Table 2 List of five variants identified and eight strong candidate variants.

From: Analysis of rare Parkinson’s disease variants in millions of people

 

rsID

Variant Name

Ref

Alt

CLNSIG

Power

OR

L95

U95

Penetrance

PL95

PU95

MAF (MAC) cases

MAF (MAC) controls

R1

rs34637584

LRRK2 p.G2019S

G

A

P/R

0.97

11.8

10.5

13.2

0.3

0.2

0.3

0.01 (470)

0.001 (3,385)

 

rs76763715

GBA1 p.N409S

T

C

P/R

1.00

2.3

2.0

2.5

0.0

0.0

0.1

0.01 (487)

0.006 (18,190)

 

rs75548401

GBA1 p.T408M

G

A

C/U/U

1.00

1.5

1.4

1.6

0.0

0.0

0.0

0.02 (206)

0.009 (1,013)

 

rs2230288

GBA1 p.E365K

C

T

C/U/U

1.00

1.4

1.3

1.5

0.0

0.0

0.0

0.03 (1,099)

0.02 (74,759)

 

rs34424986

PRKN p.R275W

G

A

P

1.00

1.3

1.1

1.5

NA

NA

NA

0.004 (138)

0.003 (8,532)

R2.1

rs34995376

LRRK2 p.R1441H

G

A

P

0.06

43.0

13.8

133.9

0.8

0.2

1.0

2e-04 (6)

0 (14)

 

rs80356771

GBA1 p.R502C

G

A

P

0.60

3.8

2.7

5.4

0.1

0.0

0.1

0.001 (45)

4e-04 (1,271)

 

rs78973108

GBA1 p.R296Q

C

T

P

0.10

3.7

2.1

6.5

0.9

0.2

1.0

1e-04 (4)

0 (10)

 

rs147138516

GBA1 p.D179H

C

G

C/U/U

0.41

3.3

2.1

5.0

0.0

0.0

0.1

2e-04 (6)

1e-04 (272)

 

rs111910483

LRRK2 p.L1795F

G

T

C/U/U

0.30

2.5

1.6

3.8

0.1

0.0

0.4

4e-04 (2)

1e-04 (53)

R2.2

rs28365216

LRRK2 p.N238I

A

T

C/U/U

0.05

9.4

1.5

58.1

0.6

0.1

1

1e-04 (2)

0 (3)

 

rs80356769

GBA1 p.V433L

C

A

P

0.13

4.18

1.99

8.77

0.11

0.05

0.2

3e-04 (9)

0 (149)

 

rs201106962

SNCA p.H50Q

A

C

C/U/U

0.64

2.0

1.2

3.5

0.05

0.02

0.1

0.001 (10)

4e-04 (18)

  1. R1 are variants in our main results, having passed 80% and Bonferroni correction. R2 describes variants not passing 80% power with ORs greater than 2. R2.1 are variants passing Bonferroni correction, R2.2 are pathological variants passing p value < 0.05, dominantly inherited genes, and previously linked to PD. Variants in the R2 group are strong candidates for a potential association with PD, based on their high ORs and p value status. More information can be found in Supplementary Table 8. Variants with wide confidence intervals should be interpreted carefully.
  2. Ref reference allele, Alt alternate allele, CLNSIG clinical significance based on ClinVar, Power statistical power at OR = 2 and alpha=0.05, OR odds ratio, L95 Lower boundary 95% confidence interval, U95 upper boundary 95% confidence interval, PL95 Lower boundary 95% confidence interval penetrance, PU95 Upper boundary 95% confidence interval penetrance, MAF minor allele frequency, MAC minor allele count, P pathogenic, P/R pathogenic/risk factor, C/U/U conflicting, uncertain, unknown.
Back to article page