Table 3.
NAFLD Progressor (N = 28) Versus Population Controls (N = 4455) Comparison: Top Associated Variants in Biologically Relevant Genes
| Gene | Variant | rs# |
NAFLD Progressors With Variant, N (MAF) |
Controls With Variant, N (MAF) |
PolyPhen Prediction | ExAC Global MAF | Genetic Model | P Value |
|---|---|---|---|---|---|---|---|---|
| PNPLA3 | P149 | rs738408 | 24 (0.61) | 1826 (0.23) | NA | 0.26 | SV allelic (and recessive) | 2.09E‐09 |
| PNPLA3 | I148M | rs738409 | 24 (0.61) | 1826 (0.23) | Probably damaging | 0.26 | SV allelic (and recessive) | 2.10E‐09 |
| PARVB | W37R | rs1007863 | 23 (0.70) | 2691 (0.40) | Benign | 0.44 | SV allelic (and recessive) | 8.20E‐06 |
| SAMM50 | D110G | rs3761472 | 17 (0.38) | 1329 (0.16) | Benign | 0.21 | SV allelic | 1.45E‐04 |
| TM6SF2 | E167K | rs58542926 | 9 (0.20) | 549 (0.06) | Probably/possibly damaging | 0.07 | SV allelic | 8.88E‐04 |
| MPO | I717V | rs2759 | 4 (0.11) | 237 (0.03) | Benign | 0.02 | SV recessive | 7.76E‐04 |
| HIST1H2BC | FS (chr6: 26124019 insT) | NA | 1 | 1 | NA | 0 | GB dominant | 0.002 |
| A22S | NA | 1 | 1 | Unknown | 2.00E‐05 | |||
| AZGP1 | H214Q | NA | 1 | 1 | Benign | 2.00E‐05 | GB dominant | 0.007 |
| A46V | rs142669146 | 1 | 0 | Benign | 1.00E‐04 | |||
| MRGPRX1 | Q307R | rs138752944 | 1 | 0 | Benign | 3.00E‐04 | GB recessive | 7.75E‐04 |
| Q307* | rs140371088 | 1 | 0 | NA | 3.00E‐04 | |||
| Y272C | NA | 1 | 0 | Probably damaging | 1.00E‐04 | |||
| CYP26B1 | A420G and R191H | rs7568553 and rs76025186 | 1 | 0 | Benign and probably damaging | 0.005 and 0.001 | GB compound‐heterozygous | 0.006 |
| EFCAB13 | K244* and T577R/T481R | NA and rs142664574 | 1 | 0 | NA and possibly damaging/benign | 2.00E‐05 and 0.005 | GB compound‐heterozygous | 0.007 |
Note: Italicized and bolded variants reached statistical significance.
Abbreviations: ExAC, exome aggregation consortium; GB, gene‐based; MAF, minor allele frequency; NA, not available; SV, single‐variant