1805E WARNING: Incorrect mutation E1806K WARNING: Incorrect mutation E1806G WARNING: Incorrect mutation E1806V WARNING: Incorrect mutation V1807M WARNING: Incorrect mutation A1808T WARNING: Incorrect mutation A1808E WARNING: Incorrect mutation A1808G WARNING: Incorrect mutation A1808V WARNING: Incorrect mutation K1810N WARNING: Incorrect mutation L1811V WARNING: Incorrect mutation L1811R WARNING: Incorrect mutation S1812N WARNING: Incorrect mutation S1813P WARNING: Incorrect mutation C1816W WARNING: Incorrect mutation H1817Y WARNING: Incorrect mutation H1817P WARNING: Incorrect mutation H1817R WARNING: Incorrect mutation S1818T WARNING: Incorrect mutation R1819W WARNING: Incorrect mutation R1819Q WARNING: Incorrect mutation R1819L WARNING: Incorrect mutation E1820D WARNING: Incorrect mutation Q1822E WARNING: Incorrect mutation A1823G WARNING: Incorrect mutation A1826G WARNING: Incorrect mutation A1826V WARNING: Incorrect mutation G1827D WARNING: Incorrect mutation E1829G WARNING: Incorrect mutation E1830G WARNING: Incorrect mutation T1831K WARNING: Incorrect mutation T1831M WARNING: Incorrect mutation S1832F WARNING: Incorrect mutation D1834N WARNING: Incorrect mutation D1834E WARNING: Incorrect mutation E1835K WARNING: Incorrect mutation E1835D WARNING: Incorrect mutation Y1837H WARNING: Incorrect mutation Y1837C WARNING: Incorrect mutation K1840E WARNING: Incorrect mutation K1840T WARNING: Incorrect mutation K1840N WARNING: Incorrect mutation M1841K WARNING: Incorrect mutation M1841T WARNING: Incorrect mutation N1842H WARNING: Incorrect mutation N1842T WARNING: Incorrect mutation N1842S WARNING: Incorrect mutation H1843R WARNING: Incorrect mutation H1843Q WARNING: Incorrect mutation T1845A WARNING: Incorrect mutation T1845M WARNING: Incorrect mutation A1847S WARNING: Incorrect mutation E1850K WARNING: Incorrect mutation E1850A WARNING: Incorrect mutation P1851T WARNING: Incorrect mutation L1853V WARNING: Incorrect mutation L1853P WARNING: Incorrect mutation L1854P WARNING: Incorrect mutation S1855A WARNING: Incorrect mutation S1855Y WARNING: Incorrect mutation T1856S WARNING: Incorrect mutation T1856R WARNING: Incorrect mutation E1857K WARNING: Incorrect mutation E1857A WARNING: Incorrect mutation D1863N WARNING: Incorrect mutation D1863G WARNING: Incorrect mutation D1864N WARNING: Incorrect mutation E1865K WARNING: Incorrect mutation E1865G WARNING: Incorrect mutation R1867W WARNING: Incorrect mutation R1867Q WARNING: Incorrect mutation T1870K WARNING: Incorrect mutation T1870R WARNING: Incorrect mutation T1870M WARNING: Incorrect mutation L1871R WARNING: Incorrect mutation E1873K WARNING: Incorrect mutation D1875H WARNING: Incorrect mutation D1875A WARNING: Incorrect mutation D1875E WARNING: Incorrect mutation K1876E WARNING: Incorrect mutation K1876N WARNING: Incorrect mutation I1879S WARNING: Incorrect mutation I1879M WARNING: Incorrect mutation R1880G WARNING: Incorrect mutation R1880W WARNING: Incorrect mutation R1880Q WARNING: Incorrect mutation Q1881K WARNING: Incorrect mutation Q1881P WARNING: Incorrect mutation S1882P WARNING: Incorrect mutation P1883L WARNING: Incorrect mutation G1886D WARNING: Incorrect mutation G1886A WARNING: Incorrect mutation G1886V WARNING: Incorrect mutation R1889S WARNING: Incorrect mutation R1889C WARNING: Incorrect mutation R1889H WARNING: Incorrect mutation S1890P WARNING: Incorrect mutation A1891P WARNING: Incorrect mutation A1891D WARNING: Incorrect mutation R1895Q WARNING: Incorrect mutation R1896K WARNING: Incorrect mutation S1898P WARNING: Incorrect mutation S1898F WARNING: Incorrect mutation E1902K WARNING: Incorrect mutation E1902Q WARNING: Incorrect mutation K1905R WARNING: Incorrect mutation R1906Q WARNING: Incorrect mutation R1906L WARNING: Incorrect mutation K1908R WARNING: Incorrect mutation D1909N WARNING: Incorrect mutation D1909V WARNING: Incorrect mutation R1910G WARNING: Incorrect mutation R1910Q WARNING: Incorrect mutation G1911R WARNING: Incorrect mutation G1911R WARNING: Incorrect mutation G1911E WARNING: Incorrect mutation G1912R WARNING: Incorrect mutation G1912E WARNING: Incorrect mutation D1913N WARNING: Incorrect mutation D1913H WARNING: Incorrect mutation D1913E WARNING: Incorrect mutation I1914F WARNING: Incorrect mutation I1914N Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method G1762C Disease 5 0.758 PhD-SNP: F[G]=45% F[C]=0% Nali=103 G1762C Neutral 2 0.421 PANTHER: F[G]=22% F[C]=1% G1762C Disease 9 0.957 SNPs&GO G1762D Disease 4 0.683 PhD-SNP: F[G]=45% F[D]=1% Nali=103 G1762D Neutral 5 0.249 PANTHER: F[G]=22% F[D]=3% G1762D Disease 9 0.941 SNPs&GO G1762R Neutral 5 0.266 PhD-SNP: F[G]=45% F[R]=24% Nali=103 G1762R Neutral 4 0.303 PANTHER: F[G]=22% F[R]=2% G1762R Disease 7 0.873 SNPs&GO G1762S Neutral 3 0.374 PhD-SNP: F[G]=45% F[S]=8% Nali=103 G1762S Neutral 9 0.066 PANTHER: F[G]=22% F[S]=29% G1762S Disease 2 0.576 SNPs&GO A1765D Disease 1 0.570 PhD-SNP: F[A]=15% F[D]=0% Nali=97 A1765D Neutral 7 0.129 PANTHER: F[A]=14% F[D]=4% A1765D Disease 7 0.868 SNPs&GO A1765T Neutral 7 0.156 PhD-SNP: F[A]=15% F[T]=8% Nali=97 A1765T Neutral 8 0.118 PANTHER: F[A]=14% F[T]=5% A1765T Disease 2 0.622 SNPs&GO N1814S Disease 2 0.608 PhD-SNP: F[N]=88% F[S]=2% Nali=82 N1814S Neutral 3 0.346 PANTHER: F[N]=53% F[S]=4% N1814S Disease 9 0.934 SNPs&GO V1839M Neutral 6 0.188 PhD-SNP: F[V]=46% F[M]=0% Nali=71 V1839M Neutral 2 0.384 PANTHER: F[V]=29% F[M]=1% V1839M Disease 6 0.806 SNPs&GO D1878N Neutral 6 0.194 PhD-SNP: F[D]=39% F[N]=7% Nali=43 D1878N Unclassified NA NA PANTHER: F[D]=NA F[N]=NA D1878N Neutral 2 0.392 SNPs&GO H1900Y Neutral 1 0.468 PhD-SNP: F[H]=51% F[Y]=0% Nali=50 H1900Y Neutral 7 0.131 PANTHER: F[H]=30% F[Y]=9% H1900Y Disease 6 0.790 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. ** ** ** **********************************************************************************************