Table 3.
Likely pathogenic missense variants of NTHL1 selected by population rarity or deleterious in silico tool predictions in case–control data of ten multi-center international cohorts.
| NTHL1 missense variants | Case n = 27,421 | Control n = 19,759 | OR | 95% CI | p Value | ||
|---|---|---|---|---|---|---|---|
| Carriers | % | Carriers | % | ||||
| Totala | 316 | 1.15 | 179 | 0.91 | 1.28 | 1.06–1.54 | 0.01 |
| Rare (MAF ≤ 0.001)b | 121 | 0.44 | 70 | 0.35 | 1.25 | 0.92–1.7 | 0.16 |
| Rare (MAF ≤ 0.0001)b | 92 | 0.34 | 49 | 0.25 | 1.35 | 0.95–1.96 | 0.09 |
| Condel (deleterious) | 175 | 0.64 | 92 | 0.47 | 1.37 | 1.06–1.79 | 0.02 |
| PolyPhen2 (damaging) | 161 | 0.59 | 83 | 0.42 | 1.4 | 1.07–1.85 | 0.01 |
| SIFT (deleterious) | 268 | 0.98 | 146 | 0.74 | 1.33 | 1.08–1.63 | 0.006 |
| CADD (≥10) | 282 | 1.03 | 155 | 0.78 | 1.31 | 1.08–1.61 | 0.006 |
| REVEL (≥0.75) | 144 | 0.53 | 72 | 0.36 | 1.44 | 1.08–1.94 | 0.01 |
aIncludes all the missense variants identified.
bMAF, minor allele frequency in non-cancer non-Finnish Europeans in gnomAD database.