ArticleNucleic acids research2007
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed.
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- Genetic diagnosis and molecular characterization of three novel variations in the phenylalanine hydroxylase gene from Chinese patients with phenylketonuria.EXCLI journal · 2026Article
- Alternative splicing events of three rare variants in CHKB gene causing megaconial congenital dystrophy.Neurogenetics · 2025Article
- A 15 bp non-canonical splice-site deletion in ABCA4 linked with retinitis pigmentosa and myopia: insights into splicing defects and phenotypic variability.Molecular biology reports · 2025Article
- EZH2 variants derived from cryptic splice sites govern distinct epigenetic patterns during embryonic development.Nucleic acids research · 2025Article
- Genetic Heterogeneity Correlated with Phenotypic Variability in 48 Patients with Cystic Fibrosis.Journal of clinical medicine · 2025Article
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- Variants in CFAP410 cause a range of retinal and skeletal phenotypes.NPJ genomic medicine · 2025Article
- Identification of deep intronic variants in junctional epidermolysis bullosa using genome sequencing and splicing assays.NPJ genomic medicine · 2025Article
- Identification of a novel variant inGastroenterology report · 2025Article
- A novel dinucleotide variant at 5' splice sites in theFrontiers in genetics · 2025Article
- Genotype Characterization and MiRNA Expression Profiling in Usher Syndrome Cell Lines.International journal of molecular sciences · 2024Article
- Genetic Testing in Patients with Autoimmune Lymphoproliferative Syndrome: Experience of 802 Patients at Cincinnati Children's Hospital Medical Center.Journal of clinical immunology · 2024Article
55 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Despite a growing number of splicing mutations found in hereditary diseases, utilization of aberrant splice sites and their effects on gene expression remain challenging to predict. We compiled sequences of 346 aberrant 5'splice sites (5'ss) that were activated by mutations in 166 human disease genes. Mutations within the 5'ss consensus accounted for 254 cryptic 5'ss and mutations elsewhere activated 92 de novo 5'ss. Point mutations leading to cryptic 5'ss activation were most common in the first intron nucleotide, followed by the fifth nucleotide. Substitutions at position +5 were exclusively G>A transitions, which was largely attributable to high mutability rates of C/G>T/A. However, the frequency of point mutations at position +5 was significantly higher than that observed in the Human Gene Mutation Database, suggesting that alterations of this position are particularly prone to aberrant splicing, possibly due to a requirement for sequential interactions with U1 and U6 snRNAs. Cryptic 5'ss were best predicted by computational algorithms that accommodate nucleotide dependencies and not by weight-matrix models. Discrimination of intronic 5'ss from their authentic counterparts was less effective than for exonic sites, as the former were intrinsically stronger than the latter. Computational prediction of exonic de novo 5'ss was poor, suggesting that their activation critically depends on exonic splicing enhancers or silencers. The authentic counterparts of aberrant 5'ss were significantly weaker than the average human 5'ss. The development of an online database of aberrant 5'ss will be useful for studying basic mechanisms of splice-site selection, identifying splicing mutations and optimizing splice-site prediction algorithms.
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