Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone
Samantha J. Bryen,
Michaela Yuen,
Himanshu Joshi,
Ruebena Dawes,
Katharine Zhang,
Jessica K. Lu,
Kristi J. Jones,
Christina Liang,
Wui-Kwan Wong,
Anthony J. Peduto,
Leigh B. Waddell,
Frances J. Evesson,
Sandra T. Cooper
Affiliations
Samantha J. Bryen
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia; Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Michaela Yuen
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Himanshu Joshi
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Ruebena Dawes
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Katharine Zhang
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Jessica K. Lu
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Kristi J. Jones
Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia; Department of Clinical Genetics, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
Christina Liang
Department of Neurology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia; Department of Neurogenetics, Northern Clinical School, Kolling Institute, University of Sydney, NSW 2065, Australia
Wui-Kwan Wong
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Anthony J. Peduto
Department of Radiology, Westmead Hospital, Western Clinical School, University of Sydney, Westmead, NSW 2145, Australia
Leigh B. Waddell
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Frances J. Evesson
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
Sandra T. Cooper
Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia; Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia; Corresponding author
Summary: Predicting the pathogenicity of acceptor splice-site variants outside the essential AG is challenging, due to high sequence diversity of the extended splice-site region. Critical analysis of 24,445 intronic extended acceptor splice-site variants reported in ClinVar and the Leiden Open Variation Database (LOVD) demonstrates 41.9% of pathogenic variants create an AG dinucleotide between the predicted branchpoint and acceptor (AG-creating variants in the AG exclusion zone), 28.4% result in loss of a pyrimidine at the −3 position, and 15.1% result in loss of one or more pyrimidines in the polypyrimidine tract. Pathogenicity of AG-creating variants was highly influenced by their position. We define a high-risk zone for pathogenicity: > 6 nucleotides downstream of the predicted branchpoint and >5 nucleotides upstream from the acceptor, where 93.1% of pathogenic AG-creating variants arise and where naturally occurring AG dinucleotides are concordantly depleted (5.8% of natural AGs). SpliceAI effectively predicts pathogenicity of AG-creating variants, achieving 95% sensitivity and 69% specificity. We highlight clinical examples showing contrasting mechanisms for mis-splicing arising from AG variants: (1) cryptic acceptor created; (2) splicing silencer created: an introduced AG silences the acceptor, resulting in exon skipping, intron retention, and/or use of an alternative existing cryptic acceptor; and (3) splicing silencer disrupted: loss of a deep intronic AG activates inclusion of a pseudo-exon. In conclusion, we establish AG-creating variants as a common class of pathogenic extended acceptor variant and outline factors conferring critical risk for mis-splicing for AG-creating variants in the AG exclusion zone, between the branchpoint and acceptor.
