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Revision as of 20:58, 25 June 2011 by Uskat (talk | contribs) (Visualisation of the Mutation)

General Information

SNP-id rs1054374
Codon 293
Mutation Codon Ser -> Ile
Mutation Triplet AGT -> ATT

Pysicochemical Properities

First of all, we explored the amino acid properties and compared them for the original and the mutated amino acid. Therefore we created the possible effect that the mutation could have on the protein.

Ser Ile consequences
polar, tiny, hydrophilic, neutral aliphatic, hydrophobic, neutra Ile is much bigger than Ser and also is branched, because it is an aliphatic amino acid. Therefore the structure of both amino acids is really different and Ile is to big for the position where Ser was. Therefore, there has to be a big change in the 3D structure of the protein and the protein probably will loose its function.

Visualisation of the Mutation

In the next step, we created the visualization of the muation with PyMol. Therefore we created a picture for the original amino acid, for the new mutated amino acid and finally for both together in one picture whereas the mutation is white colored. The following pictures display that the mutated amino acid Serine looks different to Isoleucine. Serine is very small whereas Isoleucine is bigger and has two spreadin chains. The first part of the rest agrees in both amino acids. In this case the difference is not so heavy, but can also cause some structural changes which can have affects on the protein function.

picture original aa picture mutated aa combined picture
Amino acid Serine
Amino acid Isoleucine
Picture which visualize the mutation

Subsitution Matrices Values

PAM 1 Pam 250 BLOSOUM 62
value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution
2 38 (Thr) 1 (Leu) 5 9 (Ala, Gly, Pro, Thr) 3 (Phe) -2 1 (Ala, Asn, Thr) -3 (Trp)

PSSM analysis

self-information expected self-information
Ser 1 10
Ile 1 7

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis


Comparison with the real structure:

Mutation at position 293
Mutation at position 293 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
I Neutral 2 69%

A detailed list of all possible substitutions can be found [here]

SIFT Prediction

SIFT Matrix:
Each entry contains the score at a particular position (row) for an amino acid substitution (column). Substitutions predicted to be intolerant are highlighted in red.

Sift legend.png
293 sift.png.png

SIFT Table
Threshold for intolerance is 0.05.
Amino acid color code: nonpolar, uncharged polar, basic, acidic.
Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.

Predict Not ToleratedPositionSeq RepPredict Tolerated

PolyPhen2 Prediction

HumDiv prediction
HumVar prediction