Table 3 Details of final candidates from eleven deaf subjects molecular genetically diagnosed and three subjects with only one mutant allele of recessive genes after targeted exome sequencing of 204 deafness genes
A) Highly probable cases (n=9) | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Patient | Gene | Inheritance | DP | GQ | Type | Chr | Genbank No. | Exon | Nucleotide | Protein | GERP++ | PolyPhen2 | Reference | Control |
SHJ4 | CDH23 | Homo (AR) | 218 | 99 | nonsynonymous SNV | Chr10 | NM_022124 | Exon8 | c.C719T* | p.P240L* | 5.19 | Probably damaging | rs1219083 (flagged)* | Â |
SHJ23 | MYO7A | Compound hetero (AR) | 82 | 99 | Stopgain SNV | Chr11 | NM_000260 | Exon 3 | c.C52T | p.Q18X | 3.91 | NA | This study | Â |
178 | 99 | Stopgain SNV | Chr11 | NM_000260 | Exon 18 | c.C2115A | p.C705X | 3.03 | NA | This study | Â | |||
SNUH59-133 (SHJ33) | CDH23 | Compound hetero (AR) | 238 | 99 | nonsynonymous SNV | Chr10 | NM_022124 | Exon 8 | c.C719T* | p.P240L* | 5.19 | Probably damaging | rs1219083 (flagged)* | Â |
29 | 99 | nonsynonymous SNV | Chr10 | NM_022124 | Exon 37 | c.C4853A | p.T1618K | 5.9 | Probably damaging | This study | 0/276 | |||
SH62-147 (SHJ41) | CDH23 | Compound hetero (AR) | 178 | 99 | nonsynonymous SNV | Chr10 | NM_022124 | exon42 | c.G5747A | p.R1916H | 4.28 | Probably damaging | This study | 0/276 |
237 | 99 | nonsynonymous SNV | Chr10 | NM_022124 | exon46 | c.G6604A§ | p.D2202N§ | 5.06 | Probably damaging | rs121908349 (flagged) |  | |||
SNUH72-164 (SHJ52) | PCDH15 | Compound hetero (AR) | 238 | 99 | nonsynonymous SNV | Chr10 | NM_001142769 | exon36 | c.5035G > C | p.V1679L | 3.48 | Damaging*** | This study | 0/276 |
250 | 99 | Frameshift deletion | Chr10 | NM_001142763 | exon23 | c.2927delA | p.Gln976Argfs*18 | N/A | NA | This study | Â | |||
SNUH91-202 (SHJ70) | MYO15A | Compound hetero (AR) | 76 | 99 | Stopgain SNV | Chr17 | NM_016239 | exon2 | c.G535T | p.E179X | 5.48 | NA | This study | Â |
147 | 99 | nonsynonymous SNV | Chr17 | NM_016239 | exon10 | c.G4252A | p.G1418R | 5.31 | Probably damaging | This study | 0/276 | |||
SNUBH71-123 | MYO15A | Compound hetero (AR) | 101 | 99 | Splice donor variant | Chr17 | NM_016239 | exon10 | c.4320 + 1G > A | Â | 5.84 | NA | This study | Â |
70 | 99 | nonsynonymous SNV | Chr17 | NM_016239 | exon46 | c.T8396A | p.L2799H | 5.58 | Probably damaging | This study | 0/276 | |||
SNUBH47-91** | MYO3A | Compound hetero (AR) | 100 | 99 | nonsynonymous | Chr10 | NM_017433 | exon7 | c.C580A | p.P194T | 4.30 | Probably damaging | [20] | Â |
77 | 99 | Frameshift insetion | Chr10 | NM_017433 | exon16 | c.1582_1583 insT | p.Y530Lfs*9 | N/A | N/A | [20] | Â | |||
SNUH3-7** | ACTG1 | Singe hetero(AD) | 30 | 99 | nonsynonymous | Chr17 | NM_001199954 | exon5 | c.T914C | p.M305T | 4.05 | Probably damaging | [36] | Â |
B) Possibly explained cases (n=2) | ||||||||||||||
SNUH10-28 | MYO7A | Compound hetero (AR) | 7 | 95 | nonsynonymous SNV | Chr11 | NM_000260 | exon23 | c.C2724G | p.D908E | -8.53 | Benign | This study | 0/276 |
| Â | Â | Â | 10 | 85 | nonsynonymous SNV | Chr11 | NM_000260 | exon29 | c.C3701G | p.T1234S | 5.38 | Possibly damaging | This study | 0/276 |
SHJ37 | USH2A | Compound hetero (AR) | 238 | 99 | nonsynonymous SNV | Chr1 | NM_206933 | exon64 | c.T14017C | p.Y4673H | 5.09 | Probably damaging | This study | 0/276 |
237 | 99 | nonsynonymous SNV | Chr1 | NM_206933 | exon2 | c.C419A | p.P140H | 2.26 | Benign | This study | 0/276 | |||
C) Cases with only one probably pathogenic recessive allele (n=3) | ||||||||||||||
SHJ3 | OTOA | AR | 250 | 99 | Frameshift | Chr16 | NM_170664, NM_001161683, NM_144672 | exon7, exon12, exon16 | c.792delC, c.1527delC, c.1764delC | p.Gln589Argfs*55 | NA | NA | This study | Â |
SHJ16 | MYO15A | AR | 72 | 99 | Splice site | Chr17 | NM_016239 | exon4 | c.3756+1G>A | NA | 4.19 | NA | [37] | Â |
SNUH53-118 | MYO7A | AR | 185 | 99 | Stopgain | Chr11 | NM_000260 | exon19 | c.C2254T | p.Q752X | 5.03 | NA | This study | Â |