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Table 2 Predicted pathogenicity of 12 novel mutations identified in this study

From: Molecular genetic diagnosis of Glanzmann syndrome in Iranian population; reporting novel and recurrent mutations

Gene name

Mutation at nucleotide level

Protein

SIFT

Polyphen

Mutation taster

HSF

(HumVar results)

ITGB3

c.2 T > C

p.Met1Thr

AFFECT PROTEIN FUNCTION with a score of 0.00

BENIGN with a score of 0.000

-disease causing

-no abrogation of potential splice sites

No significant splicing motif alteration detected

BENIGN with a score of 0.000

ITGB3

c.1656-1658delCTC

p.Ser553del

-

-

-disease causing

-splice site changes

-

-

ITGB3

c.1303 G > T

p.Glu435Ter

Affect protein function

-

-

Alteration of an exonic ESE site.

Potential alteration of splicing.

-

ITGB3

c.155 G > T

p.Cys52Phe

AFFECT PROTEIN FUNCTION with a score of 0.00

This mutation is predicted to be PROBABLY DAMAGING with a score of 1.000

disease causing

splice site changes

Creation of an exonic ESS site.

Potential alteration of splicing.

This mutation is predicted to be PROBABLY DAMAGING with a score of 1.000

ITGB3

c. 538 G > A

p.Gly180Arg

AFFECT PROTEIN FUNCTION with a score of 0.00

This mutation is predicted to be PROBABLY DAMAGING with a score of 1.000

disease causing

splice site changes

Activation of an exonic cryptic acceptor site, with presence of one or more cryptic branch point(s).

Potential alteration of splicing.

This mutation is predicted to be PROBABLY DAMAGING with a score of 1.000

ITGB3

c.401 del A

p.Glu134GlyfsTer10

-disease causing

-no abrogation of potential splice sites

Alteration of an intronic ESS site.

Probably no impact on splicing

ITGA2B

c.1899 del T

p.Cys633TrpfsTer17

-

-

amino acid sequence changed

frameshift

protein features might be affected

Creation of an exonic ESS site.

Potential alteration of splicing.

-

ITGA2B

c.409–3 C > G

-

-

-

Alteration of the WT acceptor site, most probably affecting splicing.

-

ITGA2B

c.1392 A > G

p.Pro464Pro

-

-

-

Alteration of the WT donor site, most probably affecting splicing.

Alteration of an exonic ESE site.

Potential alteration of splicing

-

ITGA2B

c.286 T > A

p.Cys96Ser

AFFECT PROTEIN FUNCTION with a score of 0.00.

PROBABLY DAMAGING with a score of 1.000 (sensitivity: 0.00; specificity:

1.00)

disease causing

-splice site changes

Alteration of an exonic ESE site.

Potential alteration of splicing.

PROBABLY DAMAGING with a score of 0.997 (sensitivity: 0.27; specificity: 0.98)

ITGA2B

c.842 C > T

p.Thr281Ile

TOLERATED with a score of 0.44

BENIGN with a score of 0.241 (sensitivity: 0.91; specificity: 0.88)

-disease causing

amino acid sequence changed

protein features (might be) affected

Alteration of an exonic ESE site.

Potential alteration of splicing.

This mutation is predicted to be BENIGN

ITGA2B

c.1071-1072insG

p.Arg358AlafsTer47

-

-

disease causing

amino acid sequence changed

frameshift

protein features (might be) affected

splice site changes

-

-