Currently, we can select a transcript in an LRG reference using for example t1:
LRG_321t1:c.1del
Or, if we want to describe a protein variant, we can select the protein:
LRG_321p8:p.1del
However, there can be more than one protein for a given transcript, giving rise to different CDS annotations. An example is TP53 where we have LRG_321t1 for both LRG_321p1 and LRG_321p8 with a difference in exon positions.
So, to unambiguously describe a c. variant, we should be able to do something like:
LRG_321t1p8:c.1del
This is also true in the reverse direction. A given protein might originate from more than one transcript, so it makes sense to say:
LRG_321p8t1:p.1del
Therefore, the parser should be updated to accept a transcript ID, or a protein ID, or both (in both orders).
Of course, the name checker should then also know what to do with this.
Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/150 Original date: 2013/10/16 Original reporter: martijn
Currently, we can select a transcript in an LRG reference using for example t1:
Or, if we want to describe a protein variant, we can select the protein:
However, there can be more than one protein for a given transcript, giving rise to different CDS annotations. An example is TP53 where we have LRG_321t1 for both LRG_321p1 and LRG_321p8 with a difference in exon positions.
So, to unambiguously describe a c. variant, we should be able to do something like:
This is also true in the reverse direction. A given protein might originate from more than one transcript, so it makes sense to say:
Therefore, the parser should be updated to accept a transcript ID, or a protein ID, or both (in both orders).
Of course, the name checker should then also know what to do with this.