Table 2.
Coding Variants Found in TREM2 through DNA Sequencing in Patients with Alzheimer's Disease and in Controls.*
| Variant | SNP Number | Position† | Minor Alleles | Patients with Alzheimer's Disease | Controls | Reference Allele | P Values‡ | Odds Ratio (95% CI) | PolyPhen-2§ | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of Nonreference Alleles | No. of Cases | No. of Nonreference Alleles | No. of Controls | ||||||||
| All variants | 60 | 38 | 0.02¶ | ||||||||
| L211P | rs2234256 | 41126655 | G | 0 | 281 | 3 | 503 | A | 0.56 | 0 | Benign (0.001) |
| H157Y | rs2234255 | 41127543 | A | 1 | 281 | 0 | 504 | G | 0.36 | NA | Possibly damaging (0.7) |
| R136Q | rs149622783 | 41127605 | T | 1 | 281 | 1 | 501 | C | 1.00 | 1.8 (0.1–28.6) | Benign (0.0) |
| R98W | rs147564421 | 41129100 | A | 1 | 1091 | 0 | 1107 | G | 0.50 | NA | Probably damaging (1.0) |
| T96K | rs2234253 | 41129105 | T | 4 | 1091 | 3 | 1105 | G | 0.72 | 1.4 (0.3–6.0) | Probably damaging (1.0) |
| D87N | rs142232675 | 41129133 | T | 6 | 1091 | 0 | 1105 | C | 0.02 | NA | Probably damaging (1.0) |
| N68K | NA | 41129188 | C | 0 | 1090 | 1 | 1105 | G | 1.00 | 0 | Benign (0.05) |
| T66M | rs201258663 | 41129195 | A | 1 | 1091 | 0 | 1107 | G | 0.50 | NA | Probably damaging (1.0) |
| R62H | rs143332484 | 41129207 | T | 25 | 1090 | 31 | 1104 | C | 0.50 | 0.8 (0.5–1.4) | Benign (0.02) |
| R47H | rs75932628 | 41129252 | T | 22 | 1091 | 5 | 1105 | C | <0.001 | 4.5 (1.7–11.9) | Probably damaging (1.0) |
| Y38C | NA | 41129279 | G | 3 | 1091 | 0 | 1107 | A | 0.12 | NA | Probably damaging (1.0) |
| Q33X | rs104894002 | 41129295 | A | 2 | 1084 | 0 | 1103 | G | 0.25 | NA | NA |
| Nasu–Hakola mutations | Q33X, Y38C, T66M | 6 | 0 | 0.01 | NA | Known damaging | |||||
NA denotes not applicable.
Position refers to the location of the variant in base pairs in chromosome 6 (hg19).
P values were calculated by means of Fisher's exact test with the use of PLINK software, version 1.07, except as noted. P<0.05 indicates statistical significance.
PolyPhen-2 refers to the pathogenicity prediction on Polymorphism Phenotyping, version 2 (PolyPhen-2). The numbers in parentheses are prediction scores in which 0 indicates benign and 1 damaging.
This P value was calculated with the use of a burden test in PLINK/SEQ, version 0.08. A comparison of frequencies with those in the Exome Variant Server (EVS) database is provided in Table S5 in the Supplementary Appendix.