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Table 1 nsSNPS that were predicted to be functionally significant by SIFT (Tolerance index) and PolyPhen (PSIC score).

From: Investigation on the role of nsSNPs in HNPCC genes – a bioinformatics approach

Gene ids

SNP ids

Alleles

Amino acid change

Reference

SIFT

PolyPhen

Tolerance index

Predicted impact

PSIC score

Predicted impact

MLH1

rs41295280

C/G

G22A

[45, 46]

0.03

Intolerant

1.606

Possibly damaging

 

rs11541859

C/G

E89Q

-NA-

0.04

Intolerant

1.012

Borderline

 

rs41295282

A/G

S93G

[4648]

0.07

Potentially Intolerant

1.828

Possibly damaging

 

rs35338630

C/G

R264G

[46, 49]

0.00

Intolerant

1.711

Possibly damaging

 

rs41295284

A/T

L607H

[45, 46, 50]

0.06

Potentially Intolerant

1.665

Possibly damaging

 

rs35045067

A/G

Y646C

[46]

0.00

Intolerant

2.978

Probably damaging

 

rs2020873

C/T

H718Y

[51, 52]

0.09

Potentially Intolerant

2.738

Probably damaging

MSH2

rs17217723

A/G

Y43C

[17, 46]

0.00

Intolerant

2.970

Probably damaging

 

rs33946261

C/G

H46Q

[45, 46, 53]

0.25

Tolerant

2.988

Probably damaging

 

rs17217772

A/G

N127S

[17, 46, 54]

0.01

Intolerant

2.359

Probably damaging

 

rs4987188

A/G

G322D

[17, 46, 55]

0.37

Tolerant

1.504

Possibly damaging

 

rs17224367

C/T

L390F

-NA-

0.02

Intolerant

0.949

Benign

 

rs35717997

C/T

P415S

[46]

0.05

Intolerant

1.982

Possibly damaging

 

rs180522

T/G

H639Q

[46, 56]

0.00

Intolerant

3.352

Probably damaging

 

rs41295290

A/G

D646G

-NA-

0.05

Intolerant

2.410

Probably damaging

 

rs41294982

C/T

P670L

[46, 56]

0.00

Intolerant

3.379

Probably damaging

 

rs34319539

A/T

K909I

-NA-

0.05

Intolerant

1.863

Possibly damaging

 

rs41295182

G/T

L911R

[46, 56]

0.04

Intolerant

1.961

Possibly damaging

MSH6

rs41294988

A/C

K13T

[45]

0.01

Intolerant

1.722

Possibly damaging

 

rs1042821

C/T

G39E

[57, 58]

0.82

Tolerant

1.530

Possibly damaging

 

rs41294984

C/T

S65L

[45]

0.25

Tolerant

1.620

Possibly damaging

 

rs3211299

A/C

S144I

[45]

0.02

Intolerant

1.883

Possibly damaging

 

rs41295268

A/G

R468H

[45]

0.54

Tolerant

1.954

Possibly damaging

 

rs728619

A/C

Y538S

-NA-

0.78

Tolerant

2.674

Probably damaging

 

rs41295270

C/T

S580L

[45]

0.19

Borderline

2.399

Probably damaging

 

rs35552856

A/C

K728T

[59]

0.41

Tolerant

1.539

Possibly damaging

 

rs34374438

A/T

K854M

[58, 60]

0.04

Intolerant

2.087

Probably damaging

 

rs2020912

C/T

V878A

[57, 58]

0.52

Tolerant

1.540

Possibly damaging

 

rs41295278

A/G

R1321G

[45]

0.07

Potentially Intolerant

1.975

Possibly damaging

PMS1

rs5742973

C/G

E27Q

-NA-

0.03

Intolerant

1.507

Possibly damaging

 

rs1145231

C/T

M394T

[61]

0.63

Tolerant

1.950

Possibly damaging

 

rs55726197

C/G

Q437H

-NA-

0.18

Borderline

2.057

Probably damaging

 

rs56305733

A/G

Q450R

-NA-

0.59

Tolerant

1.655

Possibly damaging

 

rs1145232

A/G

G501R

[61]

0.49

Tolerant

2.367

Probably damaging

 

rs2066456

A/G

N632S

-NA-

0.74

Tolerant

1.961

Possibly damaging

 

rs56309301

A/C

N855T

-NA-

0.53

Tolerant

1.722

Possibly damaging

PMS2

rs56203955

G/T

Q30P

[61]

0.00

Intolerant

2.838

Probably damaging

 

rs6977072

C/G

P37A

-NA-

0.02

Intolerant

1.503

Possibly damaging

 

rs34506829

A/G

E41K

-NA-

0.00

Intolerant

2.052

Probably damaging

 

rs35943120

A/T

L42I

-NA-

0.00

Intolerant

1.547

Possibly damaging

 

rs35629870

A/G

R151H

-NA-

0.04

Intolerant

2.292

Probably damaging

 

rs36038802

A/C

Q160K

-NA-

0.69

Tolerant

1.544

Possibly damaging

  1. NA-Not Available; nsSNPs which were found to be deleterious by both SIFT and PolyPhen were highlighted as bold.