What does Entrez_Gene_Id 0 mean?

Question

[haiying.kong]

I used Oncotator to annotate somatic mutations identified with MuTect2.

I found that on the column "Entrez_Gene_Id", there are rows with value "0". I checked these rows, some of them actually have gene symbols and amino acid changes, and are classified as missense mutation. Then there should be a valid Entrez ID, right?

How should I interpret the mutations with Entrez_Gene_Id==0?

[GenoMax]

Possibly this: For an intergenic mutation, set Entrez_Gene_Id to '0' Link to reference.

[haiying.kong]

For an intergenic mutation, there should not be gene symbol, and it cannot be classified as missense mutation. But some of these mutations with Entrez_Gene_Id=0 do have gene symbols and are classified as missense mutation.

Answer 1

[huwenhuo]

Would this helpful? http://gatkforums.broadinstitute.org/gatk/discussion/4157/what-does-an-error-message-mean

[haiying.kong]

Yes, this answers my question. Thank you so much.