Hello everyone,
I have a question regarding ANN[*].FEATURE
and ANN[*].FEATUREID
annotation from snpEff in case you know how to help me.
I have variants in my annotated .tsv which comes with the following annotation for the ANN[*].FEATURE
field: structural_interaction_variant
. Then, for the ANN[*].FEATUREID
I have the the following structure of transcript :
**1XMI:D_397-D_443**:ENST00000003084
.
However, I'm not sure about how to interpret this.
First of all, I have read the SnPEff documentation, which says:
Effect (Seq. Ontology) : structural_interaction_variant
Effect (Classic) : PROTEIN_STRUCTURAL_INTERACTION_LOCUS
Note & Example : Within protein interaction loci (e.g. two AA that are in contact within the same protein, possibly helping structural conformation)
Impact : HIGH
So, I understand that my variant has some sort of impact over the protein structure. And that probably the 1XMI:D_397-D_443
before the transcript ID means the protein PDB code and the amino acids affected. On the other hand, this variant doesn't generate any amino acid change in ANN[*].HGVS_P
field.
However. I'm not sure about which biological conclusions to take from this. Especially because I had some variants being annotated both like this and missense variants at the same time. Others only being annotated only like a structural interaction variants.
I leave here a line of my tsv, tough I don know how to properly copy table lines in here.
CHROM POS REF ALT ID QUAL ANN[*].ALLELE ANN[*].EFFECT ANN[*].IMPACT ANN[*].GENE ANN[*].GENEID ANN[*].FEATURE ANN[*].FEATUREID ANN[*].BIOTYPE ANN[*].RANK ANN[*].HGVS_C
7 117188812 G T rs147422190 100 T structural_interaction_variant HIGH CFTR ENSG00000001626 interaction 1XMI:A_397-A_443:ENST00000003084 protein_coding 10 c.1327G>T
Many thanks!
Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Many thanks! Next time I'll do it right