ArticleThe Journal of biological chemistry2015
The Silent Sway of Splicing by Synonymous Substitutions.
Article in The Journal of biological chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed.
- Association of Silent Variant p.17Pro = SNP in the LHX4 Gene with Litter Size in Awassi Sheep.Biochemical genetics · 2026Article
- Multiplexed assays of variant effect for clinical variant interpretation.Nature reviews. Genetics · 2026Review
- From paleness to albinism: Contribution of OCA2 exon 10 skipping to hypopigmentation.PLoS genetics · 2025Article
- Assessing Splicing Variants in the PAX6 Gene: A Comprehensive Minigene Approach.Journal of cellular and molecular medicine · 2025Article
- Synonymous edits in theProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer.BMC bioinformatics · 2023Article
- Nonsynonymous Synonymous Variants Demand for a Paradigm Shift in Genetics.Current genomics · 2023Review
- Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects.Nature reviews. Genetics · 2023Review
- Codon modification of Tuba1a alters mRNA levels and causes a severe neurodevelopmental phenotype in mice.Scientific reports · 2023Article
- When a Synonymous Variant Is Nonsynonymous.Genes · 2022Article
- Exonic splicing code and protein binding sites for calcium.Nucleic acids research · 2022Article
- Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon.Nature communications · 2022Article
- Accurate Prediction of Protein Sequences for Proteogenomics Data Integration.Methods in molecular biology (Clifton, N.J.) · 2022Article
- β-Arrestin 2 (ARRB2) Polymorphism is Associated With Adverse Consequences of Chronic Heroin Use.The American journal on addictions · 2021Article
- Therapeutic Modulation of RNA Splicing in Malignant and Non-Malignant Disease.Trends in molecular medicine · 2021Review
- Mistranslation Drives Alterations in Protein Levels and the Effects of a Synonymous Variant at the Fibroblast Growth Factor 21 Locus.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Splicing at the phase-separated nuclear speckle interface: a model.Nucleic acids research · 2021Review
- Splicing in the Diagnosis of Rare Disease: Advances and Challenges.Frontiers in genetics · 2021Review
- Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.Molecular biology and evolution · 2020Article
- PRRT2 gene variant in a child with dysmorphic features, congenital microcephaly, and severe epileptic seizures: genotype-phenotype correlation?Italian journal of pediatrics · 2019Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Alternative splicing diversifies mRNA transcripts in human cells. This sequence-driven process can be influenced greatly by mutations, even those that do not change the protein coding potential of the transcript. Synonymous mutations have been shown to alter gene expression through modulation of splicing, mRNA stability, and translation. Using a synonymous position mutation library in SMN1 exon 7, we show that 23% of synonymous mutations across the exon decrease exon inclusion, suggesting that nucleotide identity across the entire exon has been evolutionarily optimized to support a particular exon inclusion level. Although phylogenetic conservation scores are insufficient to identify synonymous positions important for exon inclusion, an alignment of organisms filtered based on similar exon/intron architecture is highly successful. Although many of the splicing neutral mutations are observed to occur, none of the exon inclusion reducing mutants was found in the filtered alignment. Using the modified phylogenetic comparison as an approach to evaluate the impact on pre-mRNA splicing suggests that up to 45% of synonymous SNPs are likely to alter pre-mRNA splicing. These results demonstrate that coding and pre-mRNA splicing pressures co-evolve and that a modified phylogenetic comparison based on the exon/intron architecture is a useful tool in identifying splice altering SNPs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.