Table 2.
De novo sequence variants in the CDH cohort
| ID | Cohort | Ph | Gene symbol | Dia | ExAC
|
Chr | Pos | Ref. | Alt. | cDNA | Protein | Category | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| pLI | mis_z | lof_z | ||||||||||||
| T2 | BOSTON | C | GRB10 | 3.4 | 0.367 | 1.854 | 3.918 | 7 | 50737473 | - | CT | NM_001001549: c.449_450insAG | p.S150fs | LGD |
| T33 | BOSTON | C | HSPD1 | 3.5 | 0.976 | 2.711 | 3.638 | 2 | 198362109 | G | A | NM_002156:c.C182T | p.T61I | D-mis |
| 01-0215 | DHREAMS | C | PTPN12 | 7.5 | 0.999 | −0.054 | 5.084 | 7 | 77221548 | C | T | NM_001131009:c.C77T | p.T26M | D-mis |
| T3 | BOSTON | C | ACTG1 | 7.6 | 0.219 | 5.131 | 2.413 | 17 | 79478517 | C | T | NM_001199954:c.G499A | p.E167K | D-mis |
| 01-0761 | DHREAMS | C | CDO1 | 9.4 | 0.020 | −0.088 | 1.586 | 5 | 115147001 | C | - | NM_001801:c.259delG | p.D87fs | LGD |
| T15 | BOSTON | C | ADD1 | 12.0 | 0.611 | 0.586 | 3.906 | 4 | 2906653 | C | T | NM_001119:c.C1324T | p.R442W | D-mis |
| T38 | BOSTON | I | NAA15 | 14.0 | 0.996 | 3.088 | 4.805 | 4 | 140258100 | AT | - | NM_057175:c.239_240del | p.H80fs | LGD |
| T57 | BOSTON | C | POGZ | 14.7 | 1.000 | 3.284 | 6.213 | 1 | 151378872 | GGAA | - | NM_145796:c.2350_2353del | p.F784fs | LGD |
| 01-0634 | DHREAMS | C | PRKACB | 15.6 | 0.612 | 2.547 | 3.179 | 1 | 84649798 | C | T | NM_001242862:c.C277T | p.R93X | LGD |
| 01-0562 | DHREAMS | C | GATA6 | 16.8 | - | - | - | 18 | 19761477 | C | T | NM_005257:c.C1366T | p.R456C | D-mis |
| 01-0147 | DHREAMS | C | STAG2 | 18.2 | 1.000 | 5.111 | 6.472 | X | 123197716 | C | T | NM_006603:c.C1840T | p.R614X | LGD |
| T49 | BOSTON | I | PLCG1 | 21.2 | 0.729 | 4.359 | 5.858 | 20 | 39797452 | G | A | NM_002660:c.G2425A | p.E809K | D-mis |
| T70 | BOSTON | C | FOXP4 | 22.4 | 0.672 | 1.628 | 3.652 | 6 | 41562624 | A | G | NM_001012426:c.A1553G | p.N518S | D-mis |
| T35 | BOS ON | C | ARL15 | 23.2 | 0.009 | 0.357 | 1.081 | 5 | 53450409 | C | T | sp | - | LGD |
| 01-0109 | DHREAMS | C | DLST | 23.5 | 0.950 | 0.277 | 3.734 | 14 | 75356621 | AG | - | NM_001244883:c.297_298del | p.E99fs | LGD |
| T36 | BOSTON | C | GINS3 | 23.8 | 0.236 | 0.613 | 1.888 | 16 | 58437236 | G | A | sp | - | LGD |
| 01-0136 | DHREAMS | C | PRR14 | 23.9 | 0.259 | 0.655 | 3.753 | 16 | 30667426 | C | T | NM_024031:c.C1552T | p.R518W | D-mis |
| 01-0083 | DHREAMS | C | TLN1 | 24.0 | 1.000 | 5.133 | 9.326 | 9 | 35725594 | C | T | NM_006289:c.G98A | p.R33H | D-mis |
Chr, chromosome. Ph, phenotype: C, complex; I, isolated CDH. Dia, expression rank in the embryonic mouse diaphragm. Allele: Ref., reference; Alt., alternative. Class: Sp, splice site variant. Category: LGD, likely gene disrupting; D-mis, predicted damaging missense variant by metaSVM, PolyPhen-2, SIFT, or CADD. DHREAMS variants are as reported in Yu et al. (2015). Human reference sequence: GRCh37/hg19.