Gaucher Disease: Task 07 - Research SNPs

From Bioinformatikpedia
Revision as of 22:13, 23 June 2013 by Gerkej (talk | contribs)

HGMD

The Glucocerebrosidase has the gene symbol GBA. A research on The Human Gene Mutation Database for GBA leads to the following results:

GBA in HGMD
Mutation Type Number of Mutations Effect of Mutation
Missense/nonsense 256 Single base-pair substitutions in coding regions are presented in terms of a triplet change with an additional flanking base included if the mutated base lies in either the first or third position in the triplet. There are currently 256 mutations available in this category.
Splicing 16 mutations with consequences for mRNA splicing are presented in brief with information specifying the relative position of the lesion with respect to a numbered intron donor or acceptor splice site. Positions given as positive integers refer to a 3' (downstream) location, negative integers refer to a 5' (upstream) location
Regulatory 0
Small deletions 26 micro-deletions (20 bp or less) are presented in terms of the deleted bases in lower case plus, in upper case, 10 bp DNA sequence flanking both sides of the lesion.
Small insertions 13 micro-insertions (20 bp or less) are presented in terms of the inserted bases in lower case plus, in upper case, 10 bp DNA sequence flanking both sides of the lesion.
Small indels 4 micro-indels (20 bp or less) are presented in terms of the deleted/inserted bases in lower case plus, in upper case, 10 bp DNA sequence flanking both sides of the lesion.

The mutations on GBA do not only result to Gaucher's disease or influence its phenotype, but in some cases, also have an effect on the phenotype of the diseases Parkinson and Alzheimer

In HGMD, look for missense and nonsense mutations (HGMD does not list silent point mutations).

dbSNP

blub

In dbSNP, look for silent (point) mutations. In most cases, significantly more than 100 mutations are known. The residue numbers in the databases may not correspond to each other.

SNPedia

SNPdbe

In SNPdbe, look for disease causing mutations and those that have no effect (often not verified). Please disregard the two colums "Predicted functional effect" for this week.

OMIM

Mutation map

Extract information for your protein/disease from the databases. Are there mutation hot-spots? Map approximately 100 point mutations onto your protein sequence (disease and non-disease causing).