frameshift enquiry

[Gordon Blackshields]

Hi I'd like to enquire as to correct representation for a frameshift variant: 

NP_003310.4:p.Glu8973Argfs*47

Mutalyzer V3 does not accept the term as-is, it returns an error message "Variant Glu8973[Arg;47] type frame_shift not supported. (EVARIANTNOTSUPPORTED)". 

Given the above error, I removed the frameshift information (NP_003310.4:p.Glu8973Arg), and it was accepted without issue. Is there any way to modify the full term so that it is accepted?   or should this be stripped from future queries? 

Thanks for your help,

Gordon 

[J.F.J. Laros]

Dear Gordon,

Thank you for using Mutalyzer.

Indeed Mutalyzer 3 can not check protein variant descriptions containing a
frameshift yet. This is still on your to do list.

The `EVARIANTNOTSUPPORTED` error means that Mutalyzer does recognise the
description as syntactically valid, but that no semantic checking can be done
because this is currently not implemented.

In the mean time I would suggest the following approach:
- Check the full variant description, if we get the `EVARIANTNOTSUPPORTED`,
we know that the variant description is syntactically valid.
- Remove the frameshift part from the description to check whether the
substitution is possible.

I hope this helps.


With kind regards,
Jeroen.

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Jeroen F.J. Laros - J.F.J...@lumc.nl