Researching SNPs (PKU)
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 dense journal, which offers only 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|
29 synonymous SNPs
use to annotate common variants/interesting SNPs (e.g. .0002)
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.
redundant to dbSNP, no additional information => ignore