Table 2:
Top-ranked genes in the primary analyses of ultra-rare functional variants.
| Analysis | URVs | HGNC | Epilepsy gene |
Qualifying Cases | Qualifying Controls | OR (95% CI) |
P value (homogeneity) |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1st Dataset |
2nd Dataset |
Both Datasets |
1st Dataset |
2nd Dataset |
Both Datasets |
||||||
| All GGEs | PPh2 | GABRG2 | yes | 7 (0.64%) | 3 (0.36%) | 10 (0.52%) | 3 (0.04%) | 1 (0.06%) | 4 (0.05%) | 12.1 (3.4 – 54.1) | 1.8 x 10−5 (0.54) |
| REVEL | 4 (0.36%) | 3 (0.36%) | 7 (0.36%) | 0 (0.00%) | 1 (0.06%) | 1 (0.01%) | 28.3 (3.4 – 1307.3) | 1.3 x 10−4 (0.15) | |||
| MTR | 4 (0.36%) | 3 (0.36%) | 7 (0.36%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | ∞ (6.1 – ∞) | 1.2 x 10−5 (0.53) | |||
| Familial GGEs | PPh2 | GABRG2 | yes | 6 (0.95%) | 2 (0.63.%) | 8 (0.85%) | 3 (0.04%) | 1 (0.06%) | 4 (0.05%) | 18.9 (5 – 86.5) | 3.0 x 10−6 (0.63) |
| REVEL | 3 (0.48%) | 2 (0.63%) | 5 (0.53%) | 0 (0.00%) | 1 (0.06%) | 1 (0.01%) | 40.6 (4.4 – 1934.3) | 1.0 x 10−4 (0.19) | |||
| MTR | 3 (0.48%) | 2 (0.63%) | 5 (0.53%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | ∞ (7.9 – ∞) | 1.4 x 10−5 (0.64) | |||
| Sporadic GGEs | PPh2 | FAM13C | - | 5 (0.81%) | 0 (0.00%) | 5 (0.50%) | 4 (0.05%) | 0 (0.00%) | 4 (0.05%) | 17.6 (3.8 – 89.0) | 1.3 x 10−4 (0.44) |
| REVEL | TNFRSF21 | - | 2 (0.47%) | 2 (0.39%) | 4 (0.40%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | ∞ (5.1 – ∞) | 2.3 x 10−4 (0.52) | |
| MTR | TRPV5 | - | 3 (0.70%) | 0 (0.00%) | 3 (0.30%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | ∞ (5.8 – ∞) | 3.0 x 10−4 (0.18) | |
Odds Ratio (OR) and p values are given from a Cochran-Mantel-Haenszel exact test. No gene reached study-wide significance (p < of 2.9 × 10−7). The accompanying homogeneity p value indicates the lowest p value from Breslow-Day & Woolf tests for homogeneity of odds, where p values < 0.05 indicate significantly different odds between the two analysis datasets. CI: Confidence Interval. HGNC: HUGO (Human Genome Organization) Gene Nomenclature Committee gene names. QVs: qualifying variants. URVs: Ultra-rare Variants. See Table 1 for the details of the PPh2, REVEL & MTR analysis models.