Sequence-based mutation analysis HEXA

Mutations

SNP-id	codon number	mutation codon	mutation triplet
rs4777505	29	Asn -> Ser	AAC -> AGC
rs121907979	39	Leu -> Arg	CTT -> CGT
rs61731240	179	His -> Asp	CAT -> GAT
rs121907974	211	Phe -> Ser	TTC -> TCC
rs61747114	248	Leu -> Phe	CTT -> TTT
rs1054374	293	Ser -> Ile	AGT -> ATT
rs121907967	329	Trp -> TER	TGG -> TAG
rs1800430	399	Asn -> Asp	AAC -> GAC
rs121907982	436	Ile -> Val	ATA -> GTA
rs121907968	485	Trp -> Arg	gTGG -> CGG

Analysis of the mutations

We created for each mutation an extra page. The summary of the analysis can be seen in the Summary Section.

• [rs4777505: Asn -> Ser]

• [rs121907979: Leu -> Arg]

• [rs61731240: His -> Asp]

• [rs121907974: Phe -> Ser]

• [rs61747114: Leu -> Phe]

• [rs1054374: Ser -> Ile]

• [rs121907967: Trp -> TER]

• [rs1800430: Asn -> Asp]

• [rs121907982: Ile -> Val]

• [rs121907968: Trp -> Arg]

Summary page

Here we sum up all analysis we did for the mutations:

• pysicochemical properitites: we called a mutation neutral, if the properitites of the mutated amino acid are very similar to them of the orginal amino acid. Otherwise, it is called non-neutral.
• visuale analysis: a mutation is called neutral, if the structure of the changed amino acid is very similar to the structure of the original amino acid.
• PAM1, PAM2, BLOSUM62 and PSSM analysis: a mutation is called neutral, if the change score is near to the score of the most frequent exchanged amino acid.
• multiple alignment: a mutation is called non-neutral if the original amino acid is very conserved in the alignment. If there is a conservation rate less than 50%, we decided to call the mutation neutral.
• analysis with JPred, PsiPred: if the mutated amino acid has no secondary structure (coil) in the prediction of the secondary structure, we called the mutation neutral.
• analysis with the real structure: here we look, if the mutation takes place in a secondary structure element or not. Instead of DSSP, we used the real structure. Normally, the real structure is not available and therefore, this value can not be used in the prediction. Therefore, we do not use this value, since we decided if the mutation is neutral or not.
• SNAP, SIFT and PolyPhen2 prediction: These are the three mutation prediction methods we used in our analysis. Here a mutation is called neutral, if the program predicts this mutation as neutral.

method	mutations
	Asn -> Ser (rs4777505)	Leu -> Arg (rs121907979)	His -> Asp (rs61731240)	Phe -> Ser (rs121907974)	Leu -> Phe (rs61747114)	Ser -> Ile (rs1054374)	Trp -> TER (rs121907967)	Asn -> Asp (rs1800430)	Ile -> Val (rs121907982)	Trp -> Arg (rs121907968)
pysiochemical properitites	neutral	non-neutral	non-neutral	non-neutral	neutral	non-neutral	non-neutral	neutral	neutral	non-neutral
visuale analysis	neutral	non-neutral	non-neutral	non-neutral	non-neutral	neutral	non-neutral	non-neutral	neutral	non-neutral
PAM1	neutral	non-neutral	non-neutral	non-neutral	no statement	non-neutral	no information	neutral	neutral	neutral
PAM250	neutral	non-neutral	no statement	non-neutral	no statement	no statement	no information	neutral	neutral	neutral
BLOSUM62	neutral	no statement	no statement	non-neutral	neutral	non-neutral	no information	neutral	neutral	non-neutral
PSSM analysis	neutral	non-neutral	non-neutral	non-neutral	non-neutral	neutral	no information	neutral	neutral	non-neutral
multiple alignment	neutral	neutral	non-neutral	non-neutral	non-neutral	neutral	neutral	neutral	neutral	non-neutral
analysis with Jpred	non-neutral	non-neutral	neutral	neutral	neutral	neutral	neutral	neutral	neutral	neutral
analysis with PsiPred	non-neutral	non-neutral	neutral	neutral	neutral	neutral	neutral	non-neutral	neutral	neutral
analysis with real structure	non-neutral	no statement	neutral	neutral	non-neutral	neutral	non-neutral	no statement	non-neutral	non-neutral
SNAP Prediction	neutral	non-neutral	non-neutral	non-neutral	neutral	neutral	no information	neutral	neutral	non-neutral
SIFT Prediction	neutral	non-neutral	non-neutral	non-neutral	neutral	neutral	no information	neutral	neutral	non-neutral
PolyPhen2 Prediction	neutral	non-neutral	non-neutral	non-neutral	neutral	neutral	no information	neutral	neutral	non-neutral

In the table above you can see the summary of all of the analysis we did to got the possibility to make a statement about the mutation. Here we want to sum it up for each mutation and write it in the end down in an extra table. In the end, we wanted to compare our summing up with the reality and therefore we compared from which database the mutation was extracted.

• Asn -> Ser

The first mutation we looked at, is a substitution from Asn to Ser. As you can see in our summary table, there was always a prediction that this mutation is silent, except of the analysis of the secondary structure. Therefore, this means that the mutation is in a secondary structure element. But these two amino acids seems to be very similar and therefore, it seems not to be that bad, if the mutation is in an secondary structure element, because the structure will not change dramatically. Therefore, in sum we predict this mutation as neutral. Also each of the prediction tools predicted this mutation as neutral. So therefore in sum, we think this is a neutral mutation.

• Leu -> Arg

It is a little bit more complicate to predict the effect of this mutation as before, because there are conflicting predictions of the single categories. In sum, most of the categories counted this mutation as non-neutral. By BLOSUM62 it was not possible to make a statement, because the score of this mutation was between the rarest and highest score and therefore, it was not possible to assign the mutation to one of the two categories. The multiple alignment was not very conserved at this position, and therefore with this analysis the mutation seems to be neutral. But on the one side, we do not know the correct alignment and therefore, perhaps we used a wrong alignment. On the other side, we did not regard which amino acid mutations are present in the alignment. Perhaps there are only substitutions between pysiochemical identical amino acids. In the case of the comparison with the real strucuture it was not possible to make a clear statement, because this amino acid is located at the boarder between a secondary structure element and a coiled region and therefore, we do not know if a mutation at the last position of the secondary structure really change the structure dramatically. But this is not that important for our prediction, because we do not attend this. So therefore, in sum we predicted this mutation as non-neutral, which is the same result as the methods gave us.

• His -> Asp

In this case we have to differ between the secondary structure analysis and the other analysis. So the other analysis showed, that this mutation might not be neutral. In the analysis with PAM250 and BLOSUM62 it was not possible to make a statement, so therefore, the amin acid mutated some times, but without a trend the a very common or very rare mutation. The secondary structure analysis predicted a neutral mutation, which means this mutation does not take place at a secondary structure element. But our analysis method for the secondary structure is very simple. We do not regard any contacts with other amino acids in the structure (which would be there). So it is not absolutly impossible, that the mutation of an amino acid in a loop region do have any effects on structure and function of the protein, especially, if the physicochemical properitites differ. Furthermore, we know that there exist disordered regions, which are essential for the function of a protein, which do not have a defined secondary structure and therefore, will be predicted as coiled regions. So this is a difficult case, but because of the different physicochemical properitites and the very different structure of the two amino acids and also the results of the multiple alignment, we decided to predict this mutation as non-neutral.

• Phe -> Ser

In this case we have the same situation as before. All our analysis gave us the hint, that these mutation is non-neutral, except the secondary structure analysis. As we mentioned before, it is also possible that there is a big impact on the structure of the protein, even if the mutation takes place in a coil-region. Especially if we keep in mind, that there is the possibility of a disordered region. So we think, the secondary structure is not that a straight criterion for function of the protein than the mutation rate or the physicochemical properities. Therefore, we decided to predict this mutation as non-neutral, which is consisently with the results of the three prediction methods.

• Leu -> Phe

This mutation is a very interessting case. Here we have a lot of methods, which gave us other hints. So first of all, both amino acids have the identical physicochemical propertites, which is always a strong hint that the mutation does not destroy the function of the protein. Otherwise, if we have a look at the structure of the amino acids, there is a big difference between Leu and Phe and therefore, this is a hint for changing the structure of the amino acid. It was no possible to make a statement about the effect of this mutation by regarding the PAM matrices, but in the BLOSUM matrix this mutation is noted as neutral. The PSSM analysis and the multiple alignment analysis, however, suggest that the mutation is non-neutral. Very interesstingly is the result of the secondary structure analysis. So if we have a look at the results of PsiPred and JPred, we have to suggest, that this mutation is neutral, because it takes place in a coiled region. But both methods predicted the secondary structure wrong, because if we have a look to the real structure, we can see, that the mutation takes place in a secondary structure element. So it is important to keep in mind, that we work on predictions, which could be wrong. But as we said before, the real structure is not regarded in our manually prediction and therefore, we decided that this mutation is neutral for the following reasons. First of all the physicochemical propertites are equal and this is a very important point. Next, the structure of the residues is not similar, but the mutation takes place at a coiled region, and therefore a wrong structure would not be that dramatically as in a secondary structure element. Furthermore, BLOSUM62 told us, that this substitution is neutral. So in sum, we have more neutral predictions that non-neutral predictions. Of course, the multiple alignment is a strong hint, that the mutation is non-neutral, but as we mentioned above, we also do not know if the alignment is right and we have two secondary structure methods, which gave us the same result. Therefore we have to trust the predictions. Therefore, we predicted the same effect as the methods did.

• Ser -> Ile

Interesstingly in this case the physicochemical properities are not identical and also the substitution matrices scored this substitutions as non-neutral, but the rest of our predictions shows that the effect of this mutation is neutral. So there is a similar structure of the residues, the alignment is not conserved and also the pssm of the PsiBlast run do not show any conservation of this residue. Furthermore, the mutation takes place in a coiled region. Although the physicochemical properitites and the substitution matrices are very important hints for the effect of the mutation we decided to predict this mutation as silent. First of all, there are 5 predictions which predict this mutations as silent and only 3 predictions which see a causing effect of this mutation. An argument for a silent mutation is, that the pysicochemical propertites perhaps are not that important for a residue which is located in a coiled region, especially if this residue does not have many connections to other residues. In general the substitution matrix showed, that this mutation is not neutral, but the PSSM predicts it as neutral. The PSSM also regards the position of the substitution in the sequence. So therefore, it is possible, that this mutation is normally no silent, but in this special case we have a neutral mutation. This prediction is equal to the predictions of the methods.

• Trp -> Ter

In this case it is not neceassry to have a look at the different predictions of the single analysis. This mutation is located at the middle of the protein and leads to a short protein, which surley could not fold in the right way and therefore could not function anymore. Therefore, this mutation is non-neutral. Sadly, it was not possible to predict the effect of a mutation which leads to shortened protein and therefore, it is not possible to compare the results of the methods with our prediction results. This is bad, because it is also possible that a mutation which leads to a shortened protein is neutral, if the mutation takes place at the very end of the protein. But in this case the mutation takes place at the middle of the protein and therefore, it is predicted as neutral from us.

• Asn -> Asp

This mutation is a clear thing, because only the visuale analysis do not predict this mutation as neutral. Furthermore, the PsiPred method does also not predict this neutral. This is not very surprisingly, because if we have a look at the real structure of the protein we can see, this amino acid is directly located at the border between a secondary structure element and a coiled region. But the rest of our predictions, especially the physicochemical propertites and the multiple alignment as well as the substitution matrices showed clearly, that this prediction is neutral. The method we used here for the prediction also gave us the same result.

• Ile -> Val

This mutation is also very easy to classify, because every of our categories predicted the mutation as neutral. Only the comparison with the real structure gave us the hint, that this prediction perhaps is not neutral, because it takes place at a secondary structure element. But firstly, we do not regard the comparison with the real structure and the secondary structure prediction methods failed and secondly, the structure of the residues and the physicochemical properitites are very similar and therefore, it should not have big effects on the structure of the protein, even if the mutation is loacted inside a secondary structure element. Therefore, we predicted this mutation as neutral, which was also the result of the three prediction methods.

• Trp -> Arg

In our last analysed mutation only the secondary structure methods predict this mutation as neutral and the substitution matrices. All other categories scored this mutation as non-neutral. As we can see, the secondary structure prediction failed, because this mutation is located at a secondary structure element. We predicted this mutation as non-neutral. First of all, we have 5 predictions for non-neutral and 4 for neutral. But only 1 categories difference is in general not enough to give a prediction. But the very important categories (physicochemical properities, alignment, pssm) predict this mutation as non-neutral and we scored these categorires as more important than for example secondary structure. Therefore, we decided to predict this mutation as non-neutral, which is consitent with the results of the three prediction methods.