Entering edit mode
3.5 years ago
avelarbio46 ▴ 20
I was hunting for a list of known false positive genes for SNPs and variants (highly variable genes). I know about many, such as TNN, mucins and olphatory proteins, but I was hoping that there might be a list of genes that are known to be highly mutated without any specific phenotype, such as mucins.
I found FLAGS, but it is a very old list.
Does anyone know a database for genes with high number of paralogues or that are very long or maybe not very conserved? Is there any up-to-date list?
What do you mean by "false positive genes"? There needs to be some sort of statistical test to have false positives and false negatives.
Edited question. I basically mean false positive calls for variants. For example, SNPs, mutations and etc.
Frequently mutated doesn't imply false positives. For example, TTN is huge so chances are high to get a mutation, and olfactory receptors are abundant and not essential.
You are correct. Just because there is a high ammount of mutations doensn't mean they are not there, but that probably they have no functional impact whatsoever. That's what I mean! They are the usual suspects for no functional impact, even with high mutation rates.
That's what Wouter rejects with "... doesn't imply false positives". False positives will depend on the biological question you ask and the cellular context you're in.
Have a look at the gnomad dataset, especially the pLI metric and the expected vs observed number of LOF/missense variants per gene. That will give you an idea of recurrence of mutations.
Another example, based on the ExAC database: http://genic-intolerance.org/