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Table 3 Bi-allelic mutations identified in recessive deaf probands

From: Genetic etiology study of the non-syndromic deafness in Chinese Hans by targeted next-generation sequencing

Proband ID

Gene

Type of variation

Nucletide change

Amino acid change

Phylop scorea

Mutation Taster

PROVEAN (score)b

SIFT (score)c

Allele frequency in controls

Novelty

D691

MYO15A

Frame-shift indel

c.6306_6307insG

p.A2104CfsX18

-

DCc

-

-

0

Novel

  

Missense

c.8183G>A

p.R2728H

3.17

DC

DC(−4.66)

DC (0.008)

0

Reported [8]

D768

MYO15A

Splicing site

c.6956+9C>G

-

-

-

-

-

0

Novel

  

In-frame indel

c.10251_10253

p.F3420del

-

DC

DC (−10.02)

-

0

Novel

delCTT

D856

MYO15A

Missense

c.8324G>A

p.R2775H

5.89

DC

DC (−4.56)

DC (0.000)

0

Novel

  

Nonsense

c.8767C>T

p.R2923X

1.323

DC

-

-

0

Novel

D37*

MYO15A

Missense

c.6340G>A

p.V2114M

2.138

DC

DC (−2.70)

DC (0.041)

0

Novel

  

Splicing site

c.6956+9C>G

-

-

-

-

-

0

Novel

D465

MYO15A

Missense

c.3026C>A

p.P1009H

0.29

POd

DC(−2.47)

DC (0.010)

0

Novel

   

c.3026C>A

p.P1009H

      

D475

USH2A

Missense

c.188G>A

p.R63Q

0.422

PO

DC (−1.30)

PO (0.260)

0

Novel

  

Missense

c.8342C>T

p.T2781I

1.606

PO

DC (−3.02)

PO (0.179)

0

Novel

D538

USH2A

Missense

c.5017C>T

p.L1673F

2.504

DC

DC(−2.27)

DC (0.014)

0

Novel

  

Missense

c.7076T>C

p.L2359S

3.941

PO

DC (−3.57)

DC (0.002)

0

Novel

D773*

USH2A

Frame-shift indel

c.1992_1993insT

p.K665X

-

DC

-

-

0

Novel

  

Splicing site

c.9570+1G>A

-

-

-

-

-

0

Novel

D121

PCDH15

Missense

c.1286T>C

p.L429P

4.774

DC

DC (−3.46)

DC (0.019)

0

Novel

   

c.1286T>C

p.L429P

      

D884*

PCDH15

Missense

c.3862T>C

p.S1288P

4.99

DC

DC(−2.33)

DC (0.010)

0

Novel

  

Missense

c.4118C>T

p.T1373I

4.488

DC

DC (−2.99)

DC (0.002)

0

Novel

D349*

PCDH15

Frame-shift indel

1438delT

p.S480RfsX1

-

DC

-

-

0

Novel

  

Missense

c.4118C>T

p.T1373I

4.488

DC

DC (−2.99)

DC (0.002)

0

Novel

C5

GPR98

Frame-shift indel

c.1379delA

p.Q462RfsX36

-

-

-

-

0

Novel

  

Frame-shift indel

c.4878_4879ins

p.A1630IfsX1

-

-

-

-

0

Novel

TTTGCTAATA

D593*

GPR98

Missense

c.6559A>G

p.I2187V

0.679

DC

PO (−0.73)

DC (0.041)

0

Novel

   

c.6559A>G

p.I2187V

      

D29*

GPR98

Missense

c.2399G>A

p.R800Q

5.497

DC

DC(−2.680)

DC (0.000)

0

Novel

  

Frame-shift indel

c.10088_10091

p.V3363DfsX10

-

-

-

-

0

Novel

delTAAG

D472

TMC1

Splicing site

c.236+1G>C

-

-

-

-

-

0

Novel

  

Missense

1334G>A

p.R445H

6.306

DC

DC (−4.97)

DC (0.000)

0

Reported [15]

D419

TMC1

Frame-shift indel

c.150delT

p.N50KfsX25

-

-

-

-

0

Reported [16]

  

Missense

c.1107C>A

p.N369K

2.211

DC

DC (−5.76)

DC (0.001)

0

Novel

D555

TMC1

Missense

c.1209G>C

p.W403C

6.376

DC

DC (−8.97)

DC (0.000)

0

Novel

   

c.1209G>C

p.W403C

      

D433

CDH23

Missense

c.2752G>C

p.D918H

6.036

DC

DC (−5.49)

DC (0.000)

0

Novel

  

Missense

c.6606C>A

p.D2202E

3.482

DC

DC (−2.90)

DC (0.013)

0

Novel

D32*

CDH23

Missense

c.7630T>G

p.L2544V

0.393

DC

PO (−0.54)

PO (0.404)

0

Novel

  

Missense

c.8257G>A

p.A2753T

5.768

DC

DC (−1.40)

DC (0.011)

0

Novel

D111

OTOF

Nonsense

c.4225A>T

p.K1409X

1.376

DC

-

-

0

Novel

  

Splicing site

c.4961-3C>G

-

-

-

-

-

0

Novel

D364

MYO7A

In-frame indel

c.1923_1931del

p.KKP642_644del

>1.783

PO

DC (−25.72)

-

0

Novel

CAAGAAGCC

  

Nonsense

c.6049C>T

p.Q2017X

5.211

DC

-

-

0

Novel

D499

ESRRB

Missense

c.1144C>T

p.R382C

6.124

DC

DC (−3.01)

DC (0.039)

0

Novel

  

Missense

c.1171T>C

p.L424P

4.995

DC

DC (−6.73)

DC (0.002)

0

Novel

D887

MARVELD2

Frame-shift indel

c.1221_1222

p.E408SfsX1

-

DC

-

-

0

Novel

delAG

  

Splicing site

c.1332-2A>G

-

-

-

-

-

0

Novel

D715

TECTA

Nonsense

c.990C>A

p.Y330X

2.723

DC

-

-

0

Novel

   

c.990C>A

p.Y330X

      

C14

WHRN

Missense

c.1292G>A

p.R431Q

4.083

DC

DC (−2.12)

DC (0.010)

0

Novel

  

Missense

c.2542A>G

p.R848G

0.487

DC

DC(−1.99)

DC (0.030)

0

Novel

D386

MYO6

Missense

c.734A>G

p.Y245C

4.416

DC

DC (−8.77)

DC (0.001)

0

Novel

  

Missense

c.1015C>T

p.R339W

1.35

DC

DC (−4.36)

DC (0.003)

0

Novel

D360*

PTPRQ

Missense

c.5786G>C

p.R1929T

2.965

DC

DC (−2.38)

DC (0.023)

0

Novel

  

Nonsense

c.6226C>T

p.Q2076X

5.726

DC

-

-

0

Novel

D366*

POU3F4

Frame-shift indel

c.644_645insG

p.L217VfsX8

-

DC

-

-

0

Novel

   

c.644_645insG

p.L217VfsX8

      
  1. *Multiplex probands with bi-allelic variants also detected in their deaf relatives; aScore ranges from −14 (not conserved) to 6 (conserved); bNegative and positive scores indicated deleterious and neutral function, respectively, with cut-off score set at −1.3; cScore ranges from 0 (deleterious) to 1 (neutral), with cut-off score set at 0.05; cDC: Disease causing; dPO: Polymorphism.
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172