Table 1 Mendelian randomization (MR) results of LRRK2-associated proteins for being causal for PD.

From: Proteome wide association studies of LRRK2 variants identify novel causal and druggable proteins for Parkinson’s disease

  

All SNPs

 

Excluding LRRK2 (Chr12)

Cis signal

 

Protein

Aptamer

# SNPs

P value

β

# SNPs

P value

β

# SNPs

P value

β

SDCBP2

X19261.12

1

7.3×10−21 B

0.562

NA

NA

NA

NA

NA

NA

GPNMB

X8606.39

1

9.03×10−20 B

0.201

1

9.03×10−20 B

0.201

1

9.03×10−20 B

0.201

CD68

X18922.27

4

7.58×1011 A

0.219

3

0.011A

0.193

1

4.01×10−5 B

0.270

CD68

X20528.23

4

0.001A

0.210

3

0.220A

0.183

NA

NA

NA

LCT

X9017.58

3

0.005A

0.050

3

0.005A

0.050

1

0.006B

0.050

ENTPD1

X3182.38

2

0.011A

0.293

1

0.793B

0.022

NA

NA

NA

ITGB2

X12750.9

3

0.022A

0.294

2

0.061A

0.134

NA

NA

NA

GPNMB

X8240.207

3

0.031A

0.189

2

7.99×10−7 A

0.147

1

9.03×10−20 B

0.153

C1QTNF1

X6304.8

2

0.041A

0.293

1

0.903B

−0.010

NA

NA

NA

GPNMB

X5080.131

3

0.049A

0.166

2

7.25×10−12 A

0.132

1

9.03×10−20 B

0.135

HLA-DQA2

X7757.5

2

0.967A

−0.013

1

8.27×1013 B

−0.195

1

8.27×10−13 B

−0.195

GRN

X4992.49

2

0.552A

0.197

1

4.78×10−5 B

−0.262

1

4.78×10−5 B

−0.262

GAA

X9385.4

1

0.141B

−0.112

1

0.141B

−0.112

1

0.141B

−0.112

LGALS9

X9197.4

2

0.200A

−0.049

2

0.200A

−0.049

NA

NA

NA

TLR3

X16918.198

2

0.746A

0.055

1

0.382B

−0.018

1

0.382B

−0.018

AGFG2

X23597.11

2

0.420A

0.034

2

0.420A

0.034

1

0.881B

0.007

TMEM106A

X10499.1

2

0.073A

0.314

1

0.436B

0.053

NA

NA

NA

CHIT1

X3600.2

4

0.730A

−0.006

4

0.730A

−0.006

1

0.803B

0.004

OLR1

X3636.37

2

0.992A

−4.63 × 10−4

1

0.793B

0.021

NA

NA

NA

OLR1

X7893.19

2

0.993A

−4.53 × 10−4

1

0.793B

0.021

NA

NA

NA

GREM2

X5598.3

2

0.115A

1.808

1

0.828B

−0.058

NA

NA

NA

  1. AIVW.
  2. BWald ratio (1 SNP MR).
  3. Number of SNPs in MR and IVW (Inverse-variance-weighted) P value. In total, 21 aptamers (17 proteins) had at least one SNP, in PD GWAS, with genome-wide significance (P < 5 × 10−8) in the aptamer’s pQTL. Ten aptamers were excluded from no genome-wide significant SNPs present in the PD GWAS. Wald ratio method performed for 1 IV. Effect size (β) with direction of effect. Significant P values are bolded. Sorted by all SNP MR P values, then MR P value without LRRK2 SNPs.