I have a question regarding
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
structural_interaction_variant. Then, for the
ANN[*].FEATUREID I have the the following structure of transcript :
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
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