Cryptic Splice Variants

Summary

Cryptic splice variants are non-canonical sequence modifications that introduce or destroy splice donor or acceptor sites at locations distant from the normal intron-exon boundaries. Although historically under-annotated, modern deep learning tools like SpliceAI have enabled systematic genome-wide predictions of these cryptic events, demonstrating that their phenotypic consequences are often indistinguishable from canonical predicted loss-of-function (pLoF) mutations.

Overview

Canonical splicing mutations typically affect the highly conserved $+1, +2$ donor or $-1, -2$ acceptor dinucleotides at exon-intron boundaries. In contrast, cryptic splice variants can occur deep within introns or exons. When activated, they lead to aberrant splicing, intron retention, or exon skipping, which can introduce premature stop codons or disrupt critical protein domains.

Characterization in Large-Scale ExWAS

In the exome-wide association study of blood lipids in 1,158,017 individuals (Koyama et al. 2026), the authors highlighted: - Identification: Cryptic splice variants were identified using SpliceAI with a Delta Score (DS) threshold $>0.8$. - Effect Size equivalence: The phenotypic effect size (median $\beta = 1.092$) of identified cryptic splice variants was equivalent to that of canonical pLoF variants ($P = 0.71$). - Splicing donor 5th base: A strong enrichment of cryptic splice variants was observed at the splice donor 5th base (e.g. APOA5 rs200831171, associated with significantly elevated triglycerides, $\beta = 1.10$).

Citations

• [1] Jaganathan, K. et al. (2019). Predicting splicing from primary sequence with deep learning. Cell, 176(3), 535–548. DOI: 10.1016/j.cell.2018.12.015
• [2] Koyama, S. et al. (2026). Exome-wide association study of blood lipids in 1,158,017 individuals from diverse populations. Nature Genetics, 58(6), 1268-1279. DOI: 10.1038/s41588-026-02613-y. Source paper: s41588-026-02613-y.pdf