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Feature #491

closed

Inconsistent amino acid positions for rs3798220

Added by Madeleine Ball almost 16 years ago. Updated about 15 years ago.

Status:
Closed
Priority:
Normal
Assigned To:
Target version:
-
Story points:
-

Description

Trait-o-matic thinks rs3798220 is http://evidence.personalgenomes.org/LPA-I1891M but all the literature thinks it is http://evidence.personalgenomes.org/LPA-I4399M

Someone should figure out where this discordant position is coming from. It looks like the refFlat file doesn't have any splice variants, although this should be double-checked.

Actions #1

Updated by Madeleine Ball almost 16 years ago

  • Status changed from New to Closed
  • Resolution set to wontfix

From Xiaodi:

This is based on NP_005568.2. As noted in that file,

"Depending on the individual, the encoded protein contains 2-43 copies
of kringle-type domains. The allele represented here contains 15
copies of the kringle-type repeats and corresponds to that found in
the reference genome sequence. [provided by RefSeq]. Sequence Note:
This gene is highly polymorphic in length and number of exons due to
variation in the number of kringle IV-2 repeats which vary from 2-43
copies among individuals. This RefSeq record was created from the
reference genome assembly based on the exon representation found in
DQ452068.1 whose sequence is consistent with the reference genome
sequence, and includes 15 copies of the kringle IV-2 repeats."

So the traditional designation of I4399M is based on a sequence with a
different number of kringle repeats, which is no longer used. There's
nothing we can do about this except to note that literature previous
to 2006 (apparently, that's when this record superseded the previous
one; I'm not sure how many kringles are in that one) I4399M refers to
the current designation of I1891M.


Based on this explanation, I'm closing this bug as "wontfix". It is biology's fault for being complicated, I guess I should trust the system more. We might consider using redirects or merging based on rsIDs to address these issues in the future. -- Madeleine

Actions #2

Updated by Ward Vandewege about 15 years ago

  • Project changed from 19 to GET-Evidence
  • Category deleted (GET-Evidence)
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