Table 1 Pathogenic or possibly pathogenic variants and variants of uncertain significance in TECTA identified in this study
From: Prevalence of TECTA mutation in patients with mid-frequency sensorineural hearing loss
|
Type of variant | Location | Amino acid change | Nucleotide change | Genomic Position(Chr11) | Domain | Evolutionary Conservationa | Allele frequency |
PolyPhen2 (Hum Var) score | PROVEAN score | Family | Reference | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1000 Genome |
ESP 6500 | ExAC | HGVD | iJGVD | |||||||||||
| Pathogenic Variants | |||||||||||||||
| Missense | Exon 18 | p.R1890C | c.5668C > T | 121038844 | ZP | 12/12, 50/50, 22/36 | 0 | 0 | 0 | 0 | 0 |
Probably damaging (0.963) |
Neutral (−1.914) | 4 | [4, 16] |
| Nonsense | Exon 8 | p.C633* | c.1899C > A | 120998585 |
ZA (TIL1) | 11/12, 47/47, 36/37 | 0 | 0 | 0 | 0 | 0 | – | – | 5 | [39] |
| Splice site | IVS1 | – | c.65-3C > T b | 120976537 | – | 12/12, 50/50, 28/33 | 0 | 0 | 0 | 0 | 0 | – | – | 5 | [39] |
| Possibly Pathogenic Variants | |||||||||||||||
| Missense | Exon 18 | p.Y1900C | c.5699A > G | 121038875 | ZP | 12/12, 50/50, 36/36 | 0 | 0 | 0 | 0 | 0 |
Probably damaging (0.999) |
Deleterious (−6.77) | 6 | this study |
| Exon 20 | p.S2017P | c.6049 T > C | 121058590 | ZP | 12/12, 49/49, 36/36 | 0 | 0 | 0 | 0 | 0 |
Probably damaging (0.998) |
Neutral (−1.781) | 7 | this study | |
| Variants of Uncertain Significance | |||||||||||||||
| Missense | Exon 9 | p.L940I | c.2818C > A | 121000797 |
ZA (vWFD2-TIL2) | 11/12, 49/49, 35/36 | 0 | 0 | 0 | 0 | 0 |
Probably damaging (0.998) |
Neutral (0.642) | 8 | this study |
| Exon 10 | p.R1033Q | c.3098G > A | 121008286 |
ZA (TIL2) | 12/12, 49/50, 31/37 | 0 | 0 | 0.00002 | 0 | 0 |
Possibly damaging (0.704) |
Neutral (−0.386) | 9 | this study | |
| Exon 13 | p.L1439I | c.4315C > A | 121028559 |
ZA (TIL3-vWFD4) | 12/12, 49/49, 34/35 | 0.001 | 0 | 0.00078 | 0.008 | 0 |
Probably damaging (0.998) |
Neutral (−0.408) | 1, 2 | [6] | |
| Exon 14 | p.V1646 M | c.4936G > A | 121031090 |
ZA (vWFD4) | 12/12, 48/49, 18/37 | 0 | 0 | 0 | 0.002 | 0 | Benign (0.365) |
Neutral (−0.207) | 10 | this study | |
| Exon 16 | p.P1791R | c.5372C > G | 121036081 |
ZA (vWFD4-ZP) | 12/12, 49/49, 20/34 | 0 | 0 | 0.00019 | 0 | 0 |
Benign (0.051) |
Neutral (0.259) | 3 | [4] | |