Table 3 of Lai, Mol Vis 2010; 16:2829-2838. Table 3 of Lai, Mol Vis 2010; 16:2829-2838.
Table 3. Sequence variants as identified by Sanger sequencing in candidate genes within the common PPCD1 of Build 37.1 and their appearance in data generated by next-generation sequencing (NGS).
| Next-generation sequencing | Sanger sequencing | ||||||
|---|---|---|---|---|---|---|---|
| Gene (refSeq) | Nucleotide change | Amino acid change | refSNP ID | Affected | Unaffected | Affected | Unaffected |
| SNX5 (NM_152227) | c.543G>A | p.Glu181Glu | rs2273448 | Y (hetero) Score=25 | Y (hetero) | Y(hetero) | Y (hetero) |
| SNORD17 (NR_003045) | 98T>A | Non-coding microRNA | rs753213 | N | Y(hetero) Score=21 | N | Y (hetero) |
| C20orf72 (NM_018152) | c.43A>T | p.Ser15Cys | rs11551768 | Y (hetero) Score=18 | N | Y (hetero) | N |
| c.794C>T | p.Thr265Ile | - | N | Y (hetero) Score=2** | N | Y (hetero) | |
| c.846T>C | p.Asp282Asp | rs28455091 | Y (hetero) Score=2* | Y (hetero) Score=9 | Y (hetero) | Y(hetero) | |
| PTMAP3 (NG_001180) | c.347T>G | p.Val116Gly | - | N* | N* | Y (hetero) | Y (hetero) |
| c.348C>G | p.Val116Val | - | N* | N* | Y (homo) | Y (homo) | |
| c.362C>G | p.Thr121Arg | - | N* | N* | Y (homo) | Y (homo) | |
| c.415T>C | p.Leu139Leu | - | N* | N* | Y (homo) | Y (homo) | |
| c.553T>C | p.Cys185Arg | rs3748493 | N* | N* | Y (hetero) | Y (homo) | |
| c.843C>T | p.Cys281Cys | rs3748492 | N* | Y (homo) Score=4** | Y (hetero) | Y (homo) | |
| LOC100287054 | No Changes | ||||||
| OVOL2 (NM_021220) | c.327C>A | p.Thr109Thr | rs6111803 | Y (hetero) Score=17 | N | Y (hetero) | N |
| RPL15P1 (NG_000975) | No Changes | ||||||
| PET117 | No Changes | ||||||
| CSRP2BP (NM_020536) | c.1199T>G | p.Val400Gly | rs1205193 | Y (homo) Score=23 | Y (homo) Score=18 | Y (homo) | Y (homo) |
| c.1437C>T | p.Pro479Pro | rs1205194 | N | N | N | N | |
| c.1499C>T | p.Ala500Val | rs41276418 | Y (hetero) Score=25 | Y (hetero) Score=21 | Y (hetero) | Y (hetero) | |
| c.2223T>C | p.Pro741Pro | rs2747404 | Y (homo) Score=25 | Y (homo) Score=21 | Y (homo) | Y (homo) | |
| LOC100287095 | No Changes | ||||||
| ZNF133 (NM_003434) | No Changes | ||||||
| MGC44328 (NM_001004344) | c.89T>C | p.Leu30Pro | rs1883938 | Y (homo) Score=27 | Y (homo) Score=20 | Y (homo) | Y(homo) |
| C20orf12 (NM_018152) | c.40T>C | p.Leu14Leu | rs6035051 | Y (hetero) Score=25 | Y (homo) Score=25 | Y (hetero) | Y (homo) |
| c.801T>C | p.Cys267Cys | rs6035042 | Y (homo) Score=29 | Y (hetero) Score=13 | Y (homo) | Y (hetero) | |
| c.1410G>C | p.Leu470Leu | rs6075337 | Y (homo) Score=26 | Y (homo)+ Score=21 | Y (homo) | Y(hetero) + | |
| GCNT1P (NG_001039) | No Changes | ||||||
| POLR3F (NM_006466) | c.840A>G | p.Thr280Thr | rs1055171 | Y (homo) Score=26 | Y (hetero) Score=13 | Y (homo) | Y (hetero) |
| RPL21P3 (NG_000976) | c.346delA | p.Arg116GlyfsX28 | - | N* | N* | Y (hetero) | Y (hetero) |
| RBBP9 (NM_006606) | No Changes | ||||||
| RPS19P1 (NG_001295) | c.136C>G | p.Pro46Ala | rs2009092 | Y (hetero) Score=12 | Y (hetero) Score=5 | Y (homo) | Y hetero) |
| c.167G>A | p.Arg56Gln | - | N* | N* | Y (hetero) | N | |
| SEC23B (NM_032985) | c.490G>A | p.Val164Met | rs36023150 | N | N | N | N |
| c.1198T>C | p.Phe400Leu | - | N | Y (hetero) Score=8 | N | Y(hetero) | |
| c.1276G>A | p.Val426Ile | - | N | N | N | N | |
| c.1467C>G | p.His489Gln | rs2273526 | N | Y (hetero) Score=27 | N | Y(hetero) | |
| LOC388789 (XM_939954) | c.48A>G | p.Arg16Arg | rs12624935 | N* | N* | N | Y (hetero) |
| DTD1 (NM_080820) | No Changes | ||||||
| DUXAP7 (NG_004846) | c.447A>C | p.Gln149His | rs6132094 | N* | N* | Y (hetero) | Y (hetero) |
| c.664A>G | p.Thr222Ala | rs6081271 | N* | N* | Y (homo) | Y (homo) | |
| c.665C>T | p.Thr222Ile | rs6081270 | N* | N* | Y (hetero) | Y (hetero) | |
| c.716T>A | p.Ile239Lys | - | N* | N* | Y (hetero) | Y (hetero) | |
| c.719delA | p.Lys240LysfsX39 | - | N* | N* | N | Y (hetero) | |
| c.720delA | p.Lys240LysfsX39 | - | N* | N* | Y (hetero) | Y (hetero) | |
| c.721insA | p.Glu241ArgfsX25 | - | N* | N* | Y (hetero) | Y (hetero) | |
| c.726_730dupGAAAA | p.Arg244ArgfsX37 | - | N* | N* | Y (hetero) | Y (hetero) | |
| c.726_730dupGAAAA [3] | p.Arg244ArgfsX25 | - | N* | N* | Y (hetero) | Y (hetero) | |
| c.943G>C | p.Val315Leu | rs6132093 | N* | N* | Y (hetero) | Y (hetero) | |
| c.1124T>C | p.Val375Ala | rs6081268 | N* | N* | Y (hetero) | Y (hetero) | |
| c.1156C>T | p.Pro386Ser | rs6075382 | N* | N* | Y (hetero) | Y (hetero) | |
| LOC100132358 (NC_000020) | c.274C>T | p.Gln92X | rs6081369 | Y (hetero) Score=24 | Y (hetero) Score=6 | Y (hetero) | Y (hetero) |
| HSPC072 (AF161557) | No Changes | ||||||
| LOC100270804 | 172C>T | p.Pro58Ser | rs41309831 | Y (hetero) Score=13 | N | Y (hetero) | N |
| c.543G>T | p.Gly181Gly | rs7262320 | Y (hetero) Score=26 | N | Y (hetero) | N | |
| 685_686insG | p. Glu229fxX23 | - | Y (hetero) Score=14 | N | Y (hetero) | N | |
| 1343G>A | p.Arg448Arg | rs80046336 | Y (hetero) Score=22 | Y (hetero) Score=17 | Y (hetero) | Y (hetero) | |
| 1360_1364delAAGAA | p.Lys484fsX18 | - | Y (hetero) Score=25 | N | Y(hetero) | N | |
| LOC100128496 (XM_001725705) | c.138C>G | p.Leu46Leu | rs56743271 | Y (hetero) Score=19 | N | Y (hetero) | N |
| C20orf79 (NM_178483) | c.255C>T | p.Thr85Thr | rs1053834 | Y (hetero) Score=25 | N | Y (hetero) | N |
| c.295C>T | p.Pro99Ser | rs1053839 | Y (hetero) Score=20 | N | Y (hetero) | N | |
| SLC24A3 (NM_020689) | c.52_54delCGC* | p.Arg18del | - | N* | N* | Y (hetero) | Y (hetero) |
| c.163G>A | p.Val55Ile | rs1569767 | N | Y (hetero) Score=17 | N | Y (hetero) | |
| c.369G>A | p.Ala123Ala | rs3790261 | Y (Hetero) Score=26 | Y (homo) Score=24 | Y (hetero) | Y (homo) | |
| c.639G>A | p.Leu213Leu | rs3790278 | Y (homo) Score=30 | Y (homo) Score=15 | Y (homo) | Y (homo) | |
| c.654T>C | p.Ile218Ile | rs3790279 | Y (homo) Score=26 | Y (homo) Score=23 | Y (homo) | Y (homo) | |
| LOC100130264 (XM_001717962) | No Changes | ||||||