Table 1.
Probable pathogenic and uncertain pathogenic variants of OTOF identified in this study
|
Exon |
DNA level |
Protein level |
Occurrence in this work (chromosome) |
Control (chromosome) |
Functional prediction |
References |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| PhyloP | SIFT (p-value) | P2 D.S. | LRT | Mutation taster | GERP ++ | ||||||
| Probable pathogenic variants |
|
|
|
|
|
|
|
|
|
||
| Exon 14 |
c.1422T>A |
p.Y474X |
2/320 |
0/374 |
N (0.072941) |
NA (0.829813) |
NA (0.58309) |
D (1) |
A (1) |
−3.78 |
[13] |
| Exon 18 |
c.2151G>A |
p.W717X |
1/320 |
0/344 |
C (0.994764) |
NA (0.90345) |
NA (0.734698) |
D (0.999998) |
A (1) |
3.83 |
This study |
| Exon 34 |
c.4103C>G |
p.S1368X |
1/320 |
0/364 |
N (0.944413) |
NA (0.915) |
NA (0.554899) |
NA (0.026679) |
A (1) |
0.571 |
This study |
| Exon 38 |
c.4748G>A |
p.R1583H |
1/320 |
0/366 |
C (0.997935) |
D (1) |
D (0.999) |
D (1) |
D (0.999661) |
4.69 |
This study |
| Exon 44 |
c.5567G>A |
p.R1856Q |
1/320 |
0/380 |
C (0.99611) |
T (0.91) |
P (0.813) |
D (1) |
D (0.999517) |
4.1 |
[11] |
| Exon 46 |
c.5816G>A |
p.R1939Q |
11/320 |
0/382 |
N (0.996658) |
T (0.92) |
NA (0.746672) |
NA (1) |
D (0.999886) |
1.38 |
[22] |
| Uncertain pathogenic variants |
|
|
|
|
|
|
|
|
|
||
| Exon 12 |
c.1194T>A |
p.D398E* |
1/320 |
1/380 |
N (0.232793) |
T (0.77) |
D (0.853) |
D (1) |
D (0.995165) |
0.981 |
[23] |
| Exon 13 |
c.1350C>G |
p.D450E* |
1/320 |
1/380 |
C (0.986229) |
T (0.74) |
D (0.853) |
D (1) |
D (0.991594) |
3.54 |
This study |
| Exon 18 |
c.2180A>G |
p.N727S* |
2/320 |
1/344 |
C (0.992986) |
T (0.27) |
P (0.386) |
D (1) |
D (0.95528) |
3.98 |
[21] |
| Exon 43 |
c.5332G>A |
p.V1778I |
1/320 |
0/378 |
C (0.997116) |
T (0.54) |
P (0.289) |
D (1) |
D (0.994783) |
4.38 |
This study |
| Exon 43 | c.5408A>C | p.E1803A | 1/320 | 0/378 | C (0.994555) | D (1) | D (0.995) | D (1) | D (0.999914) | 4.26 | This study |
*the variants found in controls.
Exon number was named based on ENST00000403946.
A, disease causing automatic; C, conserved; D, damaging or disease causing; N, not conserved; NA, not applicable; P, possibly damaging; T, tolerated; P2 D.S., Polyphen-2 damaging score. Polyphen-2, PhyloP, LRT, Mutation Taster, and GERP++ are functional prediction scores that indicate a probable mutation with increasing value.