Alzheimer's disease, late-onset (IGAP)

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Updated Genetics of Alzheimer's Disease

The below tables provide the best glimpse to date of the genetics of Alzheimer's disease. Tables (b) and on include results from the recent International Genomics of Alzheimer's Project which is the largest genetic study in AD yet.


(a) These are established AD SNPs.

SNP Gene MAF Major/Minor OR * PAF
rs4147929 ABCA7 0.16 G/A 1.15 (1.11–1.19) 2.8
rs6733839 BIN1 0.37 C/T 1.22 (1.18–1.25) 8.1
rs10948363 CD2AP 0.26 A/G 1.10 (1.07–1.13) 2.3
rs9331896 CLU 0.40 T/C 0.86 (0.84–0.89) 5.3
rs6656401 CR1 0.19 G/A 1.18 (1.14–1.22) 3.7
rs11771145 EPHA1 0.35 G/A 0.90 (0.88–0.93) 3.1
rs983392 MS4A6A 0.41 A/G 0.90 (0.87–0.92) 4.2
rs10792832 PICALM 0.37 G/A 0.87 (0.85–0.89) 5.3
rs429358 ApoE-ε4 0.12 T/C 4.89 (4.45–5.39) 27.3
rs75932628 TREM2 0.002 C/T 4.5 (1.7–11.9) 0.8
rs3865444 CD33 0.238 G/T 0.89 (0.86,0.92) --
  • ORs (Odds Ratios) are relative to the minor allele

--(This established AD SNP was not confirmed in IGAP)

[Population attributable fraction (PAF)]


(b) These are newly confirmed AD SNPs in IGAP.

SNP Gene MAF Major/Minor OR * PAF
rs7274581 CASS4 0.08 T/C 0.88 (0.84–0.92) 1.1
rs10838725 CELF1 0.31 T/C 1.08 (1.05–1.11) 2.4
rs17125944 FERMT2 0.08 T/C 1.14 (1.09–1.19) 1.5
rs9271192 HLA 0.28 A/C 1.11 (1.08–1.15) 3.2
rs35349669 INPP5D 0.46 C/T 1.08 (1.05–1.11) 4.6
rs190982 MEF2C 0.39 A/G 0.93 (0.90–0.95) 2.7
rs2718058 NME8 0.37 A/G 0.93 (0.90–0.95) 2.9
rs28834970 PTK2B 0.36 T/C 1.10 (1.08–1.13) 3.1
rs10498633 SLC24A4 0.21 G/T 0.91 (0.88–0.94) 1.5
rs11218343 SORL1 0.04 T/C 0.77 (0.72–0.82) 1.1
rs1476679 ZCWPW1 0.29 T/C 0.91 (0.89–0.94) 3.2
Total PAF 61.8
  • ORs (Odds Ratios) are relative to the minor allele


(c) TREML2 and TRIP4 were suggestive SNPs from IGAP that have now been confirmed AD SNPs.

SNP Gene MAF Major/Minor OR * P value
rs9381040 TREML2 0.297 C/T 0.93 (0.91–0.96) 1.30 ×10−6 SUG
rs74615166 TRIP4 0.02 T/C 1.29 (1.17–1.42) 9.74 ×10−9 SUG
  • ORs (Odds Ratios) are relative to the minor allele


(d) These are suggestive SNPs from IGAP that are yet to be confirmed.

SNP Gene MAF Major/Minor OR * P value
rs8035452 SPPL2A 0.339 T/C 0.93 (0.91–0.96) 3× 10-7 SUG
rs7920721 ECHDC3 0.387 A/G 1.07 (1.04–1.10) 3× 10-7 SUG
rs7818382 NDUFAF6 0.469 C/T 1.07 (1.04–1.10) 8× 10-8 SUG
rs7295246 ADAMST20 0.406 T/G 1.07 (1.04–1.10) 3× 10-7 SUG
rs7225151 SCIMP 0.121 G/A 1.10 (1.06–1.15) 3× 10-7 SUG
rs6678275 None 0.169 G/C 1.09 (1.05–1.13) 3× 10-7 SUG
rs6448799 HS3ST1 0.300 C/T 1.08 (1.05–1.11) 8× 10-8 SUG
rs72807343 SQSTM1 0.011 C/T 1.35 (1.20-1.52) 7× 10-7 SUG
rs2337406 IGH 0.178 A/G 1.15 (1.09-1.20) 3× 10-7 SUG
(chr17:61538148 corresponds to chr17:63460787 on build 37 where below SNP is located)
rs138190086 ACE 0.011 A/G 1.34 (1.20-1.50) 3× 10-7 SUG
rs10751667 AP2A2 0.439 A/T 1.07 (1.04-1.11) 6× 10-7 SUG
  • ORs (Odds Ratios) are relative to the minor allele


(e)

SNP Gene MAF Major/Minor OR * P value
rs8093731 DSG2 0.017 C/T 0.73 (0.62–0.86) 3.02 × 10−5
  • OR (Odds Ratio) is relative to minor allele

Note: It is not clear where this SNP from the second quoted study is obtained. This gene is not quoted on the commentary on the IGAP study.


Tables a and b are modified from the article: [PMID 24443964] Review: The genetics of Alzheimer's disease; putting flesh on the bones

Tables c, d, and e are modified from: [PMID 24495969] Follow-up of loci from the International Genomics of Alzheimer's Disease Project identifies TRIP4 as novel susceptibility gene


TREML2 was confirmed as an AD gene in: [PMID 24439484] Missense variant in TREML2 protects against Alzheimer's disease

Article found that rs3747742 G (minor allele) reduces AD risk