Sequence based mutation analysis of GBA
Contents
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. It was not easy to find missense mutations only listed in dbSNP, as most of them were listed in HGMD, too.
| Nr. | SNP ID/Accession Number | Database | Position | Amino Acid Change | Codon Change | Remarks |
| 1 | CM081634 | HGMD | 49 | Gly - Ser | cGGC-AGC | |
| 2 | rs74953658, CM050263 | dbSNP, HGMD | 63 | Asp-Asn | tGAC-AAC | |
| 3 | rs1141820 | dbSNP | 99 | His - Arg | CAC - CGC | suspected, status not validated |
| 4 | CM880035 | HGMD | 159 | Arg - Gln | CGG-CAG | Synonymos Mutation at this position listed in dbSNP |
| 5 | rs80205046, CM041347 | dbSNP, HGMD | 221 | Pro - Leu | CCC - CTC | |
| 6 | rs74731340, CM970620 | dbSNP, HGMD | 310 | Ser - Asn | AGT - AAT | |
| 7 | CM993703 | HGMD | 350 | His - Arg | CAT - CGT | |
| 8 | CM960698 | HGMD | 426 | Pro - Leu | CCC-CTC | |
| 9 | rs80020805, CM052245 | dbSNP, HGMD | 455 | Met - Val | cATG-GTG | |
| 10 | rs113825752 | dbSNP | 509 | Leu - Pro | CTT - CCT |
[Note that the positions of the SNPs listed in HGMD in this table are different from the corresponding codon numbers, indicated in Task 5, as this position is relative to the sequence of GBA including the signal peptide (+ 39 residues).]
Physicochemical Properties and Changes
Mutation Analysis
SNAP
SIFT
Usage
- Webserver: http://sift.jcvi.org/www/SIFT_seq_submit2.html
- Input: sequence in fasta format, substitutions of interest (Example for mutation 1:
G49S)
Results
At the moment the connection to the server gets aborted all the time. Results will be posted soon.
Polyphen2
Usage
- Webserver: http://genetics.bwh.harvard.edu/pph2/
- Input: sequence in fasta format, position and substitution of mutation
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.
| 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 | probably damaging | 1.000 | 0.00 | 1.00 |
| 8 | benign | 0.001 | 0.99 | 0.15 |
| 9 | probably damaging | 0.999 | 0.14 | 0.99 |
| 10 | probably damaging | 0.978 | 0.75 | 0.96 |
