Table 2.
TREM2 Rare Variants From the Human Exome Array
| rsID | Variant | CADD | PP | SIFT | gnomAD(MAF) | Controls(MAF) | POAG(MAF) | HTG(MAF) | NTG(MAF) | P *Case/Control | P † GnomAD |
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs200392967 | D39E | 23.4 | PS | D | 1.3E-4 | 1/6381 (1.5E-4) | 0/5628 (0.00) | 0/2866 (0.00) | 0/1158 (0.00) | 0.99 | 0.99 |
| rs143332484 | R62H‡ | 11.11 | B | T | 0.012 | 69/6347 (0.011) | 49/5623 (0.009) | 30/2836 (0.011) | 10/1148 (0.009) | 0.24 | 0.06 |
| rs142232675 | D87N‡ | 22.8 | PD | T | 0.002 | 4/6412 (6.2E-4) | 4/5668 (7.1E-4) | 0/2866 (0.00) | 1/1157 (8.6E-4) | 0.86 | 0.008 |
| rs145080901 | A105V | 24.2 | PD | D | 1.3E-4 | 0/6416 (0.00) | 3/5669 (5.3E-4) | 3/2863 (1.0E-3) | 0/1158 (0.00) | 0.07 (POAG)0.03 (HTG) | 0.05(POAG)0.008(HTG) |
| rs149622783 | R136Q | 1.841 | B | T | 1.3E-4 | 2/6414 (3.1E-4) | 3/5669 (5.3E-4) | 1/2865 (3.5E-4) | 1/1157 (8.6E-4) | 0.56 | 0.05 |
| rs79011726 | E151K | 23.2 | B | T | 1.8E-4 | 3/6413 (4.7E-4) | 1/5671 (1.8E-4) | 0/2866 (0.00) | 0/1158 (0.00) | 0.29 | 0.99 |
| rs2234255 | H157Y‡ | 23.1 | PS | D | 2.9E-4 | 3/6413 (4.7E-4) | 2/5670 (3.5E-4) | 0/2866 (0.00) | 1/1157 (8.6E-4) | 0.76 | 0.67 |
B, benign; CADD, combined annotation-dependent depletion score; D, damaging; PD, probably damaging; PP, polyphen2; PS, possibly damaging; SIFT, sorting intolerant from tolerant score; T, tolerated.
*
P value for logistic regression using cases and controls. Cases are POAG overall except for A105V, where the results are provided for both POAG overall and HTG.
†
Comparison of POAG cases to the European population distribution in GnomAD using the Fisher exact test. For A105V, the results are provided for both POAG and HTG.