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Table 3 Results of resequencing chosen variants

From: Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes

Gene

Caller

WES Predicted variant

Predicted

Confirmed variant

Patients with variant

Variant ID

MAF

Consequence

MAF

 

Heterozygote

Homozygote

NEDD4

Samtools

g.15:56208463A > C

0.0356

g.15:56208463A > C

1D 3S

 

rs113176671

0.038

Missense

NEDD4

Samtools

g.15:56208933 T > C

0.0992

g.15:56208933 T > C

3D 1S

 

rs1912403

0.108

Missense

ZAN

Dindel

g.7:100385563delC

g.7:100385563_100385597del

 

3D

rs369526619

0.456a

Frameshift deletion

ZAN

Samtools

g.7:100371417G > A

0.0451

g.7:100371417G > A

1 M 1R

 

rs12673041

0.032

Missense

ZAN

Dindel

g.7:100353014_100353016del

0.0548

g.7:100353019_100353021del

2R

 

rs377643276

Inframe deletion

ZAN

Samtools

g.7:100346094G > A

0.0476

g.7:100346094G > A

1D

 

rs117406702

0.032

Essential splice site

ZAN

Samtools

g.7:100389590C > T

0.0803

g.7:100389590C > T

1S

 

rs76325149

0.085

Missense, splice site

DNAH2

Samtools

g.17:7736480 T > A

0.0095

g.17:7736480 T > A

1D 1R

 

rs78354379

0.008

Missense

GPR98

Samtools

g.5:89925039A > C

0.0035

g.5:89925039A > C

2D

 

rs61744480

0.002

Missense

GPR98

Samtools

g.5:90106415 T > G

0.000015

g.5:90106415 T > G

1R

 

Missense

NEFH

Dindel

g.22:29885564_29885564insG

g.22:29885568_29885585dup

1R 1S

3D 2R 1S

rs147489453

0.577

Inframe duplication

NEFH

Samtools

g.22:29885016G > A

0.0971

g.22:29885016G > A

2D 1R

1D

rs59371099

0.1

Missense

WFS1

Samtools

g.4:6290798G > A

0.0004

g.4:6290798G > A

1D

 

rs147724970

0.0002

Missense

WFS1

Samtools

g.4:6296783C > T

0.0002

g.4:6296783C > T

1D

 

rs147147660

0.00013

Missense

WFS1

Samtools

g.4:6302459C > T

g.4:6302459C > T

1D

 

rs886044563

Missense

WFS1

Samtools

g.4:6302888C > T

0.000015

g.4:6302888C > T

1D

 

Missense

WFS1

Samtools

g.4:6303119C > T

0.0012

g.4:6303119C > T

1D

 

rs146132083

0.001

Missense

GRM7

Dindel

g.3:7494306delT

g.3:7494272_7494273del

1 M

 

Frameshift deletion

SIK3

Samtools

g.11:116728913G > A

0.0002

g.11:116728913G > A

1 M

 

rs61738656

0.0002

Missense

MON1B

Dindel

g.16:77228709_77228710insG

Failed

n/a

n/a

   

ADC

Dindel

g.1:33583668_33583669insG

0.0005

Failed

n/a

n/a

   

ADC

Dindel

g.1:33583674_33583675insC

3.24E-05

Failed

n/a

n/a

   

PAX2

Dindel

g.10:102587323dupC

4.58E-05

Failed

n/a

n/a

   

PAX2

Dindel

g.10:102587329dupG

Failed

n/a

n/a

   

PAX2

Dindel

g.10:102587333dupC

Failed

n/a

n/a

   

SIRPA

Dindel

g.20:1895964_1895965del

Failed

n/a

n/a

   

LRBA

Samtools

g.4:151727540C > A

0.0028

Failed

n/a

n/a

   

LRBA

Samtools

g.4:151837565G > T

0.0011

Failed

n/a

n/a

   

RBPJ

Samtools

g.4:26426018C > G

0

Failed

n/a

n/a

   
  1. Details of variant validation. The number of heterozygous and homozygous patients with each variation is annotated with the subgroups to which each belonged, where “D” stands for the 10 patients with dominantly inherited hearing loss, “R” for the 10 patients with recessive hearing loss, “M” for the 5 patients with a metabolic phenotype and “S” for the 5 patients with a sensory phenotype. Predicted variant MAF is from the 1000 Genomes data [24]; confirmed variant MAF is from gnomAD genome data [20], except for a, which is from the NHLBI GO Exome Sequencing Project [70]