ArticleNPJ genomic medicine2022
Clinical variant interpretation and biologically relevant reference transcripts.
Article in NPJ genomic medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed, 16 citations in OpenAlex.
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- Conservation assessment of human splice site annotation based on a 470-genome alignment.Nucleic acids research · 2025Article
- Conservation assessment of human splice site annotation based on a 470-genome alignment.bioRxiv : the preprint server for biology · 2025Article
- mRNA Transcript Variants Expressed in Mammalian Cells.International journal of molecular sciences · 2025Review
- The state of the human coding gene catalogues.Database : the journal of biological databases and curation · 2025Article
- GENCODE 2025: reference gene annotation for human and mouse.Nucleic acids research · 2025Article
- The rapid degradation of translated upstream regions points to an inefficient translation initiation process.bioRxiv : the preprint server for biology · 2024Article
- Re-appraising the evidence for the source, regulation and function of p53-family isoforms.Nucleic acids research · 2024Review
- Evidence for widespread translation of 5' untranslated regions.Nucleic acids research · 2024Article
- Coinheritance of HNF1A and glucokinase variants in maturity-onset diabetes of the young.Endocrinology, diabetes & metabolism case reports · 2024Article
- The impact of genetically controlled splicing on exon inclusion and protein structure.PloS one · 2024Article
- Origins and Evolution of Human Tandem Duplicated Exon Substitution Events.Genome biology and evolution · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Clinical variant interpretation is highly dependent on the choice of reference transcript. Although the longest transcript has traditionally been chosen as the reference, APPRIS principal and MANE Select transcripts, biologically supported reference sequences, are now available. In this study, we show that MANE Select and APPRIS principal transcripts are the best reference transcripts for clinical variation. APPRIS principal and MANE Select transcripts capture almost all ClinVar pathogenic variants, and they are particularly powerful over the 94% of coding genes in which they agree. We find that a vanishingly small number of ClinVar pathogenic variants affect alternative protein products. Alternative isoforms that are likely to be clinically relevant can be predicted using TRIFID scores, the highest scoring alternative transcripts are almost 700 times more likely to house pathogenic variants. We believe that APPRIS, MANE and TRIFID are essential tools for clinical variant interpretation.
Identifiers
What OpenQuestion holds
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.