Difference between revisions of "Rs121907968"

From Bioinformatikpedia
(Created page with "=== Pysicochemical Properities === {| border="1" style="text-align:center; border-spacing:0;" |Trp |Arg |consequences |- |aromatic, polar, hydrophobic, neutral |positive charged…")
 
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=== General Information ===
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{| border="1" style="text-align:center; border-spacing:0;"
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|SNP-id
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|rs121907968
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|-
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|Codon
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|485
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|-
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|Mutation Codon
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|Trp -> Arg
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|-
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|Mutation Triplet
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|gTGG -> CGG
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|-
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|}
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----
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=== Pysicochemical Properities ===
 
=== Pysicochemical Properities ===
   
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|2 (Tyr)
 
|2 (Tyr)
 
| -4 (Asn, Asp, Pro)
 
| -4 (Asn, Asp, Pro)
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|-
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|}
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----
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=== PSSM analysis ===
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{| border="1" style="text-align:center; border-spacing:0;"
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|
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|self-information
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|expected self-information
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|-
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|Trp
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|13
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|99
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|-
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|Arg
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| -6
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|0
 
|-
 
|-
 
|}
 
|}

Revision as of 20:17, 23 June 2011

General Information

SNP-id rs121907968
Codon 485
Mutation Codon Trp -> Arg
Mutation Triplet gTGG -> CGG

Pysicochemical Properities

Trp Arg consequences
aromatic, polar, hydrophobic, neutral positive charged, polar, hydrophilic Trp is very big, because of two aromatic rings in its structure. Furthermore, it is hydrophobic, whereas, Arg is a hydrophilic amino acid. Therefore, the changes in the 3D structure might be extreme and delete the function of the protein.

Visualisation of the Mutation

picture original aa picture mutated aa combined picture
Amino acid Tryptophan
Amino acid Arginine
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 2 (Arg) 0 (all, except Arg, Phe, Ser, Tyr) 2 2 (Arg) 0 (all, except Arg, His, Leu, Phe, Ser, Tyr) -3 2 (Tyr) -4 (Asn, Asp, Pro)

PSSM analysis

self-information expected self-information
Trp 13 99
Arg -6 0

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis

JPred:
...HHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCC...
PsiPred:
...HHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC...

Comparison with the real structure:

Mutation at position 485
Mutation at position 485 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
R Non-neutral 7 96%

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
485 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
yvtsrqpnmlkihgfedca485W0.97W




PolyPhen2 Prediction

HumDiv prediction
HumVar prediction