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fix: return unknown when initiation site is affected #111

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merged 1 commit into from
Dec 5, 2024

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nokara26
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I fixed N-terminal extension and to return unknown by default when initiation site is affected.
p.M1*ext-? is not valid because changing to Ter is incorrect.
And I found N-terminal extension is a variant in the 5' UTR and it is difficult to predict accurate hgvs.
So I fixed to return unknown by default when initiation site is affected.

https://hgvs-nomenclature.org/stable/recommendations/protein/extension/

p.Met1ext-5
a variant in the 5' UTR activates a new upstream translation initiation site starting with amino acid Met-5.
NOTE: modified from p.Met1extMet-5.

p.Met1_Leu2insArgSerThrVal
amino acid Met1 is changed to Val, activating an upstream translation initiation site at position -4 (Met-4), inserting amino acids ArgSerThrVal between Met1 and Leu2.
NOTE: this variant is not described as an extension (p.Met1Valext-4) since Met1, part of the normal amino acid sequence, is changed.

@@ -637,7 +659,8 @@
(let [{ppos :pos, pref :ref, palt :alt}
(if-not (#{:no-effect :unknown :overlap-exon-intron-boundary} (:type pvariant))
(common/apply-3'-rule pvariant (:ref-prot-seq seq-info))
pvariant)]
pvariant)
seq-info (merge seq-info options)]
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to use prefer-extension-for-initial-codon-alt? in protin-extension because protein-extension is called from protein-indel.

alt-aa (mut/->long-amino-acid (if (= ppos 1)
(or (last ins) (first rest-seq))
(:palt first-diff-aa-info)))
alt-aa-offset (if (and (= ppos 1) (nil? (last ins))) -1 0)
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to move one position to the N terminal side.

@nokara26 nokara26 self-assigned this Nov 27, 2024
@nokara26 nokara26 requested a review from federkasten November 27, 2024 01:47
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Sorry for the delayed reply 🙇 LGTM!

@federkasten federkasten merged commit 82f827f into master Dec 5, 2024
30 checks passed
@federkasten federkasten deleted the fix/fix-start-codon-affected branch December 5, 2024 06:17
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2 participants