Table 1.
Variants in affected patients
| ID | Gene | Variant | Variant type | Impact | Grading |
|---|---|---|---|---|---|
| C1 | CHM | c.529del; p.Glu177Lysfs*20 | Indel | Frameshift | 3 |
| C2 | CHM | g.85957852del; c.940 + 3delA | Indel | Splicing | 4 |
| C3 | CHM | g.85957852del; c.940 + 3delA | Indel | Splicing | 2 |
| C4 | CHM | c.1214_1215insC; p.Gln405Hisfs*13 | Indel | Frameshift | 2 |
| C5 | CHM | c.1780delC; p.Leu594Phefs*55 | Indel | Frameshift | 2 |
| C6 | CHM | g.86045359_86047506del; c.27_49 + 2125del | SV | Deletion | 4 |
| C7 | CHM | c.757C > T, p.Arg253Ter | SNV | Stop | 3 |
| C8 | CHM | g.85838231_85933652del; c.1167-22313_*26400del | SV | Truncation | 2 |
| C9 | CHM | g.85965588T > C; c.315-1536A > G | SNV | Splicing | 3 |
| C10 | CHM | c.1584_1587delTGTT; p.Val529Hisfs*7 | Indel | Frameshift | 2 |
| C11 | CHM | c.1584_1587delTGTT; p.Val529Hisfs*7 | Indel | Frameshift | 1 |
| C12 | CHM | g.84295184_84296004del; c.(1770 + 1_1771-1)_(*1_?)del | SV | Truncation | 3 |
| R1 | RPGR | c.2362_2366del, p.Glu788Argfs*45 | Indel | Frameshift | 4 |
| R2 | RPGR | c.619 + 5G > A | SNV | Splicing | 4 |
| R3 | RPGR | c.2442_2445del, p.Gly817Lysfs*2 | Indel | Frameshift | 4 |
| R4 | RPGR | c.2362_2366del, p.Glu788Argfs*45 | Indel | Frameshift | 4 |
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Coordinates are relative to hg38 Chr X (NC_000023.11), CHM MANE transcript NM_000390.4 and translated protein NP_000381.1, and RPGR transcript NM_001034853.1 and protein NP_001030025.1. Patient C6's deep intronic variant in CHM has been experimentally validated as creating a cryptic splice site (Carss et al. 2017). Patients C1, C4, and C8 had not received a genetic diagnosis prior to the long-read sequencing performed in this study. C2 and C3 are sisters; C10 and C11 are daughter and mother; and R1 and R4 are mother and daughter.
