Table 2.
Results of segregation analysis in kConFab families
| Gene | Group | # Families | Log likelihood |
|---|---|---|---|
| ABCA13 | 3 | 15 | 0.85 (0.32, 1.95) |
| ANKRD30A | 3 | 1 | 0.01a (0.01a, 2.17) |
| APC | 4 | 8 | 2.96 (0.86, 26.0a) |
| ARID1A | 1 | 7 | 0.58 (0.05, 1.83) |
| ASH1L | 3 | 5 | 1.24 (0.43, 2.86) |
| ATR | 5 | 4 | 1.00 (0.17, 5.65) |
| BAZ1B | 1 | 3 | >26.0 |
| C15orf42 | 3 | 5 | 0.74 (0.06, 2.55) |
| CASC5 | 2 | 2 | 1.49 (0.10, 8.82) |
| CASP8 | 4 | 1 | >26.0 |
| CDHR2 | 3 | 1 | <0.01 |
| CELSR1 | 5 | 5 | 0.50 (0.04, 1.73) |
| CEP192 | 5 | 9 | 1.22 (0.35, 3.39) |
| CHD5 | 2 | 3 | 0.96 (0.16, 3.28) |
| CHD7 | 1 | 5 | 1.17 (0.42, 2.87) |
| CHD8 | 1 | 7 | 2.40 (1.0, 7.32) |
| CHD9 | 1 | 9 | 0.62 (0.22, 1.34) |
| DGKH | 3 | 4 | 1.75 (0.80, 4.57) |
| DLEC1 | 3 | 5 | 0.01a (0.01a, 3.86) |
| DNAH5 | 5 | 16 | 0.86 (0.36, 1.79) |
| DNMT3A | 1 | 1 | >26.0 |
| EP400 | 2 | 5 | 1.65 (0.66, 4.21) |
| HECW1 | 5 | 3 | 1.41 (0.42, 4.13) |
| HUWE1 | 2 | 9 | 2.9 (0.8, 15.0) |
| IL17B | 3 | 2 | 0.85 (0.07, 2.52) |
| ITPR2 | 3 | 9 | 1.59 (0.58, 4.61) |
| KDM5B | 2 | 6 | 7.50 (0.24, 26.0a) |
| LAMA2 | 5 | 19 | 1.32 (0.75, 2.29) |
| LPHN2 | 5 | 5 | 1.60 (0.76, 3.33) |
| LRP2 | 5 | 7 | 0.73 (0.17, 2.06) |
| MAP3K1 | 4 | 6 | 1.16 (0.09, 16.17) |
| MDN1 | 5 | 11 | 0.01a (0.01a, 0.03) |
| NCOR1 | 1 | 5 | 1.59 (0.06, 26.0a) |
| NEB | 3 | 25 | 0.87 (0.40, 1.65) |
| NELL1 | 5 | 1 | 1.0 (0.04, 22.26) |
| NET1 | 3 | 3 | 1.32 (0.45, 3.30) |
| NIPBL | 2 | 5 | 1.22 (0.36, 2.86) |
| NOS1 | 2 | 6 | 0.97 (0.14, 4.39) |
| NOTCH1 | 3 | 7 | 1.82 (0.67, 5.22) |
| NUP210 | 3 | 6 | 0.58 (0.04, 2.14) |
| PAX5 | 2 | 3 | 1.52 (0.68, 3.21) |
| PDE4DIP | 5 | 1 | >26.0 |
| PIK3C2G | 3 | 1 | 2.78 (0.64, 25.47) |
| PKD1L1 | 5 | 3 | 0.94 (0.10, 2.61) |
| PLIN4 | 3 | 1 | 0.78 (0.05, 7.54) |
| PUM2 | 3 | 3 | 1.77 (0.38, 8.95) |
| RALGAPA1 | 5 | 5 | 1.22 (0.39, 3.29) |
| RBM44 | 3 | 3 | 0.30 (0.05, 1.02) |
| RIF1 | 1 | 6 | 0.39 (0.03, 1.52) |
| RNF180 | 3 | 2 | 0.01a (0.01a, 1.85) |
| SETX | 3 | 7 | 1.37 (0.48, 3.80) |
| SLC22A5 | 3 | 3 | 6.66 (0.03, 26.0a) |
| SMG5 | 5 | 2 | 0.01a (0.01a, 6.44) |
| SPHKAP | 5 | 2 | 0.67 (0.09, 4.44) |
| SUPT3H | 3 | 1 | 0.01a (0.01a–2.3) |
| SYNE1 | 5 | 22 | 0.88 (0.45, 1.50) |
| SYNE2 | 5 | 9 | 2.14 (0.94, 5.93) |
| TDO2 | 5 | 1 | 0.01a (0.01a, 1.73) |
| TET2 | 1 | 3 | 2.21 (0.07, 26.0a) |
| TMEM131 | 3 | 9 | 1.61 (0.77, 3.78) |
| TPR | 3 | 4 | 1.06 (0.31, 3.05) |
| UBAP2L | 5 | 4 | 0.70 (0.15, 2.73) |
| UBR5 | 5 | 1 | 0.01a (0.01a–6.6) |
| USH2A | 5 | 10 | 2.48 (1.11, 6.67) |
| XRN1 | 5 | 2 | <0.01 |
| ZNF558 | 3 | 2 | 1.28 (0.33, 3.22) |
| TOTAL | 366 |
Group 1: genes involved in epigenetic regulation selected from the literature
Group 2: using the GO terms ‘chromatin organization’ or ‘chromatin reorganization’
Group 3: candidate genes from whole-exome sequencing of five non-BRCA1/2 families
a
Estimate at boundary