FexSplice: A LightGBM-Based Model for Predicting the Splicing Effect of a Single Nucleotide Variant Affecting the First Nucleotide G of an Exon.
FexSplice web service program
LightGBM model
first nucleotide of an exon
splicing-affecting variants
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
06 09 2023
06 09 2023
Historique:
received:
02
08
2023
revised:
30
08
2023
accepted:
04
09
2023
medline:
29
9
2023
pubmed:
28
9
2023
entrez:
28
9
2023
Statut:
epublish
Résumé
Single nucleotide variants (SNVs) affecting the first nucleotide G of an exon (Fex-SNVs) identified in various diseases are mostly recognized as missense or nonsense variants. Their effect on pre-mRNA splicing has been seldom analyzed, and no curated database is available. We previously reported that Fex-SNVs affect splicing when the length of the polypyrimidine tract is short or degenerate. However, we cannot readily predict the splicing effects of Fex-SNVs. We here scrutinized the available literature and identified 106 splicing-affecting Fex-SNVs based on experimental evidence. We similarly identified 106 neutral Fex-SNVs in the dbSNP database with a global minor allele frequency (MAF) of more than 0.01 and less than 0.50. We extracted 115 features representing the strength of splicing
Identifiants
pubmed: 37761905
pii: genes14091765
doi: 10.3390/genes14091765
pmc: PMC10531444
pii:
doi:
Substances chimiques
Nucleotides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
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