Rs1800430

General Information

SNP-id	rs1800430
Codon	399
Mutation Codon	Asn -> Asp
Mutation Triplet	AAC -> GAC

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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.

Asn	Asp	consequences
polar, small, hydrophilic, negatively charged	polar, small, hydrophilic, negatively charged	Both amino acids have the same properities and therefore we suggest that an exchange of these two amino acids do not destroy the protein structure and 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 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. The following pictures display that the mutated amino acid Asparagine looks very different to Aspartic acid. They both agree in the first part of the rest but then go complety in opposite directions. Otherwise both rests fork at the end. All in all, the different directions prevail and will therefore probably cause big structural changes which will cause effects on the protein function.

picture original aa	picture mutated aa	combined picture
Amino acid Asparagine	Amino acid Aspartic acid	Picture which visualize the mutation

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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
36	36 (Asp)	0 (Cys, Met)	7	7 (Asp)	2 (Cys, Leu, Phe, Trp)	1	1 (Asp, His, Ser)	-4 (Trp)

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PSSM analysis

	self-information	expected self-information
Asn	0	5
Asp	0	4

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Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

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Secondary Structure Mutation Analysis

JPred:
...CCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCC...
PsiPred:
...CCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCC...

Comparison with the real structure:

Mutation at position 399

Mutation at position 399 - detailed view

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SNAP Prediction

Substitution	Prediction	Reliability Index	Expected Accuracy
D	Neutral	1	60%

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.

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 w y f c m 399N 0.72 i H v l g P t R D E Q A S K N

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PolyPhen2 Prediction

HumDiv prediction

HumVar prediction