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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]
  1. aEvolutionary conservation in up to 12 primates, 50 mammals, and 38 vertebrates
  2. bNNsplice score, 0.95. ZA, zonadhesin-like domain; TIL, three trypsin inhibitor-like repeat; vWFD, von Willebrand factor type D repeat; ZP, zona pellucida domain