Table 2.
Results of in silico analysis
|
In vitro |
No. | Exon | Variant |
In silico (missense) |
In silico |
In silico (splicing) |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Splicing | Nucleotide | Amino acid | SIFT | PolyPhen-2 | Mutation taster | Align GVGD | MaxEntScan |
ESS/ESE (count) |
HSF | EX-SKIP | SD-SCORE | ||||
| WT | Mut | WT | Mut | ||||||||||||
| Aberrant | 2 | 19 | c.1165G>A | Gly389Arg | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C25 (GV: 00.00–GD: 55.27) | 8.76 | 4.44 | 10/23 | 10/23 | Aberrant | Normal | Aberrant |
| 3 | 21 | c.1423G>A | Gly475Ser | D (score: 0.01) | Pro (score: 1.000) | DC (prob: 1) | C65 (GV: 60.00–GD: 97.30) | 5.13 | −3.12 | 2/62 | 2/61 | Aberrant | Normal | Aberrant | |
| 4 | 25 | c.1948G>T | Gly650Cys | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C65 (GV: 0.00–GD: 158.23) | 10.86 | 8.31 | 0/25 | 0/25 | Aberrant | Normal | Aberrant | |
| 5 | c.1948G>A | Gly650Ser | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C55 (GV: 0.00–GD: 55.27) | 10.86 | 10.08 | 0/25 | 0/25 | Aberrant | Normal | Normal | ||
| 6 | 28 | c.2244G>T | Lys748Asn | D (score: 0.04) | Pro (score: 0.999) | DC (prob: 1) | C0 (GV: 109.22–GD: 46.95) | 3.93 | 0 | 13/16 | 13/16 | Aberrant | Normal | Aberrant | |
| 7 | 30 | c.2509G>A | Gly837Ser | D (score: 0) | Pro (score: 0.993) | DC (prob: 1) | C55 (GV: 0.00–GD: 55.27) | 9.45 | 5.2 | 16/13 | 16/11 | Aberrant | Aberrant | Aberrant | |
| 8 | 31 | c.2677G>C | Gly893Arg | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C65 (GV: 0.00–GD: 128.13) | 8.55 | 4.34 | 4/30 | 4/30 | Aberrant | Normal | Aberrant | |
| 9 | c.2677G>A | Gly893Ser | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C55 (GV: 0.00–GD: 55.27) | 8.55 | 3.86 | 4/30 | 4/30 | Aberrant | Normal | Aberrant | ||
| 10 | 32 | c.2767G>C | Gly923Arg | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C65 (GV: 0.00–GD: 125.13) | 8.49 | 2.1 | 8/18 | 8/17 | Aberrant | Aberrant | Aberrant | |
| 12 | 37 | c.3373G>A | Gly1125Arg | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C65 (GV: 0.00–GD: 125.13) | 8.59 | 1.89 | 10/29 | 10/29 | Aberrant | Normal | Aberrant | |
| 13 | 41 | c.3790G>A | Gly1264Arg | Tole (score: 0.15) | Pro (score: 1.000) | DC (prob: 1) | C0 (GV: 170.55–GD: 2.75) | 9.8 | 7.44 | 19/19 | 19/19 | Aberrant | Normal | Aberrant | |
| 14 | 42 | c.3924G>C | Gln1308His | D (score: 0.02) | Pos (score: 0.560) | DC (prob: 1) | C0 (GV: 75.14–GD: 11.15) | 9.79 | 3.74 | 0/55 | 0/55 | Aberrant | Normal | Aberrant | |
| 15 | 43 | c.3997G>A | Gly1333Ser | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C55 (GV: 0.00–GD: 55.27) | 7.51 | 1.24 | 11/14 | 11/14 | Aberrant | Normal | Aberrant | |
| 16 | 44 | c.4069G>C | Gly1357Arg | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C65 (GV: 0.00–GD: 125.13) | 10.77 | 7.45 | 18/21 | 18/21 | Aberrant | Normal | Aberrant | |
| 17 | c.4069G>A | Gly1357Ser | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C55 (GV: 0.00–GD: 55.27) | 10.77 | 7.61 | 18/21 | 18/21 | Aberrant | Normal | Aberrant | ||
| 19 | 48 | c.4688G>A | Arg1563Glu | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C35 (GV: 0.00–GD: 42.81) | 10.48 | 5.2 | 7/12 | 7/12 | Aberrant | Normal | Aberrant | |
| 20 | 50 | c.4976G>A | Ser1659Asn | Tole (score: 0.65) | Pos (score: 0.953) | DC (prob: 1) | C0 (GV: 118.33–GD: 0.00) | 9.65 | 2.69 | 14/19 | 14/19 | Aberrant | Normal | Aberrant | |
| Normal | 1 | 15 | c.891A>T | Arg297Ser | D (score: 0.04) | Pos (score: 0.669) | DC (prob: 1) | C15 (GV: 97.59–GD: 95.93) | 9.35 | 8.46 | 5/31 | 5/29 | Aberrant | Aberrant | Normal |
| 11 | 35 | c.3106G>A | Gly1036Arg | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C65 (GV: 0.00–GD: 125.13) | 10.67 | 9.1 | 22/24 | 22/24 | Aberrant | Normal | Aberrant | |
| 18 | 46 | c.4297G>A | Gly1433Ser | D (score: 0) | Pro (score: 1.000) | DC (prob: 1) | C55 (GV: 0.00–GD: 55.27) | 10.77 | 7.61 | 1/33 | 1/34 | Aberrant | Normal | Aberrant | |
D, deleterious; DC, disease casing; ESS, exonic splicing silencer; ESE, exonic splicing enhancer; HSF, human splicing finder; Mut, mutant; No., number; Prob, probably damaging; Pos, possibly damaging; SD-SCORE, SD-SCORE algorithm; Tole, tolerated; WT, wild type.