Question: loss of function prediction
gravatar for RT
6.1 years ago by
European Union
RT350 wrote:

Hello everyone,

I am using snpeff for variant annotation and effect prediction. For my genes of interest, I am looking for the disrupted gene models in the population (snp data for 50 individuals). Loss of function analysis or gene disruption is done based on SNPeff criteria's- loss of start, stop gain etc. Few of the positions are heterozygous. My question is how should I treat these positions? Suppose for a heterozygous position C/G, G causes an early stop codon. We don't know which allele is expressed or dominating? So for these cases, I am concluding that the gene model is broken. Is this correct to say?


snpeff disrupted gene models • 2.3k views
ADD COMMENTlink modified 6.1 years ago by Devon Ryan98k • written 6.1 years ago by RT350
gravatar for Devon Ryan
6.1 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

Well, it "might" be broken. You can get dosage compensation to correct for the non-functional allele, but the only way to find that out is to do the RNAseq and/or Western blot.

ADD COMMENTlink written 6.1 years ago by Devon Ryan98k
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