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Table 3 Deafness gene variants and annotation information in this study

From: Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes

Gene symbol

Disease

Reference mRNA

Nucleotide change

Amino acid change

Genomic position (GRCh37)

dbSNP ID

MAF (1000G)

MAF (ESP6500)

MAF (ExAC)

MYO15A

DFNB3

NM_016239.3

c.419del

p.(Lys140SerfsTer304)

NC_000017.10:g.18022533del

rs750130520

0

0

8.38E−06

MYO15A

DFNB3

NM_016239.3

c.1185dup

p.(Glu396ArgfsTer36)

NC_000017.10:g.18023299dup

rs876657707

0

5.04E−04

1.49E−04

MYO15A

DFNB3

NM_016239.3

c.8450G>C

p.(Arg2817Pro)

NC_000017.10:g.18058737G>C

rs761861080

0

0

8.26E−06

MYO15A

DFNB3

NM_016239.3

c.8969del

p.(Gly2990ValfsTer44)

NC_000017.10:g.18061838del

–

0

0

0

MYO15A

DFNB3

NM_016239.3

c.9690+1G>A

p.? (splice mut)

NC_000017.10:g.18066636G>A

–

0

0

0

MYO15A

DFNB3

NM_016239.3

c.9938A>C

p.(His3313Pro)

NC_000017.10:g.18069825A>C

–

0

0

0

CDH23

DFNB12/USH1D

NM_022124.5

c.719C>T

p.(Pro240Leu)

NC_000010.10:g.73330641C>T

rs121908354

0

0

0

CDH23

DFNB12/USH1D

NM_022124.5

c.7802T>C

p.(Val2601Ala)

NC_000010.10:g.73563107T>C

–

0

0

0

CDH23

DFNB12/USH1D

NM_022124.5

c.805C>T

p.(Arg269Trp)

NC_000010.10:g.73337722C>T

rs936479651

0

0

0

PDZD7

DFNB57

NM_001195263.1

c.490C>T

p.(Arg164Trp)

NC_000010.10:g.102783245G>A

rs200664140

0

0

4.94E−05

PDZD7

DFNB57

NM_001195263.1

c.494G>C

p.(Arg165Pro)

NC_000010.10:g.102783241C>G

–

0

0

0

PDZD7

DFNB57

NM_001195263.1

c.503G>C

p.(Arg168Pro)

NC_000010.10:g.102783232C>G

–

0

0

0

OTOF

DFNB9

NM_001287489.2

c.5816G>A

p.(Arg1939Gln)

NC_000002.11:g.26681086C>T

rs201326023

0

0

2.54E−05

OTOG

DFNB18B

NM_001277269.1

c.2116+2_2116+12del

p.? (splice mut)

NC_000011.9:g.17593753_17593763del

–

A

0

0

OTOG

DFNB18B

NM_001277269.1

c.5425C>T

p.(Gln1809Ter)

NC_000011.9:g.17632236C>T

–

0

0

0

PTPN11

NS1

NM_002834.3

c.836A>G

p.(Tyr279Cys)

NC_000012.11:g.112910827A>G

rs121918456

0

0

0

PTPN11

NS1

NM_002834.4

c.1529A>G

p.(Gln510Arg)

NC_000012.11:g.112926909A>G

rs121918470

0

0

8.24E−06

SOX10

WS 2E/4C/PCWH

NM_006941.3

c.570C>A

p.(Cys190Ter)

NC_000022.10:g.38374001G>T

–

0

0

0

SOX10

WS 2E/4C/PCWH

NM_006941.3

c.1122del

p.(Thr375ProfsTer127)

NC_000022.10:g.38369782del

–

0

0

0

EYA1

BOR, BOS

NM_000503.5

c.1082G>A

p.(Arg361Gln)

NC_000008.10:g.72156896C>T

rs145219836

0.001

0

4.12E−05

ZNF335

MCPH10

NM_022095.3

c.1399T>C

p.(Cys467Arg)

NC_000020.10:g.44592246A>G

–

0

0

0

ZNF335

MCPH10

NM_022095.3

c.1505A>G

p.(Tyr502Cys)

NC_000020.10:g.44592140T>C

rs753888773

0

0

8.24E−06

STRC

DFNB16

NM_153700.2

c.(?_-1)_(*1_?)del

–

–

–

–

–

–

MYO6

DFNA22

NM_004999.3

c.1325G>A

p.(Cys442Tyr)

NC_000006.11:g.76566915G>A

rs121912557

0

0

0

Gene symbol

MAF (gnomAD)

MAF (HGVD)

MAF (in house)

REVEL†

CADD‡

UCSC conservation§

Splice site (MaxEntScan)

Splice site (HSF3.1)

ACMG criteria

References (PubMED)

MYO15A

8.40E−06

0

0

–

–

–

–

–

PVS1, PM2_Supporting

4783301

MYO15A

0

0

0

–

–

–

–

–

PVS1, PM2_Supporting, PP1

3534775

MYO15A

4.08E−06

0

0

0.772

26.7

12/12, 41/47, 28/29

–

–

PVS1, PS1, PM2_Supporting, PM5

This study

MYO15A

0

0

0

–

–

–

–

–

PVS1, PM2, PM2_Supporting, PP1

This study

MYO15A

0

0

0

–

32

12/12, 48/48, 28/29

8.59 to 0.41

Affected (− 32.17%)

PVS1, PM2_Supporting

4444116

MYO15A

0

0

0

0.83

27.3

12/12, 49/49, 35/36

–

–

PM2_Supporting, PP3

This study

CDH23

0.00004062

0.002

0.003

0.516

29.5

11/11, 49/49, 36/36

–

–

PM2_Supporting, PP1

17850630, 4451718

CDH23

0

0

0

0.777

26.4

12/12, 47/47, 36/37

–

–

PM2_Supporting, PM3

This study

CDH23

0.000008749

0

0

0.439

27.4

12/12, 49/49, 30/30

–

–

PM2_Supporting, PM3

This study

PDZD7

5.28E−05

0.002

0

0.377

24.1

12/12, 49/49, 37/37

–

–

PM2_Supporting, PP1

31454969

PDZD7

0.000004064

0

0

0.622

29.4

12/12, 49/49, 37/37

–

–

PM2_Supporting, PM3

This study

PDZD7

0

0

0

0.123

25.1

12/12, 49/49,17/38

–

–

PM2_Supporting, PM3

This study

OTOF

3.38E−05

0.002

0

0.86

20.9

11/11, 37/48, 31/34

–

–

PM2_Supporting, PP1, PP3

1735255, 22575033

OTOG

0

0

0

.

.

–

10.90 to − 9.39

Affected (− 52.79%)

PVS1, PM2_Supporting

This study

OTOG

0

0

0

.

40

–

–

–

PVS1, PM2_Supporting

This study

PTPN11

0

0

0

0.973

31

12/12, 49/49, 32/32

–

–

PS1, PS2, PM2_Supporting, PP4

11992261

PTPN11

4.06E−06

0

0

0.959

28

12/12, 49/49, 37/37

–

–

PS1, PS2, PM1, PM2_Supporting, PM5, PP1, PP3, PP5

15948193

SOX10

0

0

0

0.211

28.4

–

–

–

PVS1, PS2, PM2_Supporting, PP4

This study

SOX10

0

0

0

.

.

–

–

–

PVS1, PS2, PM2_Supporting, PP4

This study

EYA1

4.08E−05

0

0

0.642

24

12/12, 48/48, 38/38

–

–

PM1, PM2_Supporting, PP1

This study

ZNF335

0

0

0

0.808

29

–

–

–

PM2_Supporting

27540107

ZNF335

8.14E−06

0

0

0.466

29.1

–

–

–

PM2_Supporting

27540107

STRC

–

–

–

–

–

–

–

–

PVS1

26011646, 27469136

MYO6

0

0

0

0.959

29.8

12/12, 50/50, 36/36

–

–

PS1, PS2, PM2_Supporting, PP3

1235492

  1. †Rare exome variant ensemble learner
  2. ‡Combined annotation dependent depletion (v1.4)
  3. §Identity of amino acid residues (nucleotide in case of splice site variant) in up to 12 primate, 50 mammalian, and 38 vertebrate species