Researching SNPs (PKU)

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Revision as of 18:32, 9 June 2012 by Hollizeck (talk | contribs) (Overview)

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

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