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
|
|
|
|
 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 - 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 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 Tolerated | Position | Seq Rep | Predict Tolerated |
|---|
| | y | v | t | s | r | q | p | n | m | l | k | i | h | g | f | e | d | c | a | 485W | 0.97 | W | | | | | | | | | | | | | | | | | | | |
|---|
|
PolyPhen2 Prediction
