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Table 2 List of 54 rare variants predicted to be deleterious using MetaLR and MetaSVM

From: Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients

Chr

Start

Gene Symbol

Ref allele

Alt allele

Variant

MetaLR score

MetaSVM score

CountNGR patients

CountSA patients

CountAll patients

GnomAD MAF (Controls, All)

GnomAD MAF (Controls, African)

rs number

Gene linked to PD

16

70,296,316

AARS

T

A

Y535F

0.906

0.836

1

0

1

9.14e-6

0.000

rs756650948

 

22

40,755,001

ADSL

G

T

A206S

0.914

0.976

0

1

1

4.16e-4

0.005

rs148411623

 

5

125,919,688

ALDH7A1

C

T

R110Q

0.980

0.966

0

1

1

3.98e-06

0.000

rs1160207513

 

X

66,863,156

AR

A

T

T559S

0.918

0.858

0

1

1

1.14e-4

0.001

rs139756052

 

22

51,063,778

ARSA

T

C

N442S

0.847

0.816

0

1

1

3.25e-4

0.003

rs6151427

 

22

51,065,288

ARSA

G

T

P220T

0.983

0.969

1

0

1

5.82e-5

7.00e-4

rs146173768

 

1

17,313,614

ATP13A2

T

G

S1004R

0.905

0.844

0

1

1

4.032e-06

0.000

rs1230099396

Yes

16

28,912,085

ATP2A1

G

A

D525N

0.800

0.832

0

1

1

1.65e-3

0.018

rs74573581

 

11

62,458,888

BSCL2

A

G

L290P

0.880

0.818

1

0

1

N/A

N/A

rs1451786763

 

15

42,693,950

CAPN3

G

A

R441Q

0.874

0.811

1

1

2

3.33e-5

2.05e-4

rs147764579

 

10

50,828,566

CHAT

T

G

M84R

0.892

0.828

0

1

1

9.15e-5

0.001

rs376808313

 

1

154,544,030

CHRNB2

C

T

P244L

0.944

0.988

1

0

1

9.14e-6

0.000

rs1462718185

 

15

68,500,645

CLN6

T

C

S257G

0.814

0.811

1

1

2

0.001

0.014

rs151295143

 

21

47,544,826

COL6A2

G

A

G588S

1.000

0.987

0

1

1

8.23e-5

8.00e-4

rs139488626

 

2

238,258,801

COL6A3

G

A

R1683C

0.975

0.933

0

1

1

9.98e-5

3.00e-4

rs116608946

 

3

148,899,821

CP

T

C

E842G

0.931

0.934

1

0

1

0.001

0.011

rs149858116

 

19

10,893,647

DNM2

G

T

V234 L

0.933

0.860

0

1

1

4.57e-5

0.000

rs377159042

 

6

56,765,318

DST

A

C

S106R

0.825

0.858

1

0

1

5.86e-5

7.00e-4

rs375833647

Yes

6

56,765,371

DST

C

T

A89T

0.805

0.824

0

1

1

3.35e-4

3.00e-4

rs370358616

 

X

153,583,294

FLNA

C

T

G1698S

0.910

0.858

0

1

1

7.52e-5

0.000

rs781993685

Yes

X

153,592,919

FLNA

G

A

A666V

0.872

0.829

0

1

1

1.00e-4

1.76e-4

rs374295965

 

14

88,414,158

GALC

G

C

T445S

0.824

0.837

0

3

3

0.001

0.016

rs34134328

Yes

9

36,236,974

GNE

A

C

D203E

0.858

0.820

0

3

3

0.001

0.013

rs35224402

 

17

10,443,936

MYH2

T

C

D328G

0.982

0.935

0

1

1

N/A

N/A

N/A

 

17

10,314,218

MYH8

A

C

L488R

0.967

0.881

0

1

1

N/A

N/A

N/A

 

12

4,763,994

NDUFA9

G

A

R75H

0.901

0.879

1

0

1

8.97e-4

0.008

rs35263902

 

20

13,797,783

NDUFAF5

G

C

G294A

0.981

0.919

0

2

2

4.57e-5

6.98e-4

rs140825882

Yes

1

161,182,208

NDUFS2

C

G

P352A

0.928

0.865

0

1

1

0.073

0.016

rs11576415

 

11

66,618,540

PC

G

C

R732G

0.878

0.882

0

2

2

9.21e-6

0.000

rs112948607

 

15

89,868,793

POLG

G

A

H613Y

0.854

0.858

1

0

1

6.26e-4

0.006

rs147407423

Yes

3

64,133,345

PRICKLE2

T

G

Q274P

0.904

0.838

0

1

1

N/A

N/A

rs564701683

 

14

73,659,375

PSEN1

T

C

V191A

0.992

0.953

0

2

2

N/A

N/A

rs112451138

 

1

227,073,297

PSEN2

G

A

V139 M

0.963

0.948

0

1

1

1.46e-4

0.000

rs202178897

 

1

227,079,048

PSEN2

A

G

Y319C

0.950

0.914

0

1

1

2.78e-5

4.34e-4

rs547494670

 

19

12,921,137

RNASEH2A

C

T

R186W

0.957

0.910

0

1

1

4e-06

0.000

rs77103971

 

19

38,974,116

RYR1

C

T

P1632S

0.858

0.908

1

2

3

1.67e-3

0.020

rs76537615

 

19

38,998,362

RYR1

G

A

D2943N

0.904

0.895

0

2

2

8.31e-4

0.010

rs79294840

 

19

39,019,242

RYR1

C

G

H3642Q

0.873

0.853

0

2

2

9.15e-4

0.011

rs114351116

 

19

39,025,421

RYR1

C

T

A3769V

0.837

0.846

0

1

1

1.42e-4

0.001

rs146361173

 

20

35,533,822

SAMHD1

T

G

N452 T

0.828

0.822

0

1

1

N/A

N/A

N/A

 

17

62,019,123

SCN4A

C

T

V1507I

0.880

0.843

0

1

1

5.82e-5

6.16e-4

rs140517911

 

17

62,036,686

SCN4A

C

A

S653I

0.982

0.976

0

1

1

N/A

N/A

rs535473662

 

17

62,049,961

SCN4A

C

G

E81Q

0.853

0.912

2

2

4

1.34e-3

0.016

rs111926172

 

4

52,895,854

SGCB

T

C

N140S

0.847

0.872

0

1

1

4.16e-5

0

rs775409967

 

15

34,534,333

SLC12A6

C

A

G696 V

0.957

0.934

0

1

1

N/A

N/A

rs369367800

 

15

34,542,869

SLC12A6

A

C

I503M

0.859

0.910

0

1

1

N/A

N/A

N/A

 

6

152,809,602

SYNE1

A

G

W333R

0.925

0.865

0

1

1

1.34e-4

0.002

rs146668256

 

20

2,376,062

TGM6

T

A

L135H

0.984

0.957

0

1

1

9.15e-5

0.001

rs138009191

 

11

61,160,781

TMEM216

A

G

E38G

0.848

0.813

1

0

1

1.25e-4

0.001

rs568253718

 

8

94,827,551

TMEM67

G

A

S928 N

0.822

0.838

0

1

1

3.05e-5

4.45e-4

rs538380011

 

16

2,130,346

TSC2

G

T

G949 V

0.952

0.895

0

1

1

1.42e-4

3.59e-4

rs137854262

 

16

2,134,230

TSC2

C

T

S1092 L

0.871

0.819

0

1

1

1.71e-4

0.002

rs148527903

 

16

2,138,318

TSC2

C

T

R1507C

0.936

0.889

1

0

1

1.83e-5

0.000

rs781630603

 

2

179,590,564

TTN

C

T

G5585S

0.904

0.823

0

1

1

2.77e-5

2.80e-4

rs139549363

 
  1. Chr Chromosome, Start GRCh38 coordinates, Ref allele Reference allele based on GRCh38, Alt allele Alternative (variant) allele found in this study, CountNGR Number of variant alleles in the Nigerian sample, CountSA Number of variant alleles in the South African sample, CountAll Number of variant alleles in the entire study sample, GnomAD MAF (Controls, All) Minor allele frequency of healthy controls from all population groups (n = 60,146 controls) on the public database GnomAD (https://gnomad.broadinstitute.org/), GnomAD MAF (Controls, African) Minor allele frequency of healthy controls from the African/African American subset (n = 8128 controls) on the public database GnomAD, N/A Not available
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BMC Medical Genetics

ISSN: 1471-2350

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