Rs121907967

General Information

SNP-id	rs121907967
Codon	329
Mutation Codon	Trp -> TER
Mutation Triplet	TGG -> TAG

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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.

Trp	TER	consequences
aromatic, polar, hydrophobic	TER	By this change, the protein is not complete, therefore it is not possible for the protein to fold and to function.

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Visualisation of the Mutation

In the next step, we created the visualization of the muation with PyMol. Therefore we created two pictures: one which displays the original amino acid and one that displays the consequence of the resulting termination. The grey and the red parts of 3D-structure are the original protein whereas the red part shows the remaining protein if there is an exchange of Tryptophan to a stop codon. Here we can see that the remaining red part has only the half size of the protein. Furthermore, the missing part can have an effect on the folding of the remaining part, which this one can fold in a complety other way. Therefore, this muation will have engraving effects on the protein. The protein will probably loose its whole function and is not usable anymore.

picture original aa	consequence for the whole protein
Amino acid Tryptophan	Visualization of the mutated protein

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Subsitution 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 for accoding amino acid substitution, the most frequent value for the substitution of the examined amino acid and the rarest substitution.

In this case, we get no informations because there is no entry for the substitution of Tryptophan to a stop codon. Therefore we can not say what the possible consequences for the protein are only by looking at the substitution matrices. However,a stop codon will if course always have a drastical effect on the protein and its function.

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
X	2 (Arg)	0 (all, except Arg, Phe, Ser, Tyr)	X	2 (Arg)	0 (all, except Arg, His, Leu, Phe, Ser, Tyr)	X	2 (Tyr)	-4 (Asn, Asp, Pro)

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PSSM analysis

	self-information	expected self-information
Trp	12	78

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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. The regarded mutation is presented by the colored column. Here we can see, that all other mammalians have on this Position the same amino acid. Therefore, the mutation on this position is highly conserved and in a normal case this would be a indication for structural and functional changes. In this special case it will cause anyway structural and functional changes, because it is a substitution with a stop codon and therefore only a part of the protein will be translated.

Mutation in the multiple alignment

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Secondary Structure Mutation Analysis

JPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECC...
PsiPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...

Comparison with the real structure:

Mutation at position 329

Mutation at position 329 - detailed view

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SNAP Prediction

No prediction available, because the protein ends here.

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

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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.

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PolyPhen2 Prediction

In this case the mutation is from Tryptophan to a stop codon. Therefore, we made no PolyPhen2 prediction, because it is clear that it will cause a damage of the 3D-structure of the protein. Furthermore, it will of course .....