Table 1

 Mutation analysis results on the NF1 gene with in silico analysis of the sequence variations found for splice site strength and presence of ESE

Canonical splice sites (AG-GT nucleotides)Within the consensus splice site sequence
MutationSS scoreExonMutationSS score
7889−1 G→C0.64–<0.40261–12 delT1–1
7899−2 A→G0.64–<0.403288+5 G→C1–0.83
10b1527+1 G→C0.98–<0.4010c1642–3 C→G0.99–0.46
111642–2 A→G<0.40–<0.40111642–3 C→G<0.40–<0.40
12a1722 C→A<0.40–<0.40172857–16 T→A0.99–0.98
172857–2 A→G0.99–<0.40183113+3 ins A0.99–<0.40
244112–2 A→G0..99–<0.40315941C→T0.58–0.77
325944–1 G→C0.78–<0.40457907+5 G→A0.96–<0.40
11–22 G→C
7899–31 del5
111642–25 T→C
326084+8 C→G0.99–0.98
397126+37 G→C
427395–29 G→A
468050+20 G→A
ExonMutationAmino acidESEfinderRESCUE-ESE3′SS5′SS
Same sense
2168 C→TS56S↓SRp5510.99
5703 G→AL234L0.990.99
6846 G→AQ283Q↓SF2/ASFHexamer0.551
223867 C→TF1289F↓SRp40 ↓SC350.990.92
285172 G→AL1724F↓SRp40 ­SF2/ASF↓ Hexamer10.98
147 G→CR16P↑SC35<0.400.91
292 A→GH31R↓SRp5510.99
3269 T→GL90R↓SC35↓ Hexamer0.791
4a434 T→CL145P↑SRp40 ↑­SC350.81<0.40
4b526 G→AD176N↑SRp5511
4b528 T→AD176EHexamer11
81098 A→TR366S↓ Hexamer0.68<0.40
10b1466 A→GY489C↓SRp40↓ Hexamer0.980.86
10c1595 T→CP533L↓SRp40 ↑­SF2/ASF↓ Hexamer0.990.90.999
111658 A→GH553R↓ Hexamer × 3<0.400.79
111700 T→GV567G↓SRp55 ↑­SRp40Hexamer × 2<0.400.79
12b1885 G→AG629R↓SRp55 ↑­SF2/ASF<0.40<0.40
162530 C→TL844F0.460.92
162531 T→CL844P0.460.92
213610 C→GR1204↑SF2/ASF ↑­SC350.90.99
3269 T→GL90R↑SRp40,SF2/ASF↓SC35↓ Hexamer × 20.791
4b571 C→TR192X↓SRp40↓ Hexamer11
5670 del GV224X0.990.99
10a1274 G→AW425X↑SRp400.980.99
10a1318 C→TR440X↑SC35↓ Hexamer × 20.980.99
132041 C→TR681X0.720.99
19a3163 C→TQ1055X↓SRp40 ­SRp55↓ Hexamer × 20.99<0.40
223916 C→TR1306XHexamer
23.24084 C→TR1362X↑SRp40↓ Hexamer10.98
23.24103 T→AL1368X↑SRp4010.98
27a4537 C→TR1513X↓SF2/ASF0.490.53
376792 C→G*Y2264XHexamer<0.400.99
427486 C→TR2496X↓SC350.980.73
498428 A→TK2810X↑SC351<0.40
The table is broken down into the classical mutation categories. Splice site strength (SS score) was evaluated using the web tool found at and is reported in the table for the wildtype and mutated nucleotides, respectively. Where the splice site strength was below the threshold suggested by the program (<0.40) this is reported as <0.40. The presence of ESE was searched for using both ESEfinder and ESE-RESCUE. The creation or destruction of a site is highlighted by an up or down arrow, respectively. SS, splice site. The consensus is taken as bp within the area analysed by
512 bp from intron then first 7 bp of exon 5Destroy 3′ splice siteNDND0.990.99
6787–789 del253 Val 253 del, in frame deletion­ Hexamer0.551
7993 35 bp delOccurs in exon↓ 2SRp40 ↓ SC35↓ 2SRp55↓× 4 Hexamer0.640.93
132148 del AStop codon created downstream↓× 3 Hexamer0.720.99
162508 del AStop codon created downstream↓ Hexamer0.460.925
17Del 2970–2972 AATIn frame deletion of 991M↓ Hexamer0.991
37Del 6789 -TTACStop codon created downstream.
 >Known not to cause skipping<0.401
376791 ins AStop codon created downstream.<0.401
457887 del TStop codon created downstream↑SC350.520.96