Difference between revisions of "Rs121907979"

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(Polyphen2 Prediction)
 
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----
 
----
   
=== Pysicochemical Properities ===
+
=== Pysicochemical Properties ===
   
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.
+
First of all, we explored the amino acid properties and compared them for the original and the mutated amino acid. Therefore we concluded the possible effect that the mutation could have on the protein.
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 29: Line 29:
 
|aliphatic, hydrophobic, neutral
 
|aliphatic, hydrophobic, neutral
 
|positive charged, polar, hydrophilic
 
|positive charged, polar, hydrophilic
|Leucine is smaller and without a positive charge. Therefore, Arg is too big for the position of Leu, therefore, the change of Leu with Arg has to cause changes in the 3D structure of the protein. Furthermore, Leu is a hydrophobic amino acid, whereas Arg is hydrophilic. This is the complete contrary and therefore we suggest, that the protein will not function any longer.
+
|Leucine is smaller and without a positive charge. Therefore, Arg is too big for the position of Leu, which means that the exchange of Leu to Arg has to cause changes in the 3D structure of the protein. Furthermore, Leu is a hydrophobic amino acid, whereas Arg is hydrophilic. This is the complete contrary and therefore we suggest, that the protein will not function any longer.
 
|-
 
|-
 
|}
 
|}
   
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
=== Visualisation of the Mutation ===
+
=== Visualization 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.
+
In the next step, we created the visualization of the mutation with PyMol. Therefore we created a picture of the original amino acid (Figure 1), of the new mutated amino acid (Figure 2) and finally of both together in one picture whereas the mutation is white colored (Figure 3).
The following pictures display that the mutated amino acid Arginine has a longer chain than Leucine. Contrary Leucine comes to a fork at the end of its rest. This shows that the amino acids have some structural differences that are not drastical, but can be essential.
+
The following pictures display that the mutated amino acid Arginine has a longer chain than Leucine. Contrary Leucine comes to a fork at the end of its rest. This shows that the amino acids have some structural differences that are not drastic, but can be essential.
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
|picture original aa
+
|picture original amino acid
|picture mutated aa
+
|picture mutated amino acid
 
|combined picture
 
|combined picture
 
|-
 
|-
|[[Image:L39.png|thumb|150px|Amino acid Leucine]]
+
|[[Image:L39.png|thumb|150px|Figure 1: Amino acid Leucine]]
|[[Image:39R.png|thumb|150px|Amino acid Arginine]]
+
|[[Image:39R.png|thumb|150px|Figure 2: Amino acid Arginine]]
|[[Image:L39R.png|thumb|150px|Picture which visualize the mutation]]
+
|[[Image:L39R.png|thumb|150px|Figure 3: Picture which visualize the mutation]]
 
|-
 
|-
 
|}
 
|}
   
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
=== Subsitution Matrices Values ===
+
=== Substitution Matrices Values ===
   
 
Afterwards, we looked at the values of the substitution matrices PAM1, PAM250 and BLOSSUM62.
 
Afterwards, we looked at the values of the substitution matrices PAM1, PAM250 and BLOSSUM62.
Therefore we looked detailed at the three values: the value for accoding amino acid substitution, the most frequent value for the substitution of the examined amino acid and the rarest substitution.
+
Therefore we looked detailed at the three values: the value of the amino acid substitution, the most frequent value for the substitution of the examined amino acid and the rarest substitution value.
   
In this case, the substitution of Leucine to Arginine has very low values that are near the values for the rarest subsitution for PAM1 and PAM250. Furthermore, the value for the most frequent substitution differs also a lot from the value for this certain mutation for both PAMs. Contrary for BLOSUM62 the value for the amino acid subsitution Leucine to Arginine is average. This means the most frequent subsitution value is as far as the rarerest subsitution from the the underlying value.
+
In this case, the substitution of Leucine to Arginine has very low values that are near the values for the rarest substitution for PAM1 and PAM250. Furthermore, the value for the most frequent substitution differs also a lot from the value for this certain mutation for both PAMs. Contrary for BLOSUM62 the value for the amino acid substitution Leucine to Arginine is average. This means, the most frequent substitution value is as far away as the rarest substitution value.
The difference between the two PAMs and BLOSUM62 can be ascribed to the different preparations of these two kind of substitutions matrices. The PAM-matrices is an evolutionary model whereas BLOSUM is based on protein famalies. Therefore probably this mutation is evolutionary not that unlikely whereas within a protein family it is unusual.
+
The difference between the two PAMs and BLOSUM62 can be ascribed to the different preparations of these two kinds of substitutions matrices. The PAM-matrices are evolutionary models, whereas BLOSUM is based on protein families. Therefore, probably this mutation is evolutionary not that unlikely whereas within this protein family it is unusual.
  +
According to PAM1 and PAM250 a mutation at this position will almost certainly cause structural changes which can affect functional changes. The value from BLOSSUM62 is not really significant and therefore we are not able to determine effects on the protein.
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
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|colspan="3" | BLOSOUM 62
 
|colspan="3" | BLOSOUM 62
 
|-
 
|-
|value aa
+
|value amino acid
 
|most frequent substitution
 
|most frequent substitution
 
|rarest substitution
 
|rarest substitution
|value aa
+
|value amino acid
 
|most frequent substitution
 
|most frequent substitution
 
|rarest substitution
 
|rarest substitution
|value aa
+
|value amino acid
 
|most frequent substitution
 
|most frequent substitution
 
|rarest substitution
 
|rarest substitution
Line 88: Line 93:
 
|}
 
|}
   
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
=== PSSM analysis ===
+
=== PSSM Analysis ===
  +
  +
Besides, we looked additional at the position specific scoring matrix (PSSM) for our sequence. In contrast to PAM and BLOSOUM, the PSSM contains a specific substitution rate for each position in the sequence. Therefore, the PSSM is more position specific than PAM or BLOSOUM. We extracted the substitution value for the underlying mutation, the value for the most frequent substitution and the rarest substitution.
  +
  +
In this case the substitution rate for Leucine to Argenine at this position is very low and near the value for the rarest substitution. This means this substitution at this position is likely very uncommon which indicates that this substitution has bad effects as a consequence. Therefore, we concluded that this mutation will probably cause protein structure changes as well as functional changes.
  +
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
  +
|colspan="3" | PSSM
|
 
|self-information
 
|expected self-information
 
 
|-
 
|-
  +
|value amino acid
|Leu
 
  +
|most frequent substitution
|4
 
  +
|rarest substitution
|39
 
 
|-
 
|-
|Arg
 
 
| -4
 
| -4
|1
+
| 3
  +
| -6
 
|-
 
|-
 
|}
 
|}
   
  +
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== Conservation Analysis with Multiple Alignments ===
 
=== Conservation Analysis with Multiple Alignments ===
   
As a next step we created a multiple alignment which contains the HEXA sequence and 9 other mammalian homologous sequences from uniprot. Afterwards we looked at the position of the different mutations and looked at the conservation level on this position.
+
As a next step we created a multiple alignment which contains the HEXA sequence and 9 other mammalian homologous sequences from [[http://www.uniprot.org UniProt]]. Afterwards, we looked at the position of the different mutations and the conservation level at this position.
The regarded mutation is presented by the second colored column. Here we can see, that the most other mammalians have on this Position a Leucine. Only three mammalians differ and have on this position an Isoleucine. Therefore, the mutation on this position has probably a structural and functional change as a result.
+
The regarded mutation is presented by the second colored column in Figure 4. Here we can see, that the most other mammalians have a Leucine at the position. Only three mammalians differ and have an Isoleucine at this position, which is a very similar to Leucine. Therefore, the mutation at this position has probably a structural and functional change as a result.
  +
   
  +
[[Image:mut_1_2.png|thumb|center|600px|Figure 4: Mutation in the multiple alignment]]
   
[[Image:mut_1_2.png|thumb|center|600px|Mutation in the multiple alignment]]
 
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== Secondary Structure Mutation Analysis ===
 
=== Secondary Structure Mutation Analysis ===
   
As a next step we compared the different results of the secondary structure prediction tools JPred and PsiPred. Afterwards we can examine in which secondary structure element and at which therein the mutation takes place. This can give an overview of how drastical the mutation can be.
+
As a next step we compared the different results of the secondary structure prediction tools JPred and PsiPred. Afterwards we can examine in which secondary structure element and at which therein the mutation takes place. This can give an overview of how drastic the mutation can be.
In this case both tools agree and predict at the position of the mutation the end of a sheet. This means that there is almost certainly the end of the beta sheet. This has a result, that the mutation at this position would not destroy or split the whole beta-sheet. It will probably only change the end of the sheet, but it can also cause a change of the the following secondary structure. This can also have functional loose as a consequence, but we think that this is unlikely here.
+
In this case both tools agree and predict the mutation at the end of a sheet. This means that there is almost certainly the end of the beta sheet. This has a result, that the mutation at this position would not destroy or split the whole beta-sheet. It will probably only change the end of the sheet, but it can also cause a change of the following secondary structure. This can also have functional changes as a consequence, but we think that this is unlikely here.
   
 
JPred:
 
JPred:
Line 132: Line 147:
 
''' Comparison with the real Structure: '''
 
''' Comparison with the real Structure: '''
   
Afterwards we also visualize the position of the muation (red) in the real 3D-structure of PDB and compare it with the predicted secondary structure. The visualisation can therefore like above the predicted secondary structure display if the mutation is in a secondary structure element or in some other regions.
+
Afterwards, we also visualized the position of the mutation (red) in the real 3D-structure of [[http://www.pdb.org PDB]] and compared it with the predicted secondary structure. The visualization can therefore, like above the predicted secondary structure, display if the mutation is in a secondary structure element or in some other regions (Figure 5 and Figure 6).
   
Here in this case the mutationposition agree with the position of the predicted secondary structure and is at the end of a beta sheet. Like explained above this means a mutation will probably not destroy the whole beta sheet what could hase as a result that the structural change is not as drastical. Otherwise it can cause a change of the further secondary structure element which can has a functional loose as a consequence.
+
Here in this case the mutation position agrees with the position of the predicted secondary structure and is at the end of a beta sheet. Like explained above this means a mutation will probably not destroy the whole beta sheet what could have as a result that the structural change is not that drastic.
   
 
{|
 
{|
| [[Image:39_mut.png|thumb|250px|Mutation at position 39]]
+
| [[Image:39_mut.png|thumb|250px|Figure 5: Mutation at position 39]]
| [[Image:39_mut_detail.png|thumb|250px|Mutation at position 39 - detailed view]]
+
| [[Image:39_mut_detail.png|thumb|250px|Figure 6: Mutation at position 39 - detailed view]]
 
|}
 
|}
   
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== SNAP Prediction ===
 
=== SNAP Prediction ===
   
Next, we looked at the result of the SNAP prediction. For this prediction we took the amino acid of the certain position and checked every possible amino acid mutation. Afterwards we extract the result for Arginine which is the real mutation in this case.
+
Next, we looked at the result of the SNAP prediction. For this prediction we took the amino acid of the certain position and checked every possible amino acid mutation. Afterwards we extracted the result for Arginine which is the real mutation in this case.
SNAP has a result that the exhange from Leucine to Arginine at this position is not neutral whith a comparitive high accuracy. This means that this certain mutation on this position cause very likely structural and functional changes of the protein.
+
SNAP showed as result that the exchange from Leucine to Arginine at this position is not neutral with a comparative high accuracy. This means that this certain mutation at this position cause very likely structural and functional changes of the protein.
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 163: Line 180:
 
A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs121907979_SNAP here]]
 
A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs121907979_SNAP here]]
   
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== SIFT Prediction ===
 
=== SIFT Prediction ===
  +
  +
Next, we used SIFT Prediction which displays if a mutation is neutral or not. Therefore, it first shows a row which contains a score for the particular mutation position to a certain amino acid. The amino acid which are not tolerated at this position are colored red. Besides, it also constructs a table which lists the amino acids that are predicted as tolerated and not-tolerated.
  +
  +
In this case, there are only three substitutions that are tolerated: Valine, Isoleucine and Leucine. The substitution to Arginine is not-tolerated at this position, which can be seen in Figure 8. This means that the mutation here is probably not neutral and will cause structural and functional changes of the protein.
   
 
SIFT Matrix:<br>
 
SIFT Matrix:<br>
Line 171: Line 194:
   
 
{|
 
{|
| [[Image:sift_legend.png|center]]
+
| [[Image:sift_legend.png|800px|thumb|center|Figure 7: legende]]
 
|-
 
|-
| [[Image:39_sift.png.png|center]]
+
| [[Image:39_sift.png.png|center|800px|thumb|Figure 8: SIFT Table<br>
  +
Threshold for intolerance is 0.05.<BR>Amino acid color code: nonpolar, <font color=green>uncharged polar</font>, <font color=red>basic</font>, <font color=blue>acidic</font>. <BR>Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.]]
 
|}
 
|}
 
SIFT Table<br>
 
Threshold for intolerance is 0.05.<BR>Amino acid color code: nonpolar, <font color=green>uncharged polar</font>, <font color=red>basic</font>, <font color=blue>acidic</font>. <BR>Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.
 
 
<br>
 
<br>
 
{| class="wikitable centered"
 
{| class="wikitable centered"
Line 185: Line 206:
 
<br><br>
 
<br><br>
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== Polyphen2 Prediction ===
 
=== Polyphen2 Prediction ===
   
Finally, we also regarded the PolyPhen2 prediction for this muation. This prediction visualizes have strongly demaging the mutation probably will be. Therefore it gives the result for two possible cases: HumDiv and HumVar. HumDiv.... Contrary, HumVar....
+
Finally, we also regarded the PolyPhen2 prediction for this mutation. This prediction visualizes how strongly damaging the mutation probably is. Therefore it gives the result for two possible cases: HumDiv and HumVar. HumDiv is the preferred model for evaluation rare alleles, dense mapping of regions identified by genome-wide association studies and analysis of neutral selection. In contrast, HumVar is the preferred model for diagnostic of Mendelian diseases which require distinguishing mutations with drastic effects from all remaining human variations including abundant mildly deleterious alleles. We decided to look at both possible models, which agreed in the most cases.
  +
 
  +
In this case both models predict that the mutation is probably damaging (Figure 9 and Figure 10). This means that the mutation is not neutral and will probably destroy the structure and the function of the protein.
  +
   
 
{|
 
{|
| [[Image:mut_2_humdiv.png|thumb|450px|HumDiv prediction]]
+
| [[Image:mut_2_humdiv.png|thumb|450px|Figure 9: HumDiv prediction]]
| [[Image:mut_2_humvar.png|thumb|450px|HumVar prediction]]
+
| [[Image:mut_2_humvar.png|thumb|450px|Figure 10: HumVar prediction]]
 
|}
 
|}
  +
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]

Latest revision as of 16:35, 31 August 2011

General Information

SNP-id rs121907979
Codon Number 39
Mutation Codon Leu -> Arg
Mutation Triplet CTT -> CGT

Pysicochemical Properties

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

Leu Arg consequences
aliphatic, hydrophobic, neutral positive charged, polar, hydrophilic Leucine is smaller and without a positive charge. Therefore, Arg is too big for the position of Leu, which means that the exchange of Leu to Arg has to cause changes in the 3D structure of the protein. Furthermore, Leu is a hydrophobic amino acid, whereas Arg is hydrophilic. This is the complete contrary and therefore we suggest, that the protein will not function any longer.


Back to [Sequence-based mutation analysis]


Visualization of the Mutation

In the next step, we created the visualization of the mutation with PyMol. Therefore we created a picture of the original amino acid (Figure 1), of the new mutated amino acid (Figure 2) and finally of both together in one picture whereas the mutation is white colored (Figure 3). The following pictures display that the mutated amino acid Arginine has a longer chain than Leucine. Contrary Leucine comes to a fork at the end of its rest. This shows that the amino acids have some structural differences that are not drastic, but can be essential.

picture original amino acid picture mutated amino acid combined picture
Figure 1: Amino acid Leucine
Figure 2: Amino acid Arginine
Figure 3: Picture which visualize the mutation


Back to [Sequence-based mutation analysis]


Substitution Matrices Values

Afterwards, we looked at the values of the substitution matrices PAM1, PAM250 and BLOSSUM62. Therefore we looked detailed at the three values: the value of the amino acid substitution, the most frequent value for the substitution of the examined amino acid and the rarest substitution value.

In this case, the substitution of Leucine to Arginine has very low values that are near the values for the rarest substitution for PAM1 and PAM250. Furthermore, the value for the most frequent substitution differs also a lot from the value for this certain mutation for both PAMs. Contrary for BLOSUM62 the value for the amino acid substitution Leucine to Arginine is average. This means, the most frequent substitution value is as far away as the rarest substitution value. The difference between the two PAMs and BLOSUM62 can be ascribed to the different preparations of these two kinds of substitutions matrices. The PAM-matrices are evolutionary models, whereas BLOSUM is based on protein families. Therefore, probably this mutation is evolutionary not that unlikely whereas within this protein family it is unusual. According to PAM1 and PAM250 a mutation at this position will almost certainly cause structural changes which can affect functional changes. The value from BLOSSUM62 is not really significant and therefore we are not able to determine effects on the protein.

PAM 1 Pam 250 BLOSOUM 62
value amino acid most frequent substitution rarest substitution value amino acid most frequent substitution rarest substitution value amino acid most frequent substitution rarest substitution
1 22 (Ile) 0 (Asp, Cys) 4 20 (Met) 2 (Cys) -2 0 (Phe) -4 (Asp, Gly)


Back to [Sequence-based mutation analysis]


PSSM Analysis

Besides, we looked additional at the position specific scoring matrix (PSSM) for our sequence. In contrast to PAM and BLOSOUM, the PSSM contains a specific substitution rate for each position in the sequence. Therefore, the PSSM is more position specific than PAM or BLOSOUM. We extracted the substitution value for the underlying mutation, the value for the most frequent substitution and the rarest substitution.

In this case the substitution rate for Leucine to Argenine at this position is very low and near the value for the rarest substitution. This means this substitution at this position is likely very uncommon which indicates that this substitution has bad effects as a consequence. Therefore, we concluded that this mutation will probably cause protein structure changes as well as functional changes.


PSSM
value amino acid most frequent substitution rarest substitution
-4 3 -6


Back to [Sequence-based mutation analysis]


Conservation Analysis with Multiple Alignments

As a next step we created a multiple alignment which contains the HEXA sequence and 9 other mammalian homologous sequences from [UniProt]. Afterwards, we looked at the position of the different mutations and the conservation level at this position. The regarded mutation is presented by the second colored column in Figure 4. Here we can see, that the most other mammalians have a Leucine at the position. Only three mammalians differ and have an Isoleucine at this position, which is a very similar to Leucine. Therefore, the mutation at this position has probably a structural and functional change as a result.


Figure 4: Mutation in the multiple alignment


Back to [Sequence-based mutation analysis]


Secondary Structure Mutation Analysis

As a next step we compared the different results of the secondary structure prediction tools JPred and PsiPred. Afterwards we can examine in which secondary structure element and at which therein the mutation takes place. This can give an overview of how drastic the mutation can be. In this case both tools agree and predict the mutation at the end of a sheet. This means that there is almost certainly the end of the beta sheet. This has a result, that the mutation at this position would not destroy or split the whole beta-sheet. It will probably only change the end of the sheet, but it can also cause a change of the following secondary structure. This can also have functional changes as a consequence, but we think that this is unlikely here.

JPred:
CCHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCEEEEECCCEEEEECCCCCCC...
PsiPred:
CHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCEEEEECCCEEEEECCCCCCC...


Comparison with the real Structure:

Afterwards, we also visualized the position of the mutation (red) in the real 3D-structure of [PDB] and compared it with the predicted secondary structure. The visualization can therefore, like above the predicted secondary structure, display if the mutation is in a secondary structure element or in some other regions (Figure 5 and Figure 6).

Here in this case the mutation position agrees with the position of the predicted secondary structure and is at the end of a beta sheet. Like explained above this means a mutation will probably not destroy the whole beta sheet what could have as a result that the structural change is not that drastic.

Figure 5: Mutation at position 39
Figure 6: Mutation at position 39 - detailed view


Back to [Sequence-based mutation analysis]


SNAP Prediction

Next, we looked at the result of the SNAP prediction. For this prediction we took the amino acid of the certain position and checked every possible amino acid mutation. Afterwards we extracted the result for Arginine which is the real mutation in this case. SNAP showed as result that the exchange from Leucine to Arginine at this position is not neutral with a comparative high accuracy. This means that this certain mutation at this position cause very likely structural and functional changes of the protein.

Substitution Prediction Reliability Index Expected Accuracy
R Non-neutral 5 87%

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


Back to [Sequence-based mutation analysis]


SIFT Prediction

Next, we used SIFT Prediction which displays if a mutation is neutral or not. Therefore, it first shows a row which contains a score for the particular mutation position to a certain amino acid. The amino acid which are not tolerated at this position are colored red. Besides, it also constructs a table which lists the amino acids that are predicted as tolerated and not-tolerated.

In this case, there are only three substitutions that are tolerated: Valine, Isoleucine and Leucine. The substitution to Arginine is not-tolerated at this position, which can be seen in Figure 8. This means that the mutation here is probably not neutral and will cause structural and functional changes of the protein.

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.

Figure 7: legende
Figure 8: 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
hdwqpnecrgskytafm39L0.79VIL



Back to [Sequence-based mutation analysis]


Polyphen2 Prediction

Finally, we also regarded the PolyPhen2 prediction for this mutation. This prediction visualizes how strongly damaging the mutation probably is. Therefore it gives the result for two possible cases: HumDiv and HumVar. HumDiv is the preferred model for evaluation rare alleles, dense mapping of regions identified by genome-wide association studies and analysis of neutral selection. In contrast, HumVar is the preferred model for diagnostic of Mendelian diseases which require distinguishing mutations with drastic effects from all remaining human variations including abundant mildly deleterious alleles. We decided to look at both possible models, which agreed in the most cases.

In this case both models predict that the mutation is probably damaging (Figure 9 and Figure 10). This means that the mutation is not neutral and will probably destroy the structure and the function of the protein.


Figure 9: HumDiv prediction
Figure 10: HumVar prediction


Back to [Sequence-based mutation analysis]