| Literature DB >> 24164807 |
Hideki Mutai, Naohiro Suzuki, Atsushi Shimizu, Chiharu Torii, Kazunori Namba, Noriko Morimoto, Jun Kudoh, Kimitaka Kaga, Kenjiro Kosaki, Tatsuo Matsunaga1.
Abstract
BACKGROUND: Genetic tests for hereditary hearing loss inform clinical management of patients and can provide the first step in the development of therapeutics. However, comprehensive genetic tests for deafness genes by Sanger sequencing is extremely expensive and time-consuming. Next-generation sequencing (NGS) technology is advantageous for genetic diagnosis of heterogeneous diseases that involve numerous causative genes.Entities:
Mesh:
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Year: 2013 PMID: 24164807 PMCID: PMC4231469 DOI: 10.1186/1750-1172-8-172
Source DB: PubMed Journal: Orphanet J Rare Dis ISSN: 1750-1172 Impact factor: 4.123
Figure 1Pedigrees of the seven families with hearing loss. Double horizontal bars above a symbol indicate individuals who underwent genetic analysis by targeted next-generation sequencing. Single horizontal bars above a symbol indicate individuals who underwent analysis by Sanger sequencing. A-G denote pedigrees of family 1-7, respectively.
Summary of subjects with hearing loss
| 1 | III:3 | 45 | 53 | Moderate/Moderate | Yes |
| IV:2 | 10 | 16 | Mild/Normal | No | |
| 2 | III:1 | unknown | no data | Profound/Profound | Unknown |
| III:2 | unknown | no data | Moderate/Severe | Unknown | |
| IV:3 | 0 | 1 | Severe** | Yes | |
| 3 | III:1 | 0 | 9 | Severe** | Unknown |
| III:2 | 0 | 6 | Moderate/Moderate | Unknown | |
| 4 | I:2 | 0 | 30s | Profound/Profound | No |
| II:1 | 0 | 2 | Profound/Profound | No | |
| 5 | III:1 | 0 | 2 | Severe** | No |
| III:2 | 0 | 2 | Profound** | No | |
| 6 | II:1 | 5 | 14 | Profound/Severe | Yes |
| II:2 | 0 | 12 | Profound/Profound | Yes | |
| 7 | II:1 | 0 | 3 | Moderate (ASSR***) | Unknown |
| II:2 | 0 | 0 | Severe (ASSR) | Unknown |
*Hearing loss severity was evaluated based on average hearing level at 500, 1,000, 2,000, and 4,000 Hz (mild, 20–40 dB; moderate, 41–70 dB; severe, 71-95dB; profound, >95 dB) according to recommendations [3]. **Binaural hearing level. ***ASSR, auditory steady state responses.
Summary of the number of variants detected in each subject
| 1 | III:3 | 61 | 414 | 84 |
| III:4 | 61 | 370 | 74 | |
| IV:2 | 61 | 391 | 82 | |
| 2 | III:1 | 61 | 386 | 81 |
| III:2 | 61 | 422 | 87 | |
| IV:1 | 61 | 435 | 82 | |
| IV:3 | 61 | 400 | 84 | |
| 3 | II:1 | 61 | 383 | 82 |
| II:2 | 61 | 339 | 70 | |
| III:1 | 61 | 350 | 74 | |
| III:2 | 61 | 398 | 86 | |
| 4 | I:1 | 84 | 570 | 138 |
| I:2 | 84 | 569 | 126 | |
| II:1 | 84 | 546 | 131 | |
| 5 | II:2 | 61 | 388 | 72 |
| II:4 | 61 | 374 | 87 | |
| III:1 | 61 | 361 | 84 | |
| III:2 | 61 | 396 | 85 | |
| 6 | I:1 | 61 | 429 | 96 |
| I:2 | 61 | 371 | 81 | |
| II:1 | 61 | 378 | 86 | |
| II:2 | 61 | 375 | 84 | |
| 7 | I:1 | 84 | 607 | 139 |
| I:2 | 84 | 554 | 126 | |
| II:2 | 84 | 582 | 132 | |
| II:1 | 84 | 539 | 117 |
*SNV, single nucleotide variant; MNV, multiple nucleotide variant.
Summary of possible pathogenic mutations
| c.802G>A | p.G268S | NM_001199954.1 | None | - | 0 | 0/192 | Probably damaging (0.998 | Deleterious (-4.504) | Possible | 1 | | |
| c.1007delC | p.A336Vfs | NM_002700.2 | None | - | 0 | 0/192 | - | - | Possible | 2 | | |
| c.390A>C | p.R130S | NM_198999.2 | None | - | 0 | 0/192 | Benign (0.443) | Deleterious (-4.813) | Possible | 3 | | |
| c.209G>A | p.W70X | NM_198999.2 | None | - | 0 | n.t*. | - | - | Possible | 3 | | |
| c.328C>T | p.R110W | NM_005982.3 | rs80356459 | No info | 0 | n.t. | Probably damaging (1.000) | Deleterious (-7.775) | Causative | 4 | 35 | |
| c.6478T>G | p.W2160G | NM_000260.3 | None | - | 0 | 0/192 | Probably damaging (1.000) | Deleterious (-12.649) | Possible | 5 | | |
| c.6439-2A>G (intron 51) | Splice mutation | NM_000260.3 | None | - | 0 | 0/192 | | - | Possible | 5 | | |
| c.719C>T | p.P240L | NM_022124.5 | rs121908354 | 1/2183 | 0 | n.t. | Probably damaging (1.000) | Deleterious (-3.051) | Causative | 6 | 43 | |
| c.848G>A | p.R283H | NM_001142763.1 | None | - | 1/13005 | 0/192 | Probably damaging (0.998) | Neutral (-1.918) | Possible | 6 | | |
| c.12431delC | p.A4144GfsX23 | NM_206933.2 | None | - | 0 | 0/190 | - | Possible | 7 |
*n.t. = not tested
Summary of variants with uncertain pathogenicity
| c.781C>T | p.R261X | NM_004403.2 | None | - | 0 | 0/192 | - | - | Uncertain | 2 | | |
| c.1346G>A | p.R449H | NM_206933.2 | None | - | 0 | 5/378 | Benign (0.017) | Neutral (-0.880) | Uncertain | 7 |
Figure 2Molecular modeling of containing the p.G268S mutation. (A) Ribbon model of filamentous actin gamma 1. (B) Magnified ribbon model of filamentous actin gamma 1. Glycine residue 268 is shown in red and indicated by an arrow. Regions in yellow and green indicate the hydrophobic loop (262–274; a) and the corresponding interactive residues (281–289; b), respectively. (C and D) Vertical views of the regions a and b superimposed with predicted surface hydrophobicity in the wild type (C) and the p.G268S mutant (D).
Figure 3Molecular modeling of containing the p.W2160G mutation. (A) Structural motif of myosin 7A. Tryptophan 2160 on the C-terminal 4.1 protein-ezrin-radixin-moesin (FERM) domain is indicated by an arrow. Motor, myosin motor domain; IQ, Isoleucine-glutamine calmodulin-binding motif; CC, coiled-coil domain; MyTH4, myosin tail homology 4 domain; SH3, Src homology 3 domain. (B) Ribbon model of the C-terminal FERM domain consisting of three subdomains (F1, F2, F3) and an MyTH4 domain. (C, D) Magnified ribbon model of the F3 subdomain superimposed with predicted surface hydrophobicity in the wild type (C) and the p.W2160G mutant (D).