Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites

Publikation: Beitrag in FachzeitschriftForschungsartikelBeigetragenBegutachtung


  • Peng Zhang - , Rockefeller University (Autor:in)
  • Matthieu Chaldebas - , Rockefeller University (Autor:in)
  • Masato Ogishi - , Rockefeller University (Autor:in)
  • Fahd Al Qureshah - , Rockefeller University (Autor:in)
  • Khoren Ponsin - , Rockefeller University (Autor:in)
  • Yi Feng - , Rockefeller University (Autor:in)
  • Darawan Rinchai - , Rockefeller University (Autor:in)
  • Baptiste Milisavljevic - , Rockefeller University (Autor:in)
  • Ji Eun Han - , Rockefeller University (Autor:in)
  • Marcela Moncada-Vélez - , Rockefeller University (Autor:in)
  • Sevgi Keles - , Necmettin Erbakan University (Autor:in)
  • Bernd Schröder - , Institut für Physiologische Chemie (Autor:in)
  • Peter D Stenson - , Cardiff University (Autor:in)
  • David N Cooper - , Cardiff University (Autor:in)
  • Aurélie Cobat - , Technische Universität Dresden (Autor:in)
  • Bertrand Boisson - , Rockefeller University (Autor:in)
  • Qian Zhang - , Rockefeller University, INSERM - Institut national de la santé et de la recherche médicale, Institut des maladies génétiques Imagine, Université Paris Cité (Autor:in)
  • Stéphanie Boisson-Dupuis - , Rockefeller University (Autor:in)
  • Laurent Abel - , Rockefeller University (Autor:in)
  • Jean-Laurent Casanova - , Rockefeller University (Autor:in)


Human genetic variants that introduce an AG into the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) of protein-coding genes can disrupt pre-mRNA splicing. Using our genome-wide BP database, we delineated the BP-ACC segments of all human introns and found extreme depletion of AG/YAG in the [BP+8, ACC-4] high-risk region. We developed AGAIN as a genome-wide computational approach to systematically and precisely pinpoint intronic AG-gain variants within the BP-ACC regions. AGAIN identified 350 AG-gain variants from the Human Gene Mutation Database, all of which alter splicing and cause disease. Among them, 74% created new acceptor sites, whereas 31% resulted in complete exon skipping. AGAIN also predicts the protein-level products resulting from these two consequences. We performed AGAIN on our exome/genomes database of patients with severe infectious diseases but without known genetic etiology and identified a private homozygous intronic AG-gain variant in the antimycobacterial gene SPPL2A in a patient with mycobacterial disease. AGAIN also predicts a retention of six intronic nucleotides that encode an in-frame stop codon, turning AG-gain into stop-gain. This allele was then confirmed experimentally to lead to loss of function by disrupting splicing. We further showed that AG-gain variants inside the high-risk region led to misspliced products, while those outside the region did not, by two case studies in genes STAT1 and IRF7. We finally evaluated AGAIN on our 14 paired exome-RNAseq samples and found that 82% of AG-gain variants in high-risk regions showed evidence of missplicing. AGAIN is publicly available from and


Seiten (von - bis)e2314225120
FachzeitschriftProceedings of the National Academy of Sciences of the United States of America : PNAS
PublikationsstatusVeröffentlicht - 14 Nov. 2023

Externe IDs

PubMedCentral PMC10655562
Scopus 85176371368


Ziele für nachhaltige Entwicklung


  • Humans, RNA Splice Sites, Introns, RNA Splicing, Mutation, Genome