Difference between revisions of "Fabry:Mapping point mutations"
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At the time we checked [http://www.ncbi.nlm.nih.gov/snp/?term=%22synonymous-codon%22%5BFunction_Class%5D+AND+GLA%5BGENE%5D+AND+%22human%22%5BORGN%5D+AND+%22snp%22%5BSNP_CLASS%5D+&SITE=NcbiHome&submit=Go dbSNP], it listed eight silent single point mutations. |
At the time we checked [http://www.ncbi.nlm.nih.gov/snp/?term=%22synonymous-codon%22%5BFunction_Class%5D+AND+GLA%5BGENE%5D+AND+%22human%22%5BORGN%5D+AND+%22snp%22%5BSNP_CLASS%5D+&SITE=NcbiHome&submit=Go dbSNP], it listed eight silent single point mutations. |
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| − | == SNPdbe == |
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| + | == OMIM == |
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| − | A search in the SNPdbe database revealed 57 mutations ([http://www.rostlab.org/services/snpdbe/dosearch.php?id=name&val=NP_000160&organism2=human&organism1= see]) |
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| + | <figure id="fig:OMIM_SNPs">[[File:Fabry_SNPdistr_OMIM.png|400px|thumb|right|<caption>Distribution and number of SNPs along the sequence of GLA</caption>]]</figure> |
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| + | The OMIM database lists 62 (actually 63, since one entry contains 2 SNPs) allelic variants for the gene [http://omim.org/entry/300644 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 [[Fabry:Mapping_point_mutations/OMIM_data#Allelic_variants | OMIM data-Allelic variants]]). The remaining 40 variants are specified as SNPs and are listed in [[Fabry:Mapping_point_mutations/OMIM_data#SNPs | OMIM data-SNPs]].<br> |
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| + | 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. |
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== SNPedia == |
== SNPedia == |
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| − | == OMIM == |
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| + | == SNPdbe == |
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| − | <figure id="fig:OMIM_SNPs">[[File:Fabry_SNPdistr_OMIM.png|400px|thumb|right|<caption>Distribution and number of SNPs along the sequence of GLA</caption>]]</figure> |
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| − | The OMIM database lists 62 (actually 63, since one entry contains 2 SNPs) allelic variants for the gene [http://omim.org/entry/300644 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 [[Fabry:Mapping_point_mutations/OMIM_data#Allelic_variants | OMIM data-Allelic variants]]). The remaining 40 variants are specified as SNPs and are listed in [[Fabry:Mapping_point_mutations/OMIM_data#SNPs | OMIM data-SNPs]].<br> |
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| + | A search in the SNPdbe database revealed 57 mutations ([http://www.rostlab.org/services/snpdbe/dosearch.php?id=name&val=NP_000160&organism2=human&organism1= see]) |
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| − | 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. |
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Revision as of 00:09, 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.
SNPdbe
A search in the SNPdbe database revealed 57 mutations (see)
