Rs1800430

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Revision as of 20:24, 25 June 2011 by Uskat (talk | contribs) (Pysicochemical Properities)

General Information

SNP-id rs1800430
Codon 399
Mutation Codon Asn -> Asp
Mutation Triplet AAC -> GAC

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.

Asn Asp consequences
polar, small, hydrophilic, negatively charged polar, small, hydrophilic, negatively charged Both amino acids have the same properities and therefore we suggest that an exchange of these two amino acids do not destroy the protein structure and function

Visualisation of the Mutation

picture original aa picture mutated aa combined picture
Amino acid Asparagine
Amino acid Aspartic acid
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
36 36 (Asp) 0 (Cys, Met) 7 7 (Asp) 2 (Cys, Leu, Phe, Trp) 1 1 (Asp, His, Ser) -4 (Trp)

PSSM analysis

self-information expected self-information
Asn 0 5
Asp 0 4

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis

JPred:
...CCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCC...
PsiPred:
...CCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCC...

Comparison with the real structure:

Mutation at position 399
Mutation at position 399 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
D Neutral 1 60%

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
399 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
wyfcm399N0.72iHvlgPtRDEQASKN




PolyPhen2 Prediction

HumDiv prediction
HumVar prediction