Table 3

Comparison of prediction programs with 15 functional variants

Chromosome

Nucleotide position

Reference nucleotide

Variant nucleotide

Gene

rs ID number

Amino acid changea

PolyPhen-2

SIFT

MAPP

VarioWatch

Loss of function


2

138476119

C

T

HNMT

rs11558538

T105I

D

D

D

D

Yes

4

26092552

C

T

CCKAR

rs52795588

V365I

D

T

T

D

Yes

4

165337896

A

G

ANP32C

NA

Y140H

D

D

D

D

Yes

5

7923973

A

G

MTRR

rs1801394

I49M

D

D

D

D

Yes

7

5993056

C

T

PMS2

rs1805324

M622I

T

T

D

T

Yes

7

5993133

T

A

PMS2

rs1805318

T597S

T

T

D

T

Yes

7

127041823

G

A

PAX4

NA

R121W

D

D

D

D

Yes

7

127042702

G

A

PAX4

rs35155575

R37W

D

D

D

D

Yes

10

42930125

G

A

RET

rs1799939

G691S

D

T

D

D

No

10

72030393

G

A

PRF1

rs35947132

A91V

D

D

D

D

Yes

12

38989178

G

A

LRRK2

rs7133914

R1398H

D

T

T

T

Yes

12

39000112

G

C

LRRK2

rs33949390

R1628P

D

D

T

D

Yes

12

39043595

G

A

LRRK2

rs34778348

G2385R

T

T

D

D

No

13

32911463

A

G

BRCA2

rs1799944

N991D

T

T

D

D

Yes

19

15851431

C

T

CYP4F2

rs2108622

V433M

D

D

T

D

Yes


Correct predictions

11/15

10/15

9/15

10/15


This table highlights the 15 variants that were a gold standard in a functional study.

a Position of the amino acid change associated with the nucleotide change.

Jaffe et al. BMC Proceedings 2011 5(Suppl 9):S13   doi:10.1186/1753-6561-5-S9-S13

Open Data