Table 3.
Low Frequency Nonsynonymous Variants Used in SKAT Test for Gene PNPLA7 and Pleasant Modulated Startle
| Position | REF | ALT | CADD C-score |
REF/HET/ALT | MAF | Beta (SE) | p value |
|---|---|---|---|---|---|---|---|
| 140357186 | C | T | 18.41 | 3287/6/0 | .0009 | −0.061 (.41) | .88 |
| 140357972 | A | G | 0.01 | 0/23/3270 | .0035 | 0.857 (.21) | 5.7e-5 |
| 140358896 | A | T | 2.87 | 3280/13/0 | .0020 | −0.123 (.28) | .66 |
| 140372570 | G | A | 15.64 | 3290/3/0 | .0005 | −0.483 (.59) | .41 |
| 140372588 | T | C | 0.09 | 3274/15/0 | .0023 | −0.048 (.26) | .85 |
| 140374931 | C | T | 2.96 | 3288/5/0 | .0008 | −0.124 (.45) | .78 |
| 140391737 | A | G | 14.51 | 3287/4/0 | .0006 | 0.134 (.51) | .79 |
| 140391739 | G | A | 16.22 | 3292/1/0 | .0002 | −0.160 (1.0) | .87 |
| 140392656 | T | C | 18.80 | 3292/1/0 | .0002 | 0.526 (1.0) | .60 |
| 140400464 | C | T | 10.60 | 3212/80/1 | .0125 | −0.478 (.11) | 1.9e-5 |
| 140400473 | G | C | 9.15 | 3284/9/0 | .0014 | −0.234 (.34) | .49 |
| 140409842 | G | A | 15.20 | 3286/7/0 | .0011 | −0.419 (.39) | .28 |
| 140409877 | C | A | 12.90 | 3287/6/0 | .0009 | 0.284 (.42) | .50 |
| 140409891 | G | C | 11.58 | 3287/6/0 | .0009 | 0.284 (.42) | .50 |
| 140414411 | G | A | 13.75 | 3292/1/0 | .0002 | 1.776 (1.0) | .08 |
| 140414461 | C | A | 13.01 | 3291/2/0 | .0003 | 0.447 (.72) | .53 |
| 140414474 | C | T | 12.30 | 3288/5/0 | .0008 | 0.188 (.46) | .68 |
| 140417222 | C | T | 13.65 | 3291/2/0 | .0003 | 0.212 (.71) | .77 |
| 140437936 | C | T | 13.76 | 3292/1/0 | .0002 | −0.792 (1.0) | .43 |
| 140441299 | G | A | 12.18 | 3288/5/0 | .0008 | 1.014 (.45) | .03 |
| 140441302 | C | A | 14.32 | 3289/4/0 | .0006 | 1.326 (.51) | .01 |
Note. All variants were nonsynonymous missense with no stop gain/loss or start gain/loss. The CADD C-score is phred scaled (phred = −10log10(percentile rank/100)) such that a score of 20 is in the 10th percentile of predicted deleteriousness, 30 in 1st percentile, and so on. It appears that the overall gene signal is dominated by two low-frequency variants with opposite directions of effect. Both variants are not predicted to be highly deleterious, with C-scores of < 1 and 11. PolyPhen annotation for both variants is “benign”; similarly, SIFT annotated both variants as “tolerated.” SKAT = sequence kernel association test (Wu et al., 2011); REF = reference allele on reference genome GRCh37; ALT = nonreference allele observed in the present study; REF/HET/ALT = number of individuals who are homozygous for the REFerence allele, HETerozygous, and homozygous for the ALTernate allele.