Table 1.
Top 2 Genes for Each Endophenotype with Most Significant VTCMC Associations
| Endophenotype | Gene | Chr | No. SNPs with MAF < .05 |
Burden AC for SNPs with MAF < .05 |
Optimal burden MAC |
R2 (%) |
Direction | Bonferroni correction |
p value |
|---|---|---|---|---|---|---|---|---|---|
| P3 | TRIP10 | 19 | 9 | 20 | 4 | .41 | − | 3.4e-6 | 1.2e-4 |
| MADD | 11 | 13 | 174 | 3 | .41 | − | 3.4e-6 | 2.5e-4 | |
| gP3 | KARS | 16 | 8 | 54 | 21 | .56 | + | 3.5e-6 | 1.3e-4 |
| MADD | 11 | 13 | 125 | 3 | .6 | − | 3.5e-6 | 1.7e-4 | |
| SAC | AFTPH | 2 | 15 | 202 | 6 | .44 | + | 3.4e-6 | 8.0e-5 |
| ANXA3 | 4 | 8 | 138 | 104 | .39 | − | 3.4e-6 | 2.3e-4 | |
| SCL | DEFB116 | 20 | 2 | 166 | 163 | .44 | − | 3.4e-6 | 7.3e-5 |
| C6orf221 | 6 | 1 | 12 | 12 | .39 | + | 3.4e-6 | 1.8e-4 | |
| fSCR | PASK | 2 | 23 | 471 | 25 | .56 | − | 3.4e-6 | 1.2e-5 |
| CCT6A | 7 | 3 | 163 | 149 | .47 | − | 3.4e-6 | 2.6e-5 | |
| aSCR | KANK4 | 1 | 14 | 929 | 3 | .53 | − | 3.4e-6 | 2.2e-5 |
| SPAST | 2 | 4 | 80 | 2 | .48 | − | 3.4e-6 | 3.1e-5 | |
| EDA | ZNF691 | 1 | 2 | 10 | 6 | .40 | − | 3.4e-6 | 5.5e-5 |
| KANK4 | 1 | 14 | 998 | 3 | .44 | − | 3.4e-6 | 6.4e-5 | |
| STRTL | FBX022 | 15 | 2 | 21 | 2 | .48 | − | 3.5e-6 | 1.2e-4 |
| RAET1L | 6 | 2 | 14 | 2 | .48 | − | 3.5e-6 | 1.2e-4 | |
| aSTRTL | ANKRD13C | 1 | 2 | 35 | 7 | .50 | − | 3.5e-6 | 8.1e-5 |
| KCNA3 | 1 | 2 | 28 | 27 | .48 | − | 3.5e-6 | 1.6e-4 | |
| pSTRTL | SIL1 | 5 | 5 | 69 | 3 | .69 | + | 3.5e-6 | 7.0e-6 |
| BAI2 | 1 | 7 | 141 | 22 | .67 | + | 3.5e-6 | 1.6e-5 | |
| αPower | C17orf57 | 17 | 10 | 779 | 6 | .59 | − | 3.4e-6 | 1.0e-5 |
| OR5H2 | 3 | 7 | 125 | 52 | .57 | + | 3.4e-6 | 1.2e-5 | |
| βPower | GTPBP3 | 19 | 4 | 228 | 1 | .48 | − | 3.4e-6 | 3.4e-5 |
| C9orf9 | 9 | 2 | 5 | 4 | .47 | − | 3.4e-6 | 4.1e-5 | |
| θPower | MICAL2 | 11 | 23 | 189 | 27 | .59 | + | 3.4e-6 | 1.2e-5 |
| PARD3 | 10 | 10 | 98 | 19 | .49 | + | 3.4e-6 | 7.1e-5 | |
| δPower | FASN | 17 | 25 | 684 | 10 | .54 | + | 3.4e-6 | 5.4e-5 |
| EDC4 | 16 | 6 | 91 | 18 | .42 | − | 3.4e-6 | 1.8e-4 | |
| totPower | FASN | 17 | 25 | 684 | 10 | .49 | + | 3.4e-6 | 1.2e-4 |
| OCEL1 | 19 | 2 | 3 | 2 | .41 | − | 3.4e-6 | 1.5e-4 | |
| αPowerO1O2 | TFPI2 | 7 | 2 | 16 | 2 | .44 | − | 3.4e-6 | 1.3e-4 |
| GTSF1 | 12 | 1 | 13 | 13 | .34 | − | 3.4e-6 | 2.3e-4 | |
| αFreqO1O2 | RNF175 | 4 | 7 | 203 | 49 | .54 | − | 3.4e-6 | 2.1e-5 |
| SMAD1 | 4 | 2 | 5 | 3 | .44 | + | 3.4e-6 | 4.3e-5 |
Note. All endophenotype abbreviations are defined in the text. Genes with a burden allele count < 3 were not considered in arriving at these Bonferroni corrections. VTCMC = variable threshold collapsing and multivariate count burden test (Price et al., 2010); MAF = minor allele frequency; MAC = minor allele count; R2 = coefficient of determination, in this case variance accounted for in residualized, inverse-normalized endophenotype.