Table 3.
Number of carriers with loss-of-function and missense variants detected in case and control cohorts
| Gene | Selection criteria | Number of carriers with loss-of-function variants | Number of carriers with missense variants | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Case | Control | p Valuea | OR | 95% CI | Case | Control | p Valuea | OR | 95% CI | ||
| TET2 | GWAS proposed | 5 | 2 | 0.456 | 2.27 | 0.37–23.87 | 20 | 18 | 1 | 1.01 | 0.50–2.03 |
| NRIP1 | GWAS proposed | 3 | 0 | 0.251 | Und | 0.37–∞ | 21 | 17 | 0.632 | 1.12 | 0.56–2.28 |
| RAD51B | GWAS proposed | 2 | 0 | 0.501 | Und | 0.17–∞ | 6 | 4 | 0.756 | 1.36 | 0.32–6.57 |
| SNX32 | Neighbouring genes | 2 | 0 | 0.501 | Und | 0.17–∞ | 3 | 6 | 0.323 | 0.45 | 0.07–2.12 |
| ZNF226 | Neighbouring genes | 2 | 2 | 1 | 0.91 | 0.07–12.5 | 24 | 18 | 0.640 | 1.21 | 0.63–2.39 |
| ADAM29 | GWAS proposed | 1 | 0 | 1 | Und | 0.02–∞ | 13 | 11 | 1 | 1.07 | 0.44–2.65 |
| CASP8 | GWAS proposed | 1 | 0 | 1 | Und | 0.02–∞ | 8 | 2 | 0.113 | 3.64 | 0.72–35.26 |
| CDKN2A | GWAS proposed | 1 | 0 | 1 | Und | 0.02–∞ | 3 | 3 | 1 | 0.91 | 0.12–6.77 |
| DCLRE1B | Neighbouring genes | 1 | 1 | 1 | 0.91 | 0.01–71.08 | 7 | 6 | 1 | 1.06 | 0.30–3.82 |
| FTO | GWAS proposed | 1 | 0 | 1 | Und | 0.02–∞ | 10 | 11 | 0.668 | 0.82 | 0.31–2.14 |
| LGR6 | GWAS proposed | 1 | 0 | 1 | Und | 0.02–∞ | 16 | 8 | 0.217 | 1.82 | 0.73–4.94 |
| MUS81 | Neighbouring genes | 1 | 1 | 1 | 0.91 | 0.01–71.08 | 8 | 9 | 0.808 | 0.80 | 0.27–2.36 |
| NFRKB | Neighbouring genes | 1 | 1 | 1 | 0.91 | 0.01–71.08 | 17 | 12 | 0.577 | 1.29 | 0.58–2.97 |
| PDE4D | GWAS proposed | 1 | 0 | 1 | Und | 0.02–∞ | 6 | 3 | 0.512 | 1.81 | 0.39–11.24 |
| SETMAR | Neighbouring genes | 1 | 2 | 0.607 | 0.45 | 0.01–8.70 | 7 | 3 | 0.349 | 2.12 | 0.48–12.73 |
| SLC4A7 | GWAS proposed | 1 | 0 | 1 | Und | 0.02–∞ | 14 | 10 | 0.682 | 1.27 | 0.52–3.21 |
| USHBP1 | Neighbouring genes | 1 | 1 | 1 | 0.91 | 0.01–71.08 | 14 | 11 | 0.841 | 1.15 | 0.48–2.82 |
| CDKN2B | GWAS proposed | 0 | 1 | 0.475 | 0 | 0–35.30 | 1 | 1 | 1 | 0.91 | 0.01–71.08 |
| TCF7L2 | GWAS proposed | 0 | 1 | 0.475 | 0 | 0–35.30 | 5 | 8 | 0.406 | 0.56 | 0.14–1.96 |
| TPK1 | Neighbouring genes | 0 | 1 | 0.475 | 0 | 0–35.30 | 2 | 2 | 1 | 0.91 | 0.07–12.50 |
| ZNF283 | Neighbouring genes | – | – | – | – | – | 17 | 6 | 0.057 | 2.59 | 0.97–8.06 |
| HNF4G | GWAS proposed | – | – | – | – | – | 4 | 1 | 0.377 | 3.63 | 0.36–178.82 |
| TERT | GWAS proposed | – | – | – | – | – | 5 | 6 | 0.765 | 0.75 | 0.18–2.97 |
| UNC13A | Neighbouring genes | – | – | – | – | – | 17 | 8 | 0.158 | 1.94 | 0.79–5.21 |
| LSP1 | GWAS proposed | – | – | – | – | – | 11 | 15 | 0.327 | 0.66 | 0.27–1.55 |
| XRCC1 | Neighbouring genes | – | – | – | – | – | 6 | 12 | 0.153 | 0.45 | 0.14–1.30 |
| ZMIZ1 | GWAS proposed | – | – | – | – | – | 15 | 11 | 0.694 | 1.24 | 0.53–3.00 |
| EMID1 | Neighbouring genes | – | – | – | – | – | 11 | 8 | 0.654 | 1.25 | 0.46–3.59 |
| FGFR2 | GWAS proposed | – | – | – | – | – | 4 | 4 | 1 | 0.91 | 0.17–4.87 |
| CCDC88C | GWAS proposed | – | – | – | – | – | 38 | 45 | 0.219 | 0.76 | 0.47–1.20 |
| ITPR1 | Neighbouring genes | – | – | – | – | – | 17 | 20 | 0.507 | 0.77 | 0.37–1.55 |
| MKL1 | GWAS proposed | – | – | – | – | – | 26 | 19 | 0.547 | 1.24 | 0.66–2.40 |
| CHST9 | GWAS proposed | – | – | – | – | – | 7 | 9 | 0.617 | 0.70 | 0.22–2.13 |
| PEX14 | GWAS proposed | – | – | – | – | – | 9 | 6 | 0.613 | 1.36 | 0.43–4.66 |
| PAX9 | GWAS proposed | – | – | – | – | – | 3 | 7 | 0.207 | 0.39 | 0.06–1.70 |
| PTHLH | GWAS proposed | – | – | – | – | – | 3 | 1 | 0.626 | 2.72 | 0.22–142.85 |
| CDCA7 | GWAS proposed | – | – | – | – | – | 5 | 3 | 0.729 | 1.51 | 0.29–9.76 |
| MAP3K1 | GWAS proposed | – | – | – | – | – | 20 | 11 | 0.206 | 1.66 | 0.75–3.85 |
| RANBP9 | GWAS proposed | – | – | – | – | – | 10 | 5 | 0.309 | 1.82 | 0.56–6.80 |
| DNAJC1 | GWAS proposed | – | – | – | – | – | 8 | 9 | 0.808 | 0.80 | 0.27–2.36 |
| TOX3 | GWAS proposed | – | – | – | – | – | 7 | 7 | 1 | 0.90 | 0.27–3.03 |
| EPB41L5 | Neighbouring genes | – | – | – | – | – | 8 | 8 | 1 | 0.90 | 0.29–2.78 |
| ESR1 | GWAS proposed | – | – | – | – | – | 3 | 6 | 0.323 | 0.45 | 0.07–2.12 |
| MDM4 | GWAS proposed | – | – | – | – | – | 7 | 3 | 0.349 | 2.12 | 0.48–12.73 |
| CDYL2 | GWAS proposed | – | – | – | – | – | 11 | 5 | 0.217 | 2 | 0.64–7.37 |
| TNP1 | Neighbouring genes | – | – | – | – | – | 0 | 2 | 0.226 | 0 | 0–4.82 |
| BABAM1 | Neighbouring genes | – | – | – | – | – | 4 | 3 | 1 | 1.21 | 0.20–8.27 |
| TGFBR2 | GWAS proposed | – | – | – | – | – | 4 | 3 | 1 | 1.21 | 0.20–8.27 |
| ELL | GWAS proposed | – | – | – | – | – | 9 | 5 | 0.430 | 1.63 | 0.49–6.23 |
| NF2 | Neighbouring genes | – | – | – | – | – | 12 | 5 | 0.150 | 2.19 | 0.71–7.95 |
| KCNN4 | Neighbouring genes | – | – | – | – | – | 8 | 4 | 0.393 | 1.82 | 0.49–8.27 |
| DLX2 | Neighbouring genes | – | – | – | – | – | 7 | 4 | 0.553 | 1.59 | 0.40–7.42 |
| KAT5 | Neighbouring genes | – | – | – | – | – | 3 | 2 | 1 | 1.36 | 0.16–16.29 |
| COX11 | GWAS proposed | – | – | – | – | – | 2 | 1 | 1 | 1.81 | 0.09–106.93 |
| EBF1 | GWAS proposed | – | – | – | – | – | 2 | 3 | 0.673 | 0.60 | 0.05–5.27 |
| RAD23B | Neighbouring genes | – | – | – | – | – | 0 | 1 | 0.475 | 0 | 0–35.30 |
| GWAS proposed genes | – | 17 | 4 | 0.008 | 3.89 | 1.26–15.95 | 287 | 251 | 0.679b | 1.05 | 0.86–1.28 |
| Neighbouring genes | – | 9 | 9 | 1 | 0.90 | 0.32–2.58 | 168 | 138 | 0.392b | 1.12 | 0.87–1.44 |
| Total | – | 26 | 13 | 0.077 | 1.83 | 0.90–3.90 | 406 | 353 | 0.512b | 1.07 | 0.89–1.28 |
Abbreviations: GWAS Genome-wide association study, Und undefined
aFisher’s exact test, two-sided
bPearson’s chi-square test with the Yates correction