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Proteome‐Wide Analysis of Human Deletions

Zhang, Haoyang LU orcid ; Luan, Xinning LU and Vihinen, Mauno LU orcid (2025) In Proteins p.1-8
Abstract
Protein deletions are frequent among both natural and pathogenic variations. Many of them are misclassified in variation databases and the literature. Nonsense-mediated decay prevents the expression of many nucleotide deletions. Many variants classified as protein deletions are not expressed at all. We conducted an exhaustive systematic analysis of three types of deletions: N- and C-terminal deletions, as well as internal deletions within protein sequences. In addition, we compared natural and pathogenic internal deletions. We collected an extensive dataset of reliable deletions in many proteins and then performed extensive statistical analyses to investigate properties of deletions and proteins that contain them. We studied the properties... (More)
Protein deletions are frequent among both natural and pathogenic variations. Many of them are misclassified in variation databases and the literature. Nonsense-mediated decay prevents the expression of many nucleotide deletions. Many variants classified as protein deletions are not expressed at all. We conducted an exhaustive systematic analysis of three types of deletions: N- and C-terminal deletions, as well as internal deletions within protein sequences. In addition, we compared natural and pathogenic internal deletions. We collected an extensive dataset of reliable deletions in many proteins and then performed extensive statistical analyses to investigate properties of deletions and proteins that contain them. We studied the properties of protein deletions, including deletion length and position, amino acid composition, flanking amino acid sequence context, the functions and properties of deletion-containing proteins, the functional roles of the deleted regions, the positioning within protein domains and protein structure, as well as sequence conservation and involvement in protein–protein interaction networks. We found several statistically significant differences between the deletion types and between benign and pathogenic deletions. The obtained insight can be used, for example, for variation interpretation, prediction method development, and analysis of variation mechanisms and effects. (Less)
Please use this url to cite or link to this publication:
author
; and
organization
publishing date
type
Contribution to journal
publication status
epub
subject
in
Proteins
pages
1 - 8
publisher
Wiley-Liss Inc.
external identifiers
  • pmid:41215709
ISSN
0887-3585
DOI
10.1002/prot.70080
language
English
LU publication?
yes
id
cb29a294-182f-44dc-8a49-b91b5a19a90c
alternative location
https://onlinelibrary.wiley.com/doi/10.1002/prot.70080
date added to LUP
2025-11-11 10:35:04
date last changed
2025-11-12 03:48:31
@article{cb29a294-182f-44dc-8a49-b91b5a19a90c,
  abstract     = {{Protein deletions are frequent among both natural and pathogenic variations. Many of them are misclassified in variation databases and the literature. Nonsense-mediated decay prevents the expression of many nucleotide deletions. Many variants classified as protein deletions are not expressed at all. We conducted an exhaustive systematic analysis of three types of deletions: N- and C-terminal deletions, as well as internal deletions within protein sequences. In addition, we compared natural and pathogenic internal deletions. We collected an extensive dataset of reliable deletions in many proteins and then performed extensive statistical analyses to investigate properties of deletions and proteins that contain them. We studied the properties of protein deletions, including deletion length and position, amino acid composition, flanking amino acid sequence context, the functions and properties of deletion-containing proteins, the functional roles of the deleted regions, the positioning within protein domains and protein structure, as well as sequence conservation and involvement in protein–protein interaction networks. We found several statistically significant differences between the deletion types and between benign and pathogenic deletions. The obtained insight can be used, for example, for variation interpretation, prediction method development, and analysis of variation mechanisms and effects.}},
  author       = {{Zhang, Haoyang and Luan, Xinning and Vihinen, Mauno}},
  issn         = {{0887-3585}},
  language     = {{eng}},
  pages        = {{1--8}},
  publisher    = {{Wiley-Liss Inc.}},
  series       = {{Proteins}},
  title        = {{Proteome‐Wide Analysis of Human Deletions}},
  url          = {{http://dx.doi.org/10.1002/prot.70080}},
  doi          = {{10.1002/prot.70080}},
  year         = {{2025}},
}