Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites

Generation of tandem alternative splice acceptor sites and CLTC haploinsufficiency: A cause of CLTC‐related disorder

“…SSF and SpliceAI also predicted a splice acceptor gain at NM_004859.4:c.3766-27, whereas MaxEntScan and NNSPLICE predicted a splice acceptor gain at NM_004859.4:c.3766-20 (Figure 1b and Figure S1A). We hypothesized that the deletion of the polypyrimidine (ATGTTTATT) decreases preference for the exon 24 natural splice site acceptor since an alternative intronic polypyrimidine tract is more distant and AG dinucleotides intervene (Chern et al, 2006;Hiller & Platzer, 2008;Hujova et al, 2021;Smith et al, 1993). size or abundance in the propositus and his parents (Figure 1c, Table S2).…”

“…Given that potential splice acceptors closer to a polypyrimidine tract are used preferentially to those more distant (Hiller & Platzer, 2008; Hujova et al, 2021), we hypothesized that CLTC intronic deletions that do not place AG dinucleotides closer to the polypyrimidine tract than the natural splice acceptor are not pathogenic. This hypothesis is supported by the finding that one such deletion (NM_004859.4:c.1168‐38_1168‐4del) has a frequency of 0.02% among Africans and non‐Finnish Europeans in the gnomAD database (rs1221461094, Figure 1f).…”

“…Alternative splicing in which the generation of multiple diverse transcripts that are often differentially expressed and of varied stability is possible from a single gene via competition among tandem splice acceptor sites (Riepe et al, 2021). Numerous factors define this competition including the sequence of the splice region, the donor and acceptor sequences, and the branchpoint (BP) sequence and its distance from the splice site (Hujova et al, 2021). Current understanding predicts that cryptic intronic AGs are used preferentially to a distal natural splice acceptor if more proximate to the polypyrimidine tract and alternative BP.…”

“…Altering the proximity of splice acceptors to a polypyrimidine tract has been studied experimentally but is often not considered when assessing variants for clinical reporting (Chern et al, 2006; Hiller & Platzer, 2008; Hujova et al, 2021; Smith et al, 1993). Alternative splicing in which the generation of multiple diverse transcripts that are often differentially expressed and of varied stability is possible from a single gene via competition among tandem splice acceptor sites (Riepe et al, 2021).…”

Can tandem alternative splicing and evasion of premature termination codon surveillance contribute to attenuated Peutz–Jeghers syndrome?

“…The impact of variants creating an AG gain depends on splice site competition. Splice site competition is defined by the splice site region sequence itself, by constitutive splicing factors, by the distance between the splice site and branchpoint (BP) sequence, and by the donor and acceptor splice site sequences (Hujova et al, 2021). Given this understanding of tandem (NAGN n AG) splice acceptors, the AG gain reported herein and by Terkelsen et al are predicted to be used preferentially to the distal natural splice acceptor; this is based on the presence of an adenine in the +3 position of the STK11 exon 5 splice donor, an adenine in the À3 position of the STK11 exon 6 splice acceptor, and proximity of the variant AGs to the BP.…”