Question: Why do genes have multiple consequences for the same SNP?
1
gravatar for first
15 months ago by
first30
first30 wrote:

I am an IT guy developing a database for genotype data of samples and I am confused when I look up a snp in NCBI, the genes listed for that SNP sometimes have multiple consequences (intron, missense, upstream, etc.) but on the data that I received only one of those consequences is listed.

snp gene • 396 views
ADD COMMENTlink written 15 months ago by first30

As said @finswimmer that mean your data concerned only one transcript per genes. With some software you can filter results by consequences to conserved only mutation having a protein translation impact.

ADD REPLYlink modified 15 months ago • written 15 months ago by Titus910

So, I suspect the latter but are transcripts actually identified from the sample much like genotypes are or simply based on the filters set by the researcher?

ADD REPLYlink written 15 months ago by first30

I m not sure to understand your question. But do you have information about processing of you data ? pipeline used may be ?

ADD REPLYlink written 15 months ago by Titus910

Unfortunately I do not have any information on the processing of the data. But what I'm asking is whether the actual transcript or RNA of an individual is actually identified, like how genotypes of individuals are indentified, or the transcript data is just queried and filtered from a database.

ADD REPLYlink written 15 months ago by first30
5
gravatar for finswimmer
15 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

Hello ,

you have to get familiar with the concept of transcripts to understand this. In short: The sequence of the gene can encode for multiple (slightly) different protein sequences.

fin swimmer

ADD COMMENTlink modified 15 months ago • written 15 months ago by finswimmer13k

Hi! Thanks for the information. I have actually come across the concept of transcripts and RNA's a while ago. It actually made me wonder why such important information is not included in the data I received.

ADD REPLYlink modified 15 months ago • written 15 months ago by first30
2

People typically only output the consequence for the canonical transcript isoform. Depending on who you ask, the canonical isoform can relate to:

  • the longest transcript isoform
  • the most expressed transcript isoform, which may not necessarily be the longest in the tissue of interest

People working in specific areas of clinical genetics will already know these intricacies and will only look at the consequence for the isoform that has most clinical relevance.

ADD REPLYlink written 15 months ago by Kevin Blighe53k
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