Researching SNPs (PKU)
Mutants walk the earth.
There are mutants on your block. There's a mutant right next door. There's one in your shoes.
We are, face it, all mutants. Humanity amounts to a string of mutations millennia-old, tweaks that gave us an edge over the next brute down the line. Upright posture; opposable thumb; prefrontal lobes.
The all-time specifically human thing is language. Familiar yet mysterious, language is the angelic part of us angel/beasts. It is spiritual, evanescent, fugitive - even gorgeous words like those have an unearthly shimmer. - from philly.com
Short Task Description
In this weeks task, we will research SNPs in the PAH gene that cause or do not cause a different phenotype of the phenylalanine hydroxylase. The chosen databases are: The public release of the Human Gene Mutation Database (HGMD), dbSNP, SNPdbe, OMIM and SNPedia. You may find a detailed task description here. A very short journal, which offers a small overview over the things we did can be found here.
<figtable id="tab:modelling_scores"> Key Values of the different SNP databases
|Database||Last Update||Number of Entries||Number of Entries concerning PAH||Type of information||Sources||Curation/Verification||Comment|
|HGMD||public after 3 years (quarterly updated)||50,129 (only mis-/nonsense)||397 (only mis-/nonsense)||all types of mutations||current literature||manual and computerised search in current literature||too much advertising|
|dbSNP||Oct 2011||292,031,791||2590||SNPs, short in/dels, polymorphisms, others||submitted by registered sources (labs, institutes,.. )||clustering of identical submissions by NCBI|
|SNPdbe||Mar 2012||1,691,464||328||nonsyn. SNPs||Swissprot, dbSNP, PMD, OMIM, 1000 genomes||cf. sources||Predictions of functional effect, experimental evidence if available in source|
|OMIM||June 2012||21,257 (Summary entries)||1 (64 selected SNPs)||catalog of human genes and genetic disorders and traits||current literature||manually curated|
|SNPedia||continuous, Wiki-style||29,058||53||SNPs||publicly edited||publicly edited||get genotyped and predicted|
We extracted 397 disease-causing mis- and non-sense SNPs from HGMD. The reference sequence is [NM_000277.1.c].
As dbSNP offers differentiated search options, we extracted 29 synonymous SNPs and 358 missense SNPs separately. The reference sequence is again [NM_000277.1.c].
We will use OMIM to select common variants and interesting SNPs for next week's task.
Following the task description, we looked at the conservation score, to determine quickly, whether a mutation found here is disease causing or not. Our reasoning can be found at this subpage. In short, we take low PSSM scores and a low percentage of conservation as indicator for no disease effect.
The SNPs concerning PAH in SNPedia all appear in dbSNP and there is no additional information attached so we do not investigate them in any separate way.
Distribution of Mutations
<figtable id="tab:mutation_distri"> Distribution of SNPs from different databases on the PAH gene.
There appear to be less disease causing mutations at the termini of the protein sequence which is as expected as they are functionally less critical. Hotspots appear around positions 55-70, 165-180 and roughly from 250 to 400. The first region is in the center of the regulatory domain, the latter two regions span the whole catalytical domain.
Unfortunately there are too few silent mutations to draw valid conclusions, but they appear to be distributed quite randomly and at least the spikes in frequency visible in the histogram do not coincide with the spikes of the other mutation types pictured.
We want to present as much information in our map of SNPs on the PAH gene as possible. As it contains information from different sources and multiple annotations for the same positions, some of the annotations may appear to conflict. Consult the descriptions above and the raw material for more information in these cases.
Mapping at Sequence
Mapping at Structure
In order to see where the SNPs which we already mapped to the sequence are in the structure we used the PDB structure of 2PAH and marked the residues according to the colorcoding we used above. This means: red is a residue known to be disease causing, orange is a misssense-SNP with no entry in HGMD and green is a silent mutation. Just keep in mind that several residues have different annotations according to their substitution and that the PDB-structure is not the structure of the complete gene. The structure which can be found in the PDB starts with residue number 118 in the original sequence.
For the silent and the SNPs not found in HGMD, there are no surprises to be found in the structure, most of them are to be found on the outside of the protein, or in the coiled regions which can be seen in <xr id="fig:SNPMappingstructuremutation"/> and <xr id="fig:SNPMappingstructuresilent"/>. The other thing we expected was the low number of silent and noneffective mutations as disease causing mutations (visible by patients with the disease phenotype) draw more research attention.
For the disease causing residues on the other hand, we were quite surprised that we found so many and for them to be located in the coiled regions almost as often as in the structural regions(<xr id="fig:SNPMappingstructuredisease"/>). Most of the SNPs were in the inside of the protein, where the cosubstrate-, iron- and substrate-binding site is located, so in this part we found exactly what we expected.