Rs4777505

General Information

SNP-ID	Rs4777505
Codon Number	29
Mutation Codon	Asn -> Ser
Mutation Triplet	AAC -> AGC

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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	Ser	consequences
polar, small, hydrophilic, negatively charged	polar, tiny, hydrophilic, neutral	Both amino acids are polar and hydrophilic. Ser is tiny, Asn therefore is a small amino acid. The biggest difference between these two amino acid is, that Asn is negatively charged and Ser is neutral. But this is not that big difference and therefore we suggest, that this mutation do not delete the structure and function of the protein.

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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 has a much smaller chain than Serine. Contrary Serine is longer and comes to a fork at the end of its rest. Furthermore, it is also orientated in a completly different direction. This shows that the amino acids have huge structural differences which will probably cause drastical effects on the protein structure and function.

picture original aa	picture mutated aa	combined picture
Amino acid Asparagine	Amino acid Serine	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
20	36 (Asp)	0 (Cys, Met)	5	7 (Asp)	2 (Cys, Leu, Phe, Trp)	1	1 (Asp, His, Ser)	-4 (Trp)

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PSSM analysis

	self-information	expexted self-information
Asn	1	5
Ser	3	24

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Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

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Secondary Structure Mutation Analysis

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

Comparison with the real structure:

Mutation at position 29

Mutation at position 29 - detailed view

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SNAP Prediction

Substitution	Prediction	Reliability Index	Expected Accuracy
S	Neutral	8	96%

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 29N 0.78 c f M H i Y p V g L R N d Q T A S K E

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PolyPhen2 Prediction

HumDiv prediction

HumVar prediction