Table 3. Nonsynomous single-nucleotide polymorphisms (nsSNPs) from the Cargill et al. (1) and Halushka et al. (2) surveys with predicted effect on function

SNP handle

HUGO

pos

Aa1

aa2

UID

Sid, %

Prediction offset

Low frequency (<5%) [Cargill et al. (1)]

WIAF-10557

GRL

65

F

V

U78506

44

-1

WIAF-10558

GRL

363

N

S

U78506

44

-6

WIAF-10590

FSHR

524

S

R

M65085

61

6

WIAF-10591

GH1

105

S

C

V00520

45

4

WIAF-10592

GHR

179

R

H

M28462

37

1

WIAF-10605

GHR

495

P

T

M28466

37

5

WIAF-10624

CYP11A

314

E

K

CYP11A

31

-5

WIAF-10625

FSH

20

S

I

M16646

48

-4

WIAF-10651

IGF1

187

A

D

E01349

50

0

WIAF-10662

PC1

221

N

D

D73399

60

-2

WIAF-10726

HSD3B2

94

E

Q

M77144

39

-9

WIAF-10801

ADORA2

50

A

V

U40770

24

-5

WIAF-10811

NTRK1

604

H

Y

PNTRK1

53

4

WIAF-10842

NTRK1

11

G

V

Y09034

55

-3

WIAF-10846

HTR1D

265

S

L

M81589

44

-3

WIAF-10862

SLC6A4

56

G

A

X70697

58

-1

WIAF-10870

HTR1E

262

S

F

Z11166

54

-1

WIAF-10871

HTR2A

439

A

V

M86841

53

1

WIAF-10879

CNTF

182

H

R

CNTF

45

0

WIAF-10952

F2

386

P

T

M17262

56

1

WIAF-10958

F2R

166

S

G

M62424

52

-6

WIAF-10960

F3

163

R

W

J02846

33

0

WIAF-10965

F5

534

R

Q

L32764

40

-1

WIAF-10968

HCF2

7

A

T

M58600

40

-6

WIAF-10971

HCF2

208

R

H

M12849

40

3

WIAF-10973

HCF2

442

T

M

M58600

40

2

WIAF-10975

HMGCR

638

I

V

M11058

63

-4

WIAF-10978

ITGA2B

968

Y

N

M33320

46

3

WIAF-10984

LDLR

2

G

R

L29401

64

1

WIAF-10988

LDLR

468

V

I

L00344

64

-4

WIAF-11001

PTAFR

224

A

D

D10202

79

3

WIAF-11004

TFPI

292

V

M

M58650

57

4

WIAF-11006

ITGB3

169

R

Q

J02703

48

-4

WIAF-11016

CETP

331

G

S

M32996

29

-6

WIAF-11019

CETP

486

V

M

CETP

77

4

WIAF-11030

ITGA2B

40

T

I

M22568

50

2

WIAF-11033

ITGB3

453

V

I

J02703

48

-5

WIAF-11035

LDLR

814

R

Q

LDLR

64

-1

WIAF-11036

LPL

87

A

T

M76722

33

-9

WIAF-11041

PTAFR

338

N

S

L07334

77

-8

WIAF-11043

F10

30

Q

H

L00391

56

-2

WIAF-11052

F13A1

589

L

Q

M21999

43

5

WIAF-11062

F5

809

P

S

M14335

40

1

WIAF-11068

F7

413

R

Q

J02933

70

-1

WIAF-11075

PCI

121

P

A

M68516

62

1

WIAF-11076

PCI

217

G

R

M68516

62

1

WIAF-11082

APOD

115

S

L

M16696

72

-3

WIAF-11085

F13A1

35

V

L

M21987

43

-6

WIAF-11093

F5

1749

L

V

L32770

40

-6

WIAF-11102

F11

308

I

F

M18302

56

0

WIAF-11117

F7

295

V

D

J02933

70

1

WIAF-11120

ANX3

251

P

L

L20589

55

1

WIAF-11125

F11

66

P

L

M21184

56

2

WIAF-11149

F13B

49

M

V

M64554

38

2

WIAF-11168

APOD

87

T

K

S80440

66

3

WIAF-11171

F11

244

Q

R

M18301

56

-4

WIAF-11174

F13A1

551

T

I

M21998

43

0

WIAF-11177

F13B

350

H

R

M64554

38

1

WIAF-11179

F13B

569

D

E

M64554

38

0

WIAF-11192

FGA

446

K

E

J00128

26

-3

WIAF-11196

PCI

105

K

E

M68516

62

-4

WIAF-11200

ANX3

19

S

N

L20593

55

-7

WIAF-11203

F10

7

L

I

F10

56

-1

WIAF-11204

F13B

543

Y

S

M64554

38

3

WIAF-11210

ANX3

219

I

N

L20588

55

1

WIAF-11227

SELP

500

S

F

M60227

44

-1

WIAF-11234

TBXAS1

332

I

T

M80647

80

-1

WIAF-11235

TBXAS1

356

L

V

D34621

80

-3

WIAF-11236

TBXAS1

416

Q

E

D34623

80

-5

WIAF-11243

MPL

168

E

K

M90103

29

2

WIAF-11270

TBXAS1

429

A

T

D34623

80

-3

WIAF-11294

VLDLR

59

V

I

D16508

59

-2

WIAF-11301

PAI2

229

R

H

M31550

60

-2

WIAF-11304

GP1BA

72

R

H

J02940

53

-2

WIAF-11310

LIPC

440

S

N

M35432

41

-2

WIAF-11311

MPL

58

A

V

U68159

28

2

WIAF-11325

CD36

154

V

F

CD36

80

-3

WIAF-11331

SELP

365

M

V

M60225

44

-7

WIAF-11339

PAI1

17

V

I

PAI1

40

-3

WIAF-11348

F5

2222

D

G

M14335

40

0

WIAF-11349

F5

1820

M

I

L32771

40

-7

WIAF-11559

TBXAS1

162

L

I

D34618

80

1

WIAF-11562

HTR2A

197

I

V

S50113

54

-7

Medium frequency (5-15%) WI nsSNPs [Cargill et al. (1)]

WIAF-10604

GHR

440

C

F

M28466

37

-2

WIAF-10606

GHR

579

P

T

M28466

37

-7

WIAF-10665

PC1

690

S

T

D73407

60

-3

WIAF-10667

SHBG

25

R

H

X16349

31

-5

WIAF-10779

DBH

535

R

C

DBH

66

1

WIAF-10793

DBH

304

A

S

DBH

66

-2

WIAF-10826

DRD5

88

L

R

X58454

57

1

WIAF-10898

HTR2A

444

H

Y

M86841

53

3

WIAF-10948

CETP

390

A

P

M32997

29

1

WIAF-10951

F2

165

T

M

M17262

56

-1

WIAF-10961

F5

413

M

T

L32762

40

-6

WIAF-10977

ITGA2B

874

I

S

M33320

46

-6

WIAF-11057

F5

107

D

H

L32757

40

-2

WIAF-11065

F5

228

E

K

M94010

48

-10

WIAF-11074

PCI

55

A

V

M68516

62

-3

WIAF-11091

F5

817

N

T

M14335

40

5

WIAF-11109

F13A1

651

V

I

M22000

43

-3

WIAF-11140

PCI

64

N

S

M68516

62

-6

WIAF-11211

LIPC

95

V

M

M29188

41

-7

WIAF-11217

PAI1

15

A

T

J03764

40

-6

WIAF-11247

SELP

331

S

N

M60225

44

-6

WIAF-11248

SELP

756

T

P

M60231

44

1

High frequency (>15%) WI nsSNPs [Cargill et al. (1)]

WIAF-10549

FSHR

307

A

T

FSHR

61

-8

WIAF-10550

FSHR

680

S

N

M65085

61

-8

WIAF-10553

GHR

544

I

L

X06562

36

-5

WIAF-10554

GNRHR

16

W

S

X15215

50

-5

WIAF-10664

PC1

665

Q

E

D73407

60

-6

WIAF-10753

BDNF

70

V

M

M61176

44

0

WIAF-10780

DRD3

9

S

G

U32499

59

-8

WIAF-10791

COMT

34

C

S

Z26491

76

-6

WIAF-10800

NGFB

35

V

A

M21062

27

-7

WIAF-10854

HTR2C

26

C

S

X80763

29

-2

WIAF-10865

TH

85

V

M

M23597

54

-4

WIAF-10949

CETP

422

V

I

M32997

29

-7

WIAF-10964

F5

513

R

K

L32764

40

2

WIAF-11005

ITGB3

4

P

L

U03881

51

-11

WIAF-11053

F13B

115

H

R

M64554

38

-10

WIAF-11600

F5

858

R

K

M14335

40

-2

WIAF-11601

F5

865

R

H

M14335

40

-5

WIAF-11066

F5

1764

M

V

L32770

40

-12

WIAF-11070

FGA

331

T

A

M64982

26

-8

WIAF-11071

FGB

470

R

K

J00129

53

-1

WIAF-11087

F13A1

565

L

P

M21998

43

-6

WIAF-11088

F13A1

652

Q

E

M22000

43

-9

WIAF-11119

F9

194

A

T

K02402

80

-3

WIAF-11215

LIPC

215

S

N

M35429

41

-7

WIAF-11221

PAI2

404

N

K

J03603

60

-9

WIAF-11222

PAI2

413

S

C

J03603

60

0

WIAF-11229

SELP

603

N

D

M60229

44

-7

WIAF-11231

SELP

640

L

V

M60230

44

-6

WIAF-11238

PAI2

120

N

D

M31548

60

-3

Low frequency (<5%) CWRU nsSNPs [Halushka et al. (2)]

CHAK00022

DCP1

1018

I

T

J04144

50

0

CHAK00023

DCP1

1051

F

V

J04144

50

2

CHAK00026

DCP1

1279

R

Q

DCP1

50

-1

CHAK00044

ADRB3

265

T

M

X72861

42

-1

CHAK00117

NPPA

7

V

M

X01471

45

-5

CHAK00250

AGTR2

248

R

K

U20860

39

1

CHAK00424

EDNRB

17

L

F

D13162

56

-2

CHAK00428

EDNRB

244

T

M

D13164

56

1

CHAK00430

EDNRB

305

S

N

D13165

56

-9

CHAK00440

SELE

149

S

R

M61888

58

3

CHAK00582

ICAM2

37

A

T

M32332

28

-2

CHAK00583

ICAM2

199

R

H

M32333

28

0

CHAK00603

MLR

444

N

T

M16801

49

-5

CHAK00606

MLR

537

R

Q

M16801

49

2

CHAK00607

MLR

554

N

S

M16801

49

-5

CHAK00636

SLC8A1

613

R

H

AF128524

33

1

CHAK00708

PTGIS

236

R

C

D83398

20

0

CHAK00752

PTGER3

169

M

L

D86087

93

-1

CHAK00799

SAH

359

S

N

AC004381

69

-2

CHAK00833

TBXA2R

160

A

T

D15055

21

-7

CHAK00835

TBXA2R

217

V

I

D15055

21

-7

Medium frequency (5-15%) CWRU nsSNPs [Halushka et al. (2)]

CHAK00002

ADD1

460

G

W

L29294

31

2

CHAK00027

DCP1

1286

R

S

DCP1

50

0

CHAK00043

ADRB3

64

W

R

X72861

42

-1

CHAK00092

AGT

207

T

M

X15324

30

-2

CHAK00108

ALDR1

15

I

F

M59856

54

-1

CHAK00274

KCNJ11

337

I

V

KCNJ11

55

-9

CHAK00386

CYP11B2

386

V

A

D13752

64

-2

CHAK00402

DBH

304

A

S

DBH

66

-2

CHAK00433

SELE

575

L

F

M61892

58

-1

CHAK00479

SLC2A2

110

T

I

SLC2A2

40

-8

CHAK00849

TBXAS1

429

A

T

D34623

80

-3

CHAK00860

TBXAS1

356

L

V

D34621

80

-3

High frequency (>15%) CWRU nsSNPs [Halushka et al. (2)]

CHAK00004

ADD1

617

S

C

L29295

31

-1

CHAK00016

DCP1

32

S

P

DCP1

49

-6

CHAK00017

DCP1

49

S

G

DCP1

49

-1

CHAK00094

AGT

268

M

T

X15324

30

-10

CHAK00164

APOA4

380

H

Q

J02758

60

1

CHAK00166

APOC1

16

I

M

J03217

68

-6

CHAK00181

APOC2

77

K

Q

J02698

69

3

CHAK00226

APOC4

96

L

R

U32576

60

1

CHAK00278

KCNJ11

23

E

K

KCNJ11

55

-9

CHAK00312

CLCNKB

334

V

L

Z30644

47

-6

CHAK00357

CYP11B1

293

L

V

M32878

64

0

CHAK00373

CYP11B2

173

K

R

D13752

64

-1

CHAK00382

CYP11B2

339

I

T

D13752

64

-4

CHAK00449

EDN1

198

E

N

Z98050

37

-2

CHAK00570

ICAM1

56

K

M

ICAM1

31

-1

CHAK00577

ICAM1

469

E

K

ICAM1

31

-8

CHAK00596

KLK1

145

Q

E

M33107

67

-3

CHAK00602

MLR

180

I

V

M16801

49

-6

nsSNPs are grouped according to the allele frequencies low (<5%), medium (5-15%), and high (>15%). The column headings are: the SNP identifier from each survey (SNP handle), the Human Genome Organisation locus identifier (HUGO), the position of the polymorphic amino acid in the protein sequence (pos), the reference amino acid (aa1), the alternative amino acid (aa2), the unique identifier for the coding DNA sequence in GenBank (UID), the fraction of shared amino acid identity between the most distantly related sequence in the chosen subalignment and the query sequence (sid), and the predicted effect on function in terms of the group rank offset from the cutoff separating groups of amino acids predicted to be either tolerated or deleterious (prediction offset). Prediction offsets of zero (0) and above are polymorphisms predicted to affect function (higher confidence with larger positive values; see Fig. 4), and offsets below zero are polymorphisms predicted to be functionally tolerated (higher confidence with larger negative values).

 

1. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C. R., Lim, E. P., Kalyanaraman, N., et al. (1999) Nat. Genet. 22, 231-238.

2. Halushka, M. K., Fan, J. B., Bentley, K., Hsie, L., Shen, N., Weder, A., Cooper, R., Lipshutz, R. & Chakravarti, A. (1999) Nat. Genet. 22, 239-247.