Extended Data Table 2.
Sequence variants found in PLD3 in the NIA-LOAD, Knight-ADRC and NIA-UK datasets.
| Chr. position | AA | NIA LOAD | Knight ADRC | NIA-UK | total | MAF % | p-value | OR (95% CI) | EVS MAF% | SIFT | Polyphen | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40872407 | M6R | CA | 0 | 8 | 1 | 9 | 0.19 | 0.02 | 7.73 (1.09-61) | NP | tolerated | deleterious |
| CO | 0 | 1 | 0 | 1 | 0.02 | |||||||
| 40872764 | S63G | CA | 3 | 1 | 0 | 4 | 0.08 | 0.74 | 0.68 (0.18-2.55) | 0.16 | tolerated | neutral |
| CO | 5 | 0 | 0 | 5 | 0.12 | |||||||
| 40872803 | P76A | CA | 3 | 1 | 0 | 4 | 0.08 | 0.12 | NA | 0.03 | tolerated | benign |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40873764 | T136M | CA | 0 | 1 | 0 | 1 | 0.02 | 0.54 | NA | NP | tolerated | deleterious |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40876055 | H197Y | CA | 0 | 1 | 0 | 1 | 0.02 | 0.49 | 0.85 (0.05-13-7) | NP | damaging | benign |
| CO | 0 | 1 | 0 | 1 | 0.02 | |||||||
| 40877584 | K228R | CA | 1 | 1 | 1 | 3 | 0.06 | 0.25 | NA | NP | damaging | deleterious |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40877595 | V232M | CA | 29 | 16 | 1 | 46 | 0.99 | 1.05×10−05 | 3.99 (2.01-7.94) | 0.48 | damaging | deleterious |
| CO | 8 | 2 | 0 | 10 | 0.25 | |||||||
| 40877608 | N236S | CA | 0 | 2 | 0 | 2 | 0.04 | 0.40 | 1.71 (0.15-18.91) | 0.01 | damaging | deleterious |
| CO | 0 | 1 | 0 | 1 | 0.02 | |||||||
| 40877752 | N284S | CA | 0 | 1 | 0 | 1 | 0.02 | 0.54 | NA | NP | tolerated | deleterious |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40880407 | C300Y | CA | 2 | 3 | 0 | 5 | 0.10 | 0.46 | 2.14 (0.41-11.06) | 0.09 | tolerated | deleterious |
| CO | 1 | 0 | 1 | 2 | 0.04 | |||||||
| 40880481 | A325T | CA | 0 | 1 | 0 | 1 | 0.02 | 0.54 | NA | NP | damaging | deleterious |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40883725 | Q406H | CA | 1 | 0 | 0 | 1 | 0.02 | 0.54 | NA | NP | tolerated | neutral |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40883783 | T426A | CA | 1 | 0 | 0 | 1 | 0.02 | 0.54 | NA | NP | tolerated | neutral |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40883911 | G435V | CA | 0 | 0 | 0 | 0 | 0.00 | 0.46 | NA | 0.02 | damaging | deleterious |
| CO | 1 | 0 | 0 | 1 | 0.02 | |||||||
| 40883933 | A442A | CA | 48 | 35 | 12 | 95 | 2.09 | 1.08×10−05 | 2.31 (1.56-3.41) | 1.59 | - | - |
| CO | 17 | 12 | 7 | 36 | 0.90 | |||||||
| 40883956 | Q450L | CA | 0 | 0 | 0 | 0 | 0.00 | 0.46 | NA | NP | tolerated | neutral |
| CO | 0 | 0 | 1 | 1 | 0.02 | |||||||
| 40883962 | G452E | CA | 4 | 6 | 0 | 10 | 0.21 | 0.16 | 2.86 (0.78-10.4) | 0.09 | tolerated | deleterious |
| CO | 0 | 2 | 1 | 3 | 0.07 | |||||||
| 40883967 | G454C | CA | 0 | 1 | 0 | 1 | 0.02 | 0.54 | NA | NP | damaging | deleterious |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| 40884037 | D477G | CA | 0 | 1 | 0 | 1 | 0.02 | 0.49 | 0.42 (0.04- 4.72) | 0.02 | damaging | deleterious |
| CO | 0 | 1 | 0 | 1 | 0.02 | |||||||
| 40884069 | R488C | CA | 0 | 3 | 0 | 3 | 0.06 | 0.25 | NA | 0.02 | damaging | deleterious |
| CO | 0 | 0 | 0 | 0 | 0.00 | |||||||
| total | CA | 1106 | 1114 | 143 | 2363 | |||||||
| total | CO | 928 | 913 | 183 | 2024 |
The coding region of PLD3 was sequenced in 2,363 AD cases and 2,024 controls (see materials and methods) from the Knight-ADRC, NIA-LOAD and the NIA-UK datasets. The table shows the coding variants identified as well as the number of carriers in each dataset. The minor allele frequency (MAF) in cases and in controls, the p-value and the OR for the association with case-control status is shown. The MAF of the identified variants in the Exome Variant Server (EVS) is shown. We also used SIFT and Polyphen to predict the impact of the non-synonymous changes on protein function. NA: not available. NP: not present