Table 2.
PML cohort variant burden results for 669 immune function genes and all genes analyses.
| Analysisa | Gene symbol | Variant (hg19) | Ethnicity | gnomAD subjectsb | Discovery | Replication | Combined | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PML cases | p-value | OR | PML cases | p-value | OR | PML cases | p-value | OR | OR 95% CI | |||||
| 1 | IGLL1 | 22-23915745-G-A | EUR | 0/48/64410 | 2/49 | 6.77E-04 | 57.02 | 1/87 | 6.40E-02 | 15.59 | 3/136 | 1.77E-04 | 30.23 | 5.95–95.84 |
| 2 | MDC1 | 6-30673359-T-G | EUR | 0/347/60562 | 2/49 | 3.25E-02 | 7.38 | 6/87 | 1.27E-05 | 12.85 | 8/136 | 1.55E-06 | 10.85 | 4.55–22.25 |
| 2 | STXBP2 | 19-7712287-G-C | EUR | 0/311/63507 | 2/49 | 2.44E-02 | 8.65 | 2/87 | 6.88E-02 | 4.78 | 4/136 | 4.81E-03 | 6.16 | 1.64–16.31 |
| 3 | FCN2 | 9-137779251-G-A | EUR | 2/505/64168 | 3/49 | 7.00E-03 | 8.19 | 3/87 | 3.23E-02 | 4.48 | 6/136 | 8.21E-04 | 5.79 | 2.08–13.04 |
| 2, 3 | MCM5 | 22-35806756-G-A | EUR | 7/736/64588 | 3/49 | 1.90E-02 | 5.60 | 4/87 | 1.85E-02 | 4.14 | 7/136 | 1.10E-03 | 4.66 | 1.83–9.93 |
| 2 | IGLL1 | 22-23915583-T-C | EUR | 0/541/64515 | 2/49 | 6.41E-02 | 5.03 | 3/87 | 3.74E-02 | 4.22 | 5/136 | 6.14E-03 | 4.51 | 1.44–10.87 |
| 2 | IFIH1 | 2-163136505-C-G | EUR | 6/1367/64143 | 6/49 | 6.18E-04 | 6.38 | 5/87 | 3.95E-02 | 2.79 | 11/136 | 1.86E-04 | 4.02 | 1.95–7.47 |
| 2 | PLCG2 | 16-81939089-T-C | EUR | 3/610/64302 | 2/49 | 7.99E-02 | 4.42 | 3/87 | 5.12E-02 | 3.71 | 5/136 | 1.03E-02 | 3.97 | 1.26–9.54 |
| 4 | PLCG2 | 16-81942175-A-G | EUR | 2/934/64000 | 3/49 | 3.52E-02 | 4.39 | 3/87 | 1.36E-01 | 2.41 | 6/136 | 1.56E-02 | 3.11 | 1.12–6.98 |
| 5 | LY9 | 1-160769595-AG-A | AFR | 0/0/12479 | 1/21 | 1.68E-03 | 1826.27 | 1/28 | 2.24E-03 | 1361.40 | 2/49 | 1.50E-05 | 1313.63 | 48.37–Inf |
| 6 | LIG1 | 19-48643270-C-T | AFR | 0/10/12484 | 1/21 | 1.83E-02 | 62.11 | 1/28 | 2.44E-02 | 46.02 | 2/49 | 9.64E-04 | 52.87 | 5.49–260.10 |
| 6 | PKHD1 | 6-51798908-C-T | AFR | 0/17/12485 | 2/21 | 4.51E-04 | 76.87 | 1/28 | 3.95E-02 | 27.12 | 3/49 | 6.11E-05 | 47.68 | 8.66–173.38 |
| 6 | AIRE | 21-45708278-G-A | AFR | 0/23/12433 | 1/21 | 3.97E-02 | 26.94 | 1/28 | 5.26E-02 | 19.95 | 2/49 | 4.28E-03 | 22.94 | 2.55–97.1 |
| 6 | GFI1 | 1-92946625-G-C | AFR | 0/30/12105 | 1/21 | 5.24E-02 | 20.09 | 1/28 | 6.92E-02 | 14.89 | 2/49 | 7.31E-03 | 17.11 | 1.93–70.83 |
| 6 | NQO2 | 6-3015818-G-A | AFR | 0/54/12484 | 1/21 | 8.85E-02 | 11.50 | 2/28 | 6.90E-03 | 17.69 | 3/49 | 1.42E-03 | 15.00 | 2.9–49.01 |
| 6 | C8B | 1-57409459-C-A | AFR | 0/38/12483 | 1/21 | 6.35E-02 | 16.35 | 1/28 | 8.38E-02 | 12.12 | 2/49 | 1.06E-02 | 13.93 | 1.58–56.58 |
| 6 | CFHR2 | 1-196918605-A-G | AFR | 0/58/12384 | 1/21 | 9.53E-02 | 10.62 | 2/28 | 8.01E-03 | 16.33 | 3/49 | 1.76E-03 | 13.85 | 2.68–45.01 |
| 6 | DNASE1L3 | 3-58191230-G-T | AFR | 0/44/12483 | 1/21 | 7.30E-02 | 14.12 | 1/28 | 9.61E-02 | 10.46 | 2/49 | 1.39E-02 | 12.02 | 1.37–48.52 |
| 6 | TCIRG1 | 11-67818269-G-A | AFR | 2/490/12463 | 4/21 | 8.60E-03 | 5.72 | 3/28 | 9.76E-02 | 2.92 | 7/49 | 3.09E-03 | 4.05 | 1.53–9.17 |
| 4 | PLCG2 | 16-81942175-A-G | AFR | 0/194/12067 | 4/21 | 3.36E-04 | 14.39 | 1/28 | 3.66E-01 | 2.27 | 5/49 | 1.21E-03 | 6.95 | 2.13–17.76 |
| 4 | PLCG2 | 16-81942175-A-G | EUR+AFR | 2/1128/76067 | 7/70 | 8.60E-05 | 7.37 | 4/115 | 9.34E-02 | 2.39 | 11/185 | 1.22E-04 | 4.19 | 2.05–7.72 |
a
Analysis source of the variant: 1, ad-hoc EUR for 669-genes; 2, 669-genes EUR; 3, all-genes EUR; 4, 669-genes EUR+AFR; 5, all-genes AFR; 6, 669-genes AFR.
b
Allele data are reported as homozygotes/heterozygotes/total subjects (allele number/2).