Difference between revisions of "Fabry:Mapping point mutations"
Rackersederj (talk | contribs) m (rearranging order of databases) |
Rackersederj (talk | contribs) m (→SNPedia) |
||
| Line 36: | Line 36: | ||
In SNPedia exists a site for the disease, that is caused by mutations in the gene we are examining, [http://www.snpedia.com/index.php/Fabry_disease Fabry Disease], but not for the gene itself (GLA). |
In SNPedia exists a site for the disease, that is caused by mutations in the gene we are examining, [http://www.snpedia.com/index.php/Fabry_disease Fabry Disease], but not for the gene itself (GLA). |
||
Thus we performed a query with the search term "Gene=GLA", which resulted in 40 hits (see [[Fabry:Mapping_point_mutations/SNPedia_data | SNPedia_data]]). Again, only one hit was in the signal peptide part of the sequence and none of the important residues is mutated (see <xr id="fig:SNPedia_SNPs"/>).<br> |
Thus we performed a query with the search term "Gene=GLA", which resulted in 40 hits (see [[Fabry:Mapping_point_mutations/SNPedia_data | SNPedia_data]]). Again, only one hit was in the signal peptide part of the sequence and none of the important residues is mutated (see <xr id="fig:SNPedia_SNPs"/>).<br> |
||
| − | The gap of no variation between position 66 and 112 can be observed as well and besides from that a rather even distribution without big peaks. |
+ | The gap of no variation between position 66 and 112 can be observed as well and besides from that a rather even distribution without big peaks. <br> |
| + | Without deeper look, it can be said, that the results from OMIM and SNPedia are very similar, comparing <xr id="fig:SNPedia_SNPs"/> and <xr id="fig:OMIM_SNPs"/> |
||
<br style="clear:both;"> |
<br style="clear:both;"> |
||
| − | |||
== SNPdbe == |
== SNPdbe == |
||
Revision as of 00:10, 10 June 2012
Fabry Disease » Mapping point mutations
The following analyses were performed on the basis of the α-Galactosidase A sequence. Please consult the journal for the commands used to generate the results.
HGMD
Mutation types:
- Missense/nonsense
- Splicing
- Regulatory
- Small deletions
- Small insertions
- Small indels
- Gross deletions
- Gross insertions
- Complex
- Repeats
dbSNP
At the time we checked dbSNP, it listed eight silent single point mutations.
OMIM
<figure id="fig:OMIM_SNPs">
</figure>
The OMIM database lists 62 (actually 63, since one entry contains 2 SNPs) allelic variants for the gene GLA. Of these, 6 are exon deletions, 10 are base pair deletions, 4 are located in non-coding regions, 1 was an exon duplication and 2 Insertions (see OMIM data-Allelic variants). The remaining 40 variants are specified as SNPs and are listed in OMIM data-SNPs.
Of course, all of the mentioned mutations are disease causing. In <xr id="fig:OMIM_SNPs"/> we show the distribution of SNPs along the sequence of the α-galactosidase A coding gene. There seems to be no real "hotspot" of SNPs, but a long strip of sequence without any point mutation (position 66-112). In the signal peptide only one mutation is listed, and in at the active site amino acids (170 and 231), as well as the binding site (203-207) there are none.
SNPedia
<figure id="fig:SNPedia_SNPs">
</figure>
In SNPedia exists a site for the disease, that is caused by mutations in the gene we are examining, Fabry Disease, but not for the gene itself (GLA).
Thus we performed a query with the search term "Gene=GLA", which resulted in 40 hits (see SNPedia_data). Again, only one hit was in the signal peptide part of the sequence and none of the important residues is mutated (see <xr id="fig:SNPedia_SNPs"/>).
The gap of no variation between position 66 and 112 can be observed as well and besides from that a rather even distribution without big peaks.
Without deeper look, it can be said, that the results from OMIM and SNPedia are very similar, comparing <xr id="fig:SNPedia_SNPs"/> and <xr id="fig:OMIM_SNPs"/>
SNPdbe
A search in the SNPdbe database revealed 57 mutations (see)
