Fig. 9

Interpretation of the three c.55 SNVs and the c.11C > G variant in exon 1 by reference to SpliceAI predictions and FLGSA results. a Illustration of the (partial) disruption of the physiological 5’ splice donor site of SPINK1 intron 1 caused by the three potential SNVs at the last nucleotide of exon 1 (c.55). This disruption is shown in the context of the corresponding 9-bp 5’ splice signal sequence, which interacts with the 3’-GUCCAUUCA-5’ sequence at the 5’ end of U1snRNA. SpliceAI predicted this disruption (DL scores, 0.34 to 0.51) and the activation of an upstream cryptic splice donor site within exon 1 (DG scores, 0.33 and 0.37). However, our FLGSA assay revealed the activation of a downstream cryptic splice donor site. Vertical lines indicate paired bases between the 9-bp 5’ splice signal sequence and the 5’ end sequence of U1snRNA. The GT dinucleotides involved are highlighted in blue, with their positions (in accordance with NM_001379610.1) indicated. The 9-bp 5' splice site signal sequence position weight matrices (PWM) were sourced from Leman et al. [52], an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. Note that the 9-bp 5’ splice signal sequences, whether in the context of the consensus sequence or SPINK1 sequences, are presented in DNA. b Illustration of the c.11C > G variant in the context of the aforementioned upstream cryptic splice donor site. A dotted line represents the new base pairing derived from the variant, enhancing the interaction between the 9-bp 5’ splice signal sequence and the 5’ end sequence of U1snRNA