Table 2.
NAFLD Protective (N = 54) Versus Population Controls (N = 4455) Comparison: Top Associated Variants in Biologically Relevant Genes
| Gene | Variant | rs# |
NAFLD Protective With Variant, N (MAF) |
Controls With Variant, N (MAF) |
PolyPhen Prediction | ExAC Global MAF | Genetic Model | P Value |
|---|---|---|---|---|---|---|---|---|
| OIT3 | Y60 | NA | 2 (0.02) | 0 (0) | NA | 0 | SV allelic | 1.42E‐04 |
| ABCA8 | P1396L | rs148226092 | 2 (0.02) | 0 (0) | Probably damaging | 8.68E‐05 | SV allelic | 1.42E‐04 |
| SLAMF7 | I13V | NA | 2 (0.02) | 0 (0) | Benign | 7.15E‐05 | SV allelic | 1.42E‐04 |
| PINK1 | L288 | NA | 2 (0.02) | 0 (0) | NA | 3.95E‐05 | SV allelic | 1.42E‐04 |
| PINK1 | P289T | NA | 2 (0.02) | 0 (0) | Probably damaging | 3.95E‐05 | SV allelic | 1.42E‐04 |
| IL32 | C161 | NA | 2 (0.02) | 0 (0) | NA | 1.61E‐05 | SV allelic | 1.42E‐04 |
| SMEK2 | T723A/ T808A | rs76512669 | 4 (0.04) | 20 (0.002) | Benign | 0.001 | SV allelic | 1.72E‐04 |
| ORM1 | T151 | NA | 2 (0.02) | 1 (0.0001) | NA | 5.54E‐05 | SV allelic | 4.24E‐04 |
| HNF1A | P379A | NA | 2 (0.02) | 1 (0.0001) | Probably damaging | 2.10E‐04 | SV allelic | 4.30E‐04 |
| PKD2L1 | L138* | NA | 1 (0.02) | 2 (0.0002) | NA | 1.90E‐04 | SV allelic | 8.39E‐04 |
| IL6 | D162V | rs2069860 | 5 | 75 | Benign | 0.006 | GB dominant | 0.004 |
| THEM5 | P246L | NA | 1 | 0 | Benign | 8.00E‐06 | GB dominant | 0.006 |
| E168K | NA | 1 | 0 | Probably/possibly damaging | 2.00E‐04 | |||
| CYP26B1 | V456L | NA | 1 | 0 | Benign | 0 | GB recessive | 0.012 |
Abbreviations: ExAC, exome aggregation consortium; GB, gene‐based; MAF, minor allele frequency; NA, not available; SV, single‐variant.