Question

I would like to know how many synonimous mutations affect alternative spicing in immune diseases.

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9.2 years ago

ferga88 • 0

I am looking for a database that I can find all synonymous mutations which affect alternative splicing in immune disease.

Thanks! :)

splicing • 2.0k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 9.2 years ago by ferga88 • 0

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I seriously doubt such a database exists.

ADD REPLY • link 9.2 years ago by Devon Ryan 104k

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But maybe a database where you can use some filters...?

ADD REPLY • link 9.2 years ago by ferga88 • 0

Ram · Answer 1 · 2015-10-06

You could try pulling the Splicing variants with a "DM", "DM?", "FTV" annotation from HGMD (public version is a bit out of date http://www.hgmd.cf.ac.uk/ac/index.php). Then maybe generate a list candidate genes involved in Immunodeficiency by running the term through phenotype to gene mappers like Phenolyzer (http://phenolyzer.usc.edu/), OMIM genemap (http://www.omim.org/), or maybe Phenomizer (http://compbio.charite.de/phenomizer/) then cross reference with the splicing variants by gene symbols or maybe genomic coordinates.

If you're using Phenolyzer and a popular term like "Immunodeficiency" on it's own, maybe just use the Seed Gene list (which still weighs in at over 1000 genes...).