Table 2.
Genetic causes of disease in the pericentral RP cohort, including probands whose cause of disease was solved by panel-based sequencing (top) or whole exome sequencing (WES) (middle). Unsolved probands with VUS are shown below. Also, see Supplemental Table S1 for a more fully annotated version including genomic coordinates, pathogenicity predictions, and references.
| Solved by Panel-Based Sequencing | |||||
|---|---|---|---|---|---|
| Family# | Gene | Protein Variant | DNA Variant Description | Type | Sanger/Correct Segregation |
| 1 | PDE6B | p.(Cys458Tyr) | NM_000283.3:c.1373G>A | HET | proband |
| 1 | PDE6B | p.(Lys518Ile) | NM_000283.3:c.1553A>T | HET | proband |
| 4 | RHO | p.(Gly101Val) | NM_000539.3:c.302G>T | HET | |
| 5 | PDE6B | p.(Gln298*) | NM_000283.3:c.892C>T | HET | proband |
| 5 | PDE6B | p.(Arg100His) | NM_000283.3:c.299G>A | HET | proband |
| 6 | CNGA1 | p.(Thr586Serfs*17) | NM_000087.3:c.1755 _1758delAACT | HET | proband |
| 6 | CNGA1 | p.(Ser320Phe) | NM_000087.3:c.959C>T | HET | proband |
| 7 | RHO | p.(Gly18Asp) | NM_000539.3:c.53G>A | HET | proband |
| 8 | RHO | p.(Thr58Arg) | NM_000539.3:c.173C>G | HET | proband |
| 12 | USH2A | p.(Glu3448Lys) | NM_206933.2:c.10342G>A | HOM | proband, het in unaffected son |
| 14 | RHO | p.(Gly106Arg) | NM_000539.3:c.316G>A | HET | proband |
| 17 | NR2E3 | p.(Val118Met) | NM_014249.3:c.352G>A | HET | proband, affected sister |
| 18 | PRPF31 | p.? | NM_015629.3:c.421-1G>A | HET | proband, 3 affected children |
| 23 | RHO | p.(Gly51Arg) | NM_000539.3:c.151G>C | HET | proband |
| 26 | USH2A | p.(Cys870*) | NM_206933.2:c.2610C>A | HET | proband |
| 26 | USH2A | p.(Asn42Lys) | NM_206933.2:c.126C>G | HET | proband |
| 26 | USH2A | p.(Gly2313Cys) | NM_206933.2:c.6937G>T | HET | proband |
| 30 | USH2A | p.? | NM_206933.2:c.9571-2A>G | HET | proband |
| 30 | USH2A | p.? | NM_206933.2:c.7595-3C>G | HET | proband |
| 31 | RP2 carrier | p.(Gly163Glu) | NM_006915.2:c.488G>A | HET | proband |
| 33 | TULP1 | p.? | NM_003322.3:c.1496-6C>A | HET | proband |
| 33 | TULP1 | p.(Gln163*) | NM_003322.3:c.487C>T | HET | proband |
| 37 | USH2A | p.? | NM_206933.2:c.12067-2A>G | HET | proband |
| 37 | USH2A | p.(Cys3306Trp) | NM_206933.2:c.9918T>G | HET | proband |
| 37 | USH2A | p.(Ala1953Gly) | NM_206933.2:c.5858C>G | HET | proband |
| 40 | CNGB1 | p.(Arg396Gln) | NM_001297.4:c.1187G>A | HET | |
| 40 | CNGB1 | p.? | NM_001297.4:c.1801+5G>A | HET | |
| Solved by Exome Sequencing | |||||
| 15 | HGSNAT | p.(Ala615Thr) | NM_152419.2:c.1843G>A | HET | |
| 15 | HGSNAT | p.? | NG_009552.1(NM_152419.2):c.1464 + 1G>A | HET | |
| 34 | HGSNAT | p.(Ser318Asn) | NM_152419.2:c.953G>A | HOM | |
| Not Solved or Partially Solved Due to Variants of Uncertain Significance (VUS) | |||||
| 3 | ROM1 | p.(Leu238Cysfs*78) | NM_000327.3:c.708delC | HET | |
| 3 | COL11A1 | p.(Arg762Gln) | NM_001854.3:c.2285G>A | HET | |
| 13 | HGSNAT | p.(Ala615Thr) | NM_152419.2:c.1843G>A | HOM | |
| 16 | USH2A | p.(Leu1378Pro) | NM_206933.2:c.4133T>C | HET | proband, affected brother |
| 16 | USH2A | p.(Ser1369Leu) | NM_206933.2:c.4106C>T | HET | proband, affected brother |
| 20 | TRPM1 | p.(Gln1161His) | NM_002420.5:c.3483G>C | HET | |
| 20 | TRPM1 | p.(Ser157Phe) | NM_002420.5:c.470C>T | HET | |
| 24 | HGSNAT | p.(Ala615Thr) | NM_152419.2:c.1843G>A | HOM | |
| 25 | MKS1 | p.(Thr423Ile) | NM_017777.3:c.1268C>T | HOM | |
| 29 | BBS9 | p.(Pro419Ala) | NM_198428.2:c.1255C>G | HET | proband |
| 29 | BBS9 | p.(Glu753Val) | NM_198428.2:c.2258A>T | HET | proband |
| 42 | OPA1 | p.(Ala115Val) | NM_015560.2: c.344C>T | HET | |
ExAC AF = allele frequency [38], HET = heterozygous, HOM = homozygous.