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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]