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PMUT: a web-based tool for the annotation of pathological mutations on proteins.
To give priority to the identification of deleterious mutations (missense, nonsense and splice variants), a series of filtering strategies, including HapMap 28, SNP databases and multiple algorithms (PolyPhen, SIFT, PANTHER and PMut) were adopted.
We used SIFT , PolyPhen2 , PMUT , SNP&GO , PhD-SNP , and MutPred  to examine the disease-associated nsSNP in the PMP22 protein coding region.
PMUT is a neural network-based program that is trained on large database of neutral and pathological mutations.
Prediction of Deleterious nsSNPs Using SIFT, PolyPhen2, and PMUT Programs.
Total 11 nsSNPs are commonly predicted in SIFT, PolyPhen 2.0, and PMUT. To these 11 mutations, we applied PhD-SNP which is based on support vector machine tool to further classify the predicted deleterious nsSNPs as disease associated.
A total of 26 SNPs got from dbSNP were selected for this study which were subjected to SIFT, PolyPhen2, PMUT, PhD-SNP, SNP&GO, and MutPred to examine and predict the CMT1A associated mutations with a relatively higher accuracy.
All 5 prediction tools used in this study predicted this variant as "damaging (pathological)," with the PMut tool predicting the most pathologic (i.e., maximum) effect at position 77.
We found good agreement in general among the results obtained with the SIFT, PolyPhen-2, SNPs3D, PMut, and SNPs&GO tools.
To predict the pathological character of p.E209 K, p.R401C, p.A933T, p.G2160S, p.R2336H, p.T4294M, and p.R4645Q SVs, I tested them with 3 different prediction programs, namely, PMut (http://mmb.pcb.ub.es/PMut/) , SIFT (http://sift.jcvi.org/) , and PolyPhen-2 (http://genetics .bwh.harvard.edu/pph2/) .
Sequence PMut SIFT Polyphen-2 variant p.E209K 0.6598# 0.29 Possibly damaging p.R401C 0.8400# 0.04# Probably damaging p.A933T 0.5969# 0.01# Probably damaging p.G2160S 0.2159 0.49 Possibly damaging p.R2336H 0.8377# 0.00# Probably damaging p.T4294M 0.8994# 0.11 Benign p.R4645Q 0.8261# 0.00# Benign Scores predicting pathological effect are in bold: PMut, > 0.5; SIFT [less than or equal to] 0.05.
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