Difference between revisions of "Sequence based mutation analysis of GBA"

From Bioinformatikpedia
(→‎Subset of SNPs)
(→‎SNAP)
Line 65: Line 65:
   
 
=== SNAP ===
  
=== SNAP ===
  +
  +
''' Usage '''
  +
* command line: snapfun -i gbaseq.fasta -m mutations.txt -o snapfun_out.out
  +
<br/>
  +
{| border="1" style="text-align:center; border-spacing:0" align="center" cellpadding="3" cellspacing="3"
  +
!Mutation Nr.
  +
!Prediction
  +
!Reliability Index
  +
!Expected Accuracy
  +
|-
  +
|'''1''' (G49S)||Neutral||2||69%
  +
|-
  +
|'''2''' (D63N)||Non-neutral||5||87%
  +
|-
  +
|'''3''' (H99R)||Neutral||6||92%
  +
|-
  +
|'''4''' (R159Q)||Non-neutral||6||93%
  +
|-
  +
|'''5''' (P221L)||Non-neutral||5||87%
  +
|-
  +
|'''6''' (S310N)||Non-neutral||1||63%
  +
|-
  +
|'''7''' (N409S)||Non-neutral||0||58%
  +
|-
  +
|'''8''' (H350R)||Non-neutral||6||93%
  +
|-
  +
|'''9''' (M455V)||Non-neutral||3||78%
  +
|-
  +
|'''10''' (L509P)||Neutral||2||69%
  +
|}
   
 
=== SIFT ===
  
=== SIFT ===

Revision as of 10:40, 22 June 2011

TODO: Change Mutation 8 to mutation at 311 (His). as it is one resiude forming hydrogen bonds with the active site. Change overview, images and results of SIFT and Polyphen.

Subset of SNPs

The ten SNPs shown in the table below and highlighted in Figure 1 were chosen for the analysis in this task. It was tried to include SNPs all over the protein, in order to investigate the influence of mutations in several parts of the protein. The mutated residues forming hydrogenbonds with the active site of glucocerebrosidase are included, as these should result in either a mal- or nonfunctioning protein [TODO: Insert mutation at position 311 (His)]. It was not easy to find missense mutations only listed in dbSNP, as most of them were listed in HGMD, too.

Figure 1: Selected mutations highlighted on structure of 10GS. The different colors indicate, in which database the mutation is listed: dbSNP (blue), HGMD (red), both (green) CHANGE (Mut. 8)
Nr. SNP ID/Accession Number Database Position
including SP		 Position
 without SP		 Amino Acid Change Codon Change Remarks
1 CM081634 HGMD 49 10 Gly - Ser cGGC-AGC
2 rs74953658, CM050263 dbSNP, HGMD 63 24 Asp-Asn tGAC-AAC
3 rs1141820 dbSNP 99 60 His - Arg CAC - CGC suspected, status not validated
4 CM880035 HGMD 159 120 Arg - Gln CGG-CAG synonymos mutation at this position listed in dbSNP; forming hydrogen bond with active site
5 rs80205046, CM041347 dbSNP, HGMD 221 182 Pro - Leu CCC - CTC
6 rs74731340, CM970620 dbSNP, HGMD 310 271 Ser - Asn AGT - AAT
7 CM880036 HGMD 409 370 Asn - Ser AAC-AGC most common mutation found in gaucher disease type 1 patients
8 HGMD 350 311 His - Arg CAT-CGT
9 rs80020805, CM052245 dbSNP, HGMD 455 416 Met - Val cATG-GTG
10 rs113825752 dbSNP 509 470 Leu - Pro CTT - CCT



Physicochemical Properties and Changes

Figure 2: Comparison of the wildtype (red) and mutated (blue) amino acids mapped to the structure of 1OGS. CHANGE (Mut. 8)

Mutation 1

The wildtype amino acid, Glycine is nonpolar, whereas the mutated amino acid Serin is polar. This different polarity, could be an indication, that the mutation is damaging. Looking at the structure, one can see, that this residue (pos. 10 in mature protein) is situated in a loop at the exterior of the protein. Therefore a substitution should not affect the function of the protein that much.

Mutation 2

...

Mutation 3

Mutation 4

Mutation 5

Mutation 6

Mutation 7

Mutation 8

Mutation 9

Mutation 10

Mutation Analysis

SNAP

Usage

  • command line: snapfun -i gbaseq.fasta -m mutations.txt -o snapfun_out.out


Mutation Nr. Prediction Reliability Index Expected Accuracy
1 (G49S) Neutral 2 69%
2 (D63N) Non-neutral 5 87%
3 (H99R) Neutral 6 92%
4 (R159Q) Non-neutral 6 93%
5 (P221L) Non-neutral 5 87%
6 (S310N) Non-neutral 1 63%
7 (N409S) Non-neutral 0 58%
8 (H350R) Non-neutral 6 93%
9 (M455V) Non-neutral 3 78%
10 (L509P) Neutral 2 69%

SIFT

Usage

Results


Mutation Nr. Prediction Score Sequence Conservation
1 tolerated 0.51 3.05
2 tolerated 0.06 3.05
3 tolerated 0.62 3.04
4 affect protein function 0.03 3.01
5 affect protein function 0.00 3.01
6 tolerated 0.54 3.01
7 affect protein function 0.05 3.02
8
9 tolerated 0.12 3.01
10 affect protein function 0.01 3.09

Coming soon: Multiple alignment of sequence with its homologs + Conditional Probability Matrix


Polyphen2

Usage

Results

The results of PolyPhen-2 (HumDiv) are listed in the table below. Three mutations (Numbers 3, 6 and 8) have been predicted to be harmless. Interestingly, the most common mutation found in gaucher disease patients is only classified as possibly damaging.


Mutation Nr. Prediction Score Sensitivity Specificity
1 probably damaging 0.997 0.40 0.98
2 probably damaging 1.000 0.00 1.00
3 benign 0.000 1.00 0.00
4 probably damaging 1.000 0.00 1.00
5 probably damaging 1.000 0.00 1.00
6 benign 0.100 0.94 0.85
7 possibly damaging 0.573 0.88 0.91
8 probably damaging 1.0 0.00 1.00
9 probably damaging 0.999 0.14 0.99
10 probably damaging 0.978 0.75 0.96

Discussion

Retrieved from "https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Sequence_based_mutation_analysis_of_GBA&oldid=6555"