Table 1 FLGSA data and Illumina precomputed SpliceAI Δ scores for 27 known and 35 newly selected potential SPINK1 coding SNVs
Exon | Varianta | Illumina precomputed SpliceAI scoresb | Generation of aberrantly spliced transcripts as determined by FLGSAc | Study | ||||
|---|---|---|---|---|---|---|---|---|
Nucleotide change | Amino acid change | AG | AL | DG | DL | |||
1 | c.9A > C | p.Val3Val | 0.00 | 0.00 | 0.04 | 0.55 (3 bp)d | No | This study |
1 | c.9A > G | p.Val3Val | 0.00 | 0.00 | 0.04 | 0.54 (3 bp)d | No | This study |
1 | c.9A > T | p.Val3Val | 0.00 | 0.00 | 0.04 | 0.55 (3 bp)d | No | This study |
1 | c.11C > G | p.Thr4Arg | 0.00 | 0.00 | 0.44 (5 bp) | 0.45 (-44 bp) | No | This study |
1 | c.15C > T | p.Gly5Gly | 0.00 | 0.00 | 0.52 (2 bp) | 0.13 (-40 bp) | No | This study |
1 | c.26 T > G | p.Leu9Arg | 0.00 | 0.00 | 0.03 | 0.29 (20 bp)d | No | [38] |
1 | c.29G > A | p.Ser10Asn | 0.00 | 0.00 | 0.11 (23 bp) | 0.03 | No | [38] |
1 | c.36G > C | p.Leu12Phe | 0.00 | 0.00 | 0.02 | 0.10 (30 bp)d | No | [38] |
1 | c.41 T > C | p.Leu14Pro | 0.00 | 0.00 | 0.01 | 0.04 | No | [38] |
1 | c.41 T > G | p.Leu14Arg | 0.00 | 0.00 | 0.02 | 0.09 (35 bp)d | No | [38] |
1 | c.43 T > A | p.Leu15Met | 0.00 | 0.00 | 0.02 | 0.12 (37 bp)d | No | This study |
1 | c.43 T > C | p.Leu15 = | 0.00 | 0.00 | 0.03 | 0.14 (37 bp)d | No | This study |
1 | c.43 T > G | p.Leu15Val | 0.00 | 0.00 | 0.38 (1 bp) | 0.00 | No | This study |
1 | c.55G > A | p.Gly19Ser | 0.00 | 0.00 | 0.36 (49 bp) | 0.40 (0 bp) | Yes (Intron 1 retentione/normally spliced: 1/9.03) | This study |
1 | c.55G > C | p.Gly19Arg | 0.00 | 0.00 | 0.33 (49 bp) | 0.34 (0 bp) | Yes (Intron 1 retentione/normally spliced: 1/21.72) | This study |
1 | c.55G > T | p.Gly19Cys | 0.00 | 0.00 | 0.37 (49 bp) | 0.51 (0 bp) | Yes (Intron 1 retentione/normally spliced: 1/9.38) | This study |
2 | c.56G > A | p.Gly19Asp | 0.01 | 0.10 (0 bp) | 0.00 | 0.07 | No | This study |
2 | c.56G > C | p.Gly19Ala | 0.01 | 0.40 (0 bp) | 0.00 | 0.29 (−31 bp) | Yes (E2 skipping/normally spliced: 1/1.32) | This study |
2 | c.56G > T | p.Gly19Val | 0.01 | 0.61 (0 bp) | 0.00 | 0.46 (−31 bp) | Yes (E2 skipping/normally spliced: 2.97/1) | This study |
2 | c.65G > T | p.Gly22Val | 0.00 | 0.31 (9 bp) | 0.00 | 0.17 (−22 bp) | Yes (E2 skipping/normally spliced: 1/5.16) | This study |
2 | c.75C > T | p.Ser25 = | 0.00 | 0.02 | 0.00 | 0.02 | No | [38] |
2 | c.80G > T | p.Gly27Val | 0.00 | 0.09 | 0.61 (2 bp) | 0.10 (−7 bp) | No | This study |
2 | c.84A > C | p.Arg28Ser | 0.00 | 0.01 | 0.00 | 0.00 | No | This study |
2 | c.84A > G | p.Arg28 = | 0.00 | 0.49 (28 bp) | 0.00 | 0.25 (−3 bp) | Yes (E2 skipping/normally spliced: 10.80/1) | This study |
2 | c.84A > T | p.Arg28Ser | 0.00 | 0.04 | 0.01 | 0.02 | No | This study |
2 | c.85G > T | p.Glu29* | 0.00 | 0.25 (29 bp) | 0.00 | 0.17 (−2 bp) | No | This study |
2 | c.86A > C | p.Glu29Ala | 0.00 | 0.51 (30 bp) | 0.01 | 0.23 (−1 bp) | No | This study |
2 | c.86A > G | p.Glu29Gly | 0.00 | 0.84 (30 bp) | 0.00 | 0.67 (−1 bp) | Yes (E2 skipping/normally spliced: 4.13/1) | This study |
2 | c.86A > T | p.Glu29Val | 0.00 | 0.81 (30 bp) | 0.00 | 0.58 (−1 bp) | Yes (E2 skipping/normally spliced: 1/5.31) | This study |
2 | c.87G > A | p.Glu29 = | 0.00 | 0.87 (31 bp) | 0.00 | 0.92 (0 bp) | Yes (Complete E2 skipping) | This study |
2 | c.87G > C | p.Glu29Asp | 0.00 | 0.84 (31 bp) | 0.01 | 0.93 (0 bp) | Yes (Complete E2 skipping) | This study |
2 | c.87G > T | p.Glu29Asp | 0.00 | 0.88 (31 bp) | 0.00 | 0.93 (0 bp) | Yes (Complete E2 skipping) | This study |
3 | c.88G > A | p.Ala30Thr | 0.00 | 0.00 | 0.00 | 0.00 | No | This study |
3 | c.88G > C | p.Ala30Pro | 0.00 | 0.00 | 0.00 | 0.00 | No | This study |
3 | c.88G > T | p.Ala30Ser | 0.00 | 0.01 | 0.00 | 0.00 | No | This study |
3 | c.101A > G | p.Asn34Ser | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.110A > G | p.Asn37Ser | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.123G > C | p.Lys41Asn | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.126A > G | p.Ile42Met | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.133C > T | p.Pro45Ser | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.137 T > A | p.Val46Asp | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.143G > A | p.Gly48Glu | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.150 T > G | p.Asp50Glu | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.160 T > C | p.Tyr54His | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.163C > T | p.Pro55Ser | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.174C > T | p.Cys58 = | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.178 T > G | p.Leu60Val | 0.00 | 0.00 | 0.26 (1 bp) | 0.00 | No | This study |
3 | c.190A > G | p.Asn64Asp | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.193C > T | p.Arg65Trp | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
3 | c.194G > A | p.Arg65Gln | 0.00 | 0.00 | 0.00 | 0.00 | No | [8] |
3 | c.194G > C | p.Arg65Pro | 0.00 | 0.00 | 0.00 | 0.00 | No | This study |
3 | c.194G > T | p.Arg65Leu | 0.00 | 0.00 | 0.00 | 0.00 | No | This study |
4 | c.195G > A | p.Arg65 = | 0.00 | 0.03 | 0.00 | 0.00 | No | This study |
4 | c.195G > C | p.Arg65 = | 0.00 | 0.10 (0 bp) | 0.00 | 0.00 | No | This study |
4 | c.195G > T | p.Arg65 = | 0.00 | 0.23 (0 bp) | 0.00 | 0.00 | No | This study |
4 | c.198A > C | p.Lys66Asn | 0.01 | 0.00 | 0.00 | 0.00 | No | [38] |
4 | c.199C > T | p.Arg67Cys | 0.00 | 0.01 | 0.00 | 0.00 | No | [38] |
4 | c.200G > A | p.Arg67His | 0.00 | 0.00 | 0.00 | 0.00 | No | [38] |
4 | c.203A > G | p.Gln68Arg | 0.01 | 0.00 | 0.00 | 0.00 | No | [38] |
4 | c.206C > T | p.Thr69Ile | 0.00 | 0.01 | 0.00 | 0.00 | No | [38] |
4 | c.231G > A | p.Gly77 = | 0.01 | 0.00 | 0.00 | 0.00 | No | [38] |
4 | c.236G > T | p.Cys79Phe | 0.00 | 0.02 | 0.00 | 0.00 | No | [38] |