Genotypes of people recruited to the UK 100,000 Genomes Project as non-cystic fibrosis bronchiectasis carrying variants suggestive of primary ciliary dyskinesia
| Family code | Gene | Genomic location (GRCh38) | Mat/pat origin | cDNA change | Protein change | Tier | ACMG/AMP class# | GEL#/literature reported | dbSNP [reference] |
| 1 | CCDC39 (NM_181426.2) | 3:180659582T>C 3:180616872TTAC>TA | Mat Pat | c.610-2A>G c.2357_2359delinsT | Splice variant p.(Ser786fs) | Tier 1 Tier 1 | 5 5 | GMC exit questionnaire GMC exit questionnaire | rs756235547 [29] rs587778821 [29] |
| 2 | CCDC39 (NM_181426.2) | 3:180651496delT 3:180616604CTG>C | Unknown phase | c.1072del c.2497_2498del | p.(Thr358fs) p.(Gln833fs) | Tier 1 Tier 1 | 5 5 | Tiered only Tiered only | rs587778822 [29] rs1007345781 [30] |
| 3 | DNAI1 (NM_012144.4) | 9:34514436G>A 9:34514436G>A | Mat Pat | c.1612G>A c.1612G>A | p.(Ala538Thr) p.(Ala538Thr) | Tier 2 Tier 2 | 4 4 | GMC exit questionnaire GMC exit questionnaire | rs368248592 [31] rs368248592 [31] |
| 4 | DNAI1 (NM_012144.4) | 9:34459054G>GT 9:34513112G>A | Unknown phase | c.48+2dup c.1490G>A | Splice variant p.(Gly497Asp) | NT NT | 5 3 | RIPD form¶ RIPD form¶ | rs397515363 [32] rs376252276 [32] |
| 5 | DNAI2 (NM_023036.6) | 17:74309345G>A 17:74309345G>A | Mat Pat | c.1304G>A c.1304G>A | p.(Trp435+) p.(Trp435+) | Tier 1 Tier 1 | 5 5 | Tiered only Tiered only | rs752924362 [32] rs752924362 [32] |
| 6 | DNAH5 (NM_001369.2) | 5:13708286A>C 5:13870868G>A | Unknown phase | c.13175T>G c.3733C>T | p.(Phe4392Cys) p.(Arg1245Cys) | Tier 2 Tier 2 | 3 3 | Tiered only Tiered only | rs145400611 NR rs149609746 NR |
| 7 | DNAH5 (NM_001369.2) | 5:13753290delT 5:13780960C>A | Mat Pat | c.10815del c.8821-1G>T | p.(Pro3606fs) Splice variant | Tier 1 Tier 1 | 5 5 | Tiered only Tiered only | rs397515540 [33] rs1060501454 NR |
| 8 | DNAH11 (NM_001277115.2) | 7:21620016C>T 7:21899361C>T | Unknown phase | c.4438C>T c.13075C>T | p.(Arg1480+) p.(Arg4359+) | Tier 1 Tier 1 | 5 5 | Tiered only Tiered only | rs72657321 [34] rs774903187 [34] |
| 9 | FOXJ1 (NM_001454.4) | 17:76137652delG | De novo, dominant | c.967del | p.(Glu323fs) | Tier 3 | 5 | RIPD form¶ | rs1598372791 [35] |
| 10 | FOXJ1 (NM_001454.4) | 17:76137652delG | De novo, dominant | c.967del | p.(Glu323fs) | Tier 3 | 5 | GMC exit questionnaire (VUS+) | rs1598372791 [35] |
| 11 | OFD1 (NM_003611.3) | X:13735074G>A | Parental unknown | c.3G>A | p.(Met1?) | Tier 3 | 3 | RIPD form¶ | rs778840618 NR |
| 12 | RPGR (NM_000328.3) | X:38317333T>C | Parental unknown | c.602A>G | p.(His201Arg) | Tier 2 | 3 | Tiered only | NR |
| 13 | RSPH1 (NM_080860.4) | 21:42486463T>G 21:42486463T>G | Mat Pat | c.275-2A>C c.275-2A>C | Splice variant Splice variant | Tier 1 Tier 1 | 5 5 | Tiered only Tiered only | rs151107532 [36] rs151107532 [36] |
| 14 | RSPH4A (NM_001010892.3) | 6:116630553G>GTT 6:116628100C>T | Mat Pat | c.1916+2_1916+3insTT c.1393C>T | Splice variant p.(Arg465+) | Tier 3 Tier 3 | 4 5 | RIPD form¶ RIPD form¶ | NR rs755782051 [37] |
| 15 | CEP164 (NM_014956.5) | 11:117387204C>T 11:117411859C>T | Mat Pat | c.1726C>T c.4228C>T | p.(Arg576+) p.(Gln1410+) | Tier 3 Tier 3 | 5 4 | RIPD form¶ RIPD form¶ | rs145646425 [38] rs147398904 NR |
| 16 | CFAP53 (NM_145020.5) | 18:50262051G>A 18:50242969C>A | Unknown phase | c.238C>T c.1144G>T | p.(Arg80+) p.(Glu382+) | Tier 3 Tier 3 | 5 5 | RIPD form¶ RIPD form¶ | rs374898373 NR rs200321140 NR |
| 17 | NEK10 (NM_152534.4) | 3:27352882T>C 3:27304746C>A | Unknown phase | c.1A>G c.1028+1G>T | p.(Met1?) Splice variant | Tier 3 Tier 3 | 4 4 | RIPD form¶ RIPD form¶ | rs1363654282 NR rs1323610713 NR |
Mat: maternal; pat: paternal; ACMG: American College of Medical Genetics and Genomics; AMP: Association for Molecular Pathology; GEL: Genomics England Ltd; GMC: National Health Service Genomics Medical Centre; NT: not tiered; RIPD: researcher-identified potential diagnosis; NR: not reported; VUS: variant of unknown significance. #: ACMG/AMP classification and GEL tiering criteria are outlined in the methods section; ¶: notification submitted by researchers from within the GEL research environment for potential mutations that are not tier 1 or tier 2 and have not already been reported in a GMC exit questionnaire; +: initially classified as a VUS, done prior to the finding of additional patients and further studies describing FOXJ1 as a new ciliopathy gene [35].