********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** WARNING: Incorrect mutation I1914S WARNING: Incorrect mutation T1918S WARNING: Incorrect mutation P1921S WARNING: Incorrect mutation H1923Y WARNING: Incorrect mutation H1923R WARNING: Incorrect mutation L1924P WARNING: Incorrect mutation V1925I WARNING: Incorrect mutation H1927N WARNING: Incorrect mutation H1927D WARNING: Incorrect mutation H1927Y WARNING: Incorrect mutation L1930V WARNING: Incorrect mutation L1930F WARNING: Incorrect mutation A1933S WARNING: Incorrect mutation G1934D WARNING: Incorrect mutation L1935P WARNING: Incorrect mutation S1936R WARNING: Incorrect mutation L1939V WARNING: Incorrect mutation Q1940R WARNING: Incorrect mutation Q1940H WARNING: Incorrect mutation S1942N WARNING: Incorrect mutation H1943Y WARNING: Incorrect mutation H1943P WARNING: Incorrect mutation S1944T WARNING: Incorrect mutation A1946V WARNING: Incorrect mutation S1947T WARNING: Incorrect mutation S1947P WARNING: Incorrect mutation P1949S WARNING: Incorrect mutation P1949R WARNING: Incorrect mutation P1951R WARNING: Incorrect mutation P1951L WARNING: Incorrect mutation F1952S WARNING: Incorrect mutation A1953P WARNING: Incorrect mutation A1953S WARNING: Incorrect mutation A1953D WARNING: Incorrect mutation A1953V WARNING: Incorrect mutation T1954P WARNING: Incorrect mutation A1957P WARNING: Incorrect mutation A1957D WARNING: Incorrect mutation T1958K WARNING: Incorrect mutation T1958I WARNING: Incorrect mutation P1959A WARNING: Incorrect mutation P1959S WARNING: Incorrect mutation P1959L WARNING: Incorrect mutation G1960D WARNING: Incorrect mutation G1960V WARNING: Incorrect mutation R1962Q WARNING: Incorrect mutation G1963S WARNING: Incorrect mutation G1963C WARNING: Incorrect mutation W1964R WARNING: Incorrect mutation W1964C WARNING: Incorrect mutation P1965A WARNING: Incorrect mutation P1965S WARNING: Incorrect mutation P1965L WARNING: Incorrect mutation Q1967R WARNING: Incorrect mutation P1968H WARNING: Incorrect mutation P1968L WARNING: Incorrect mutation V1969I WARNING: Incorrect mutation V1969A WARNING: Incorrect mutation P1970L WARNING: Incorrect mutation T1971P WARNING: Incorrect mutation T1971A WARNING: Incorrect mutation T1971N WARNING: Incorrect mutation L1972M WARNING: Incorrect mutation R1973G WARNING: Incorrect mutation R1973W WARNING: Incorrect mutation R1973Q WARNING: Incorrect mutation L1974F WARNING: Incorrect mutation E1975A WARNING: Incorrect mutation G1976R WARNING: Incorrect mutation G1976E WARNING: Incorrect mutation V1977I WARNING: Incorrect mutation V1977L WARNING: Incorrect mutation V1977G WARNING: Incorrect mutation E1978K WARNING: Incorrect mutation E1978G WARNING: Incorrect mutation S1980G WARNING: Incorrect mutation S1980N WARNING: Incorrect mutation K1982N WARNING: Incorrect mutation S1985N WARNING: Incorrect mutation S1986G WARNING: Incorrect mutation S1986N WARNING: Incorrect mutation P1988S WARNING: Incorrect mutation P1988L WARNING: Incorrect mutation I1990T WARNING: Incorrect mutation I1990M WARNING: Incorrect mutation H1991Y WARNING: Incorrect mutation H1991R WARNING: Incorrect mutation C1992F WARNING: Incorrect mutation C1992W WARNING: Incorrect mutation G1993S WARNING: Incorrect mutation G1993D WARNING: Incorrect mutation A1996V WARNING: Incorrect mutation T1998P WARNING: Incorrect mutation T1998A WARNING: Incorrect mutation T1998N WARNING: Incorrect mutation T1999P WARNING: Incorrect mutation T1999A WARNING: Incorrect mutation T1999I WARNING: Incorrect mutation P2000A WARNING: Incorrect mutation P2000S WARNING: Incorrect mutation G2001S WARNING: Incorrect mutation G2001D WARNING: Incorrect mutation G2003R WARNING: Incorrect mutation G2004V WARNING: Incorrect mutation S2005G WARNING: Incorrect mutation S2006N WARNING: Incorrect mutation S2006R WARNING: Incorrect mutation A2007T WARNING: Incorrect mutation A2008T WARNING: Incorrect mutation R2009W WARNING: Incorrect mutation R2009Q WARNING: Incorrect mutation R2010I WARNING: Incorrect mutation V2011I WARNING: Incorrect mutation V2011F WARNING: Incorrect mutation V2011A WARNING: Incorrect mutation R2012W WARNING: Incorrect mutation R2012Q WARNING: Incorrect mutation P2013L WARNING: Incorrect mutation V2014I WARNING: Incorrect mutation V2014F WARNING: Incorrect mutation L2016F WARNING: Incorrect mutation L2016R WARNING: Incorrect mutation M2017T WARNING: Incorrect mutation V2018M WARNING: Incorrect mutation P2019A WARNING: Incorrect mutation P2019H WARNING: Incorrect mutation S2020N WARNING: Incorrect mutation A2022P WARNING: Incorrect mutation A2022S WARNING: Incorrect mutation G2023E WARNING: Incorrect mutation P2025L WARNING: Incorrect mutation G2026R WARNING: Incorrect mutation Q2028H WARNING: Incorrect mutation Q2028H WARNING: Incorrect mutation F2029L WARNING: Incorrect mutation G2031S WARNING: Incorrect mutation S2032T WARNING: Incorrect mutation S2032R WARNING: Incorrect mutation S2034G WARNING: Incorrect mutation S2034C WARNING: Incorrect mutation S2034R WARNING: Incorrect mutation S2035G WARNING: Incorrect mutation S2035N WARNING: Incorrect mutation V2037L WARNING: Incorrect mutation V2037G WARNING: Incorrect mutation L2041S WARNING: Incorrect mutation L2041F WARNING: Incorrect mutation S2043P WARNING: Incorrect mutation L2046P WARNING: Incorrect mutation G2047E WARNING: Incorrect mutation Q2048L WARNING: Incorrect mutation A2050V WARNING: Incorrect mutation Q2051K WARNING: Incorrect mutation Q2051E WARNING: Incorrect mutation D2052N WARNING: Incorrect mutation K2054E WARNING: Incorrect mutation K2054T WARNING: Incorrect mutation K2054R WARNING: Incorrect mutation I2056M WARNING: Incorrect mutation E2057K WARNING: Incorrect mutation E2057Q WARNING: Incorrect mutation T2060P WARNING: Incorrect mutation T2060S WARNING: Incorrect mutation Q2061K WARNING: Incorrect mutation Q2061L WARNING: Incorrect mutation E2062V WARNING: Incorrect mutation E2062D WARNING: Incorrect mutation L2063P WARNING: Incorrect mutation A2064V WARNING: Incorrect mutation D2065N WARNING: Incorrect mutation D2065Y WARNING: Incorrect mutation A2066V WARNING: Incorrect mutation C2067Y WARNING: Incorrect mutation D2068A WARNING: Incorrect mutation D2068E WARNING: Incorrect mutation T2070I WARNING: Incorrect mutation I2071T WARNING: Incorrect mutation E2073K WARNING: Incorrect mutation M2074T WARNING: Incorrect mutation E2075A WARNING: Incorrect mutation S2076R WARNING: Incorrect mutation A2077T WARNING: Incorrect mutation D2079N WARNING: Incorrect mutation N2080S WARNING: Incorrect mutation I2081V WARNING: Incorrect mutation A2086T WARNING: Incorrect mutation A2086S WARNING: Incorrect mutation P2087L WARNING: Incorrect mutation Q2088E WARNING: Incorrect mutation P2090A Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method S1915F Neutral 3 0.331 PhD-SNP: F[S]=53% F[F]=17% Nali=69 S1915F Neutral 9 0.063 PANTHER: F[S]=7% F[F]=9% S1915F Disease 3 0.668 SNPs&GO Q1916R Neutral 2 0.403 PhD-SNP: F[Q]=21% F[R]=3% Nali=69 Q1916R Neutral 9 0.068 PANTHER: F[Q]=7% F[R]=9% Q1916R Disease 4 0.701 SNPs&GO R1950K Neutral 5 0.251 PhD-SNP: F[R]=54% F[K]=11% Nali=69 R1950K Neutral 7 0.137 PANTHER: F[R]=28% F[K]=8% R1950K Disease 6 0.785 SNPs&GO P2053L Neutral 4 0.317 PhD-SNP: F[P]=85% F[L]=4% Nali=81 P2053L Disease 5 0.739 PANTHER: F[P]=77% F[L]=1% P2053L Disease 9 0.946 SNPs&GO P2053S Neutral 2 0.410 PhD-SNP: F[P]=85% F[S]=0% Nali=81 P2053S Disease 2 0.624 PANTHER: F[P]=77% F[S]=2% P2053S Disease 9 0.944 SNPs&GO G2084E Neutral 3 0.327 PhD-SNP: F[G]=55% F[E]=5% Nali=43 G2084E Neutral 8 0.122 PANTHER: F[G]=10% F[E]=3% G2084E Disease 7 0.827 SNPs&GO G2084R Neutral 3 0.362 PhD-SNP: F[G]=55% F[R]=0% Nali=43 G2084R Neutral 7 0.156 PANTHER: F[G]=10% F[R]=2% G2084R Disease 6 0.804 SNPs&GO G2085D Disease 0 0.504 PhD-SNP: F[G]=53% F[D]=0% Nali=50 G2085D Neutral 8 0.086 PANTHER: F[G]=8% F[D]=5% G2085D Disease 6 0.819 SNPs&GO G2085S Neutral 7 0.163 PhD-SNP: F[G]=53% F[S]=12% Nali=50 G2085S Neutral 8 0.108 PANTHER: F[G]=8% F[S]=20% G2085S Neutral 1 0.453 SNPs&GO S2089R Neutral 6 0.183 PhD-SNP: F[S]=34% F[R]=0% Nali=86 S2089R Neutral 2 0.402 PANTHER: F[S]=37% F[R]=2% S2089R Disease 7 0.858 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. ** ** ** **********************************************************************************************