How to judge severity of variants in genes

Question

[mschmid]

I did some variant calling on a 9MB genome we assembled and compared to another genome. We just got a few SNPs and single nucleotide indels.

With SnpEff I assessed the severity of the variants. We just got a few indels in genes.

Interestingly most of the indels are close to the stop codon. And most of them are in areas where we did not find known motifs with InterProScan...

I want to further assess the severity of the indels which are in genes. Any papers or other suggestions?

It is realy interesting that I see a strong bias of indels towards the end of the genes. Did you ever observe the same picture?

Answer 1

[Michael Schubert]

There are plenty of tools out there that try to assess the impact of different mutations (including indels) in proteins.

Have a look at VEP

The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the coordinates of your variants and the nucleotide changes to find out the [...]

and ANNOVAR

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform [...]

[mschmid]

Thanks Michael! Unfortunately, you not really answered my question. I was more asking if it is possible to asses the severity of a indel based on its position on a CDS. Or if there is any resources out there. I do not have much knowlegede about that.

Also, I would be interested if it is normal that the indels occur more to the end of a CDS. Did anyone ever see such a bias?

[Michael Schubert]

Unless I understand something wrong, the "severity" you are looking for is functional impact. This is exactly what the tools above do. I am not aware of any systematic bias if short indels closer to the stop codon as opposed to other segments of the gene.

Answer 2

[Jeremy Schwartzentruber]

One reason you might find indels in the last exon of genes is that they are much less likely to lead to nonsense-mediated decay, in the case that they are frame-shifting indels.

How many genes are you talking about? If you have other organisms to compare to, you could look at the conservation across those genes. It might be that you are just looking at poorly-conserved regions.

Have you checked whether the indels are occurring in repetitive sequence, e.g. poly-A or poly-Q repeats? Replication errors at such sites often lead to short (in-frame) indels that are less likely to affect protein function.

Answer 3

[mkulecka]

For simple check of deleteriousness in silico I strongly recommend CADD - it provides you with a lot of annotations and can be used for more than one type of variant. For indels only there's SIFT Indel.