Table 2. Genotype and clinical characteristics of patients with USH2A-related disease (replication cohort).
| Subject | USH2A sequencing results | Likely effect of allele | Diagnosis | ||
|---|---|---|---|---|---|
| Variant 1 | Variant 2 | Variant 1 | Variant 2 | ||
| R1 | c.2276G>T, p.(Cys759Phe) | c.2276G>T, p.(Cys759Phe) | Retina-specific | Retina-specific | Nonsyndromic retinitis pigmentosa |
| R2 | c.2276G>T, p.(Cys759Phe) | c.1225T>C, p.(Trp409Arg) | Retina-specific | Unknown (novel) | Nonsyndromic retinitis pigmentosa |
| R3 | c.2276G>T, p.(Cys759Phe) | c.9912dup, p.(Glu3305Argfs*41) | Retina-specific | Unknown | Nonsyndromic retinitis pigmentosa |
| R4 | c.2276G>T, p.(Cys759Phe) | c.2299delG, p.(Glu767Serfs*21) | Retina-specific | Usher | Nonsyndromic retinitis pigmentosa |
| R5 | c.99_100insT, (p.Arg34Serfs*41) | c.2802T>G, p.(Cys934Trp) | Unknown | Retina-specific | Nonsyndromic retinitis pigmentosa |
| R6 | c.5776G>A, p.(Glu1926Lys) | c.10073G>A, p.(Cys3358Tyr) | Usher | Retina-specific | Nonsyndromic retinitis pigmentosa |
| R7 | c.5776G>A, p.(Glu1926Lys) | c.10073G>A, p.(Cys3358Tyr) | Usher | Retina-specific | Nonsyndromic retinitis pigmentosa |
| R8 | c.1256G>T, p.(Cys419Phe) | c.11156G>A, p.(Arg3719His) | Usher | Retina-specific | Nonsyndromic retinitis pigmentosa |
| R9 | c.1256G>T, p.(Cys419Phe) | c.11156G>A, p.(Arg3719His) | Usher | Retina-specific | Nonsyndromic retinitis pigmentosa |
| R10 | c.11864G>A, p.(Trp3955*) | c.12580T>C, p.(Cys4194Arg) | Usher | Unknown (novel) | Nonsyndromic retinitis pigmentosa |
| R11 | c.8254G>A, p.(Gly2752Arg) | c.15178T>C, p.(Ser5060Pro) | Usher | Unknown (novel) | Nonsyndromic retinitis pigmentosa |
| R12 | c.4378G>A, p.(Gly1460Arg) | c.9424G>T, p.(Gly3142*) | Unknown (novel) | Usher | Nonsyndromic retinitis pigmentosa |
| R13 | c.6904_6920dup17 | c.12877G>A, p.(Gly4293Ser) | Unknown (novel) | Unknown (novel) | Nonsyndromic retinitis pigmentosa |
| R14 | c.9611A>G, p.(His3204Arg) | c.13768G>A, p.(Gly4590Ser) | Unknown (novel) | Unknown (novel) | Nonsyndromic retinitis pigmentosa |
| R15 | c.1876C>T, p.(Arg626*) | c.1876C>T, p.(Arg626*) | Usher | Usher | Usher syndrome |
| R16 | c.1256G>T, p.(Cys419Phe) | c.2299delG, p.(Glu767Serfs*21) | Usher | Usher | Usher syndrome |
| R17 | c.2299delG, p.(Glu767Serfs*21) | c.14287G>A, p.(Gly4763Arg) | Usher | Usher | Usher syndrome |
| R18 | c.2299delG, p.(Glu767Serfs*21) | c.14287G>A, p.(Gly4763Arg) | Usher | Usher | Usher syndrome |
| R19 | c.2209C>T, p.(Arg737*) | c.2299delG, p.(Glu767Serfs*21) | Usher | Usher | Usher syndrome |
| R20 | c.2299delG, p.(Glu767Serfs*21) | c.5168-2A>G | Usher | Unknown (novel) | Usher syndrome |
| R21 | c.2299delG, p.(Glu767Serfs*21) | c.5858-1G>A | Usher | Unknown (novel) | Usher syndrome |
| R22 | c.2299delG, p.(Glu767Serfs*21) | c.14180G>A, p.(Trp4727*) | Usher | Unknown (novel) | Usher syndrome |
| R23 | c.1679delC, p.(Pro560Leufs*31) | c.11549-1G>A | Unknown | Unknown (novel) | Usher syndrome |
| R24 | c.854T>C, p.(Ile285Thr) | c.10724G>A, p.(Cys3575Tyr) | Unknown (novel) | Usher | Usher syndrome |
| R25 | c.2081G>C, p.(Cys694Ser) | c.10612C>T, p.(Arg3538*) | Unknown (novel) | Unknown (novel) | Usher syndrome |
Retina-specific corresponds to likely ‘retinal disease-specific' alleles (shown in bold).
Usher corresponds to likely ‘Usher syndrome type II'-specific alleles.
Novel corresponds to alleles that are novel to this study. Of these novel changes, the following are found in the Exome Aggregation Consortium (ExAC) browser (accessed 31 December 2014): c.12580T>C (1/122018), c.15178T>C (4/122952 alleles), c.4378G>A (3/122140) and c.9611A>G (22/122680). Segregation analysis was performed in subjects R12, R20 and R22 and has confirmed that the reported variants are in trans.
Numbering of USH2A variants has been assigned in accordance with NCBI Reference Sequence NM_206933.2.