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Table 3 Predictive analysis using bioinformatics packages for new mutations of unknown clinical significance for the BRCA1 gene and exon 11 of the BRCA2 gene

From: Mutational analysis of BRCA1 and BRCA2 genes in women with familial breast cancer from different regions of Colombia

     

Prediction Aminotacidic Change

Splice Signal Detection

Gene

Exon

cDNA

Protein Change

Align-GVGD

PANTHER

(SubSPEC)

PROVEAN (Score)

SIFT

(Score)

PolyPhen-2

(Prob.)

MutPred

(Prob.)

SNP&GO

(RI, EA)

5’or 3′ score modification (% variation)

BRCA1

7

c.412C > A

p.Leu138Ile

Prob. Not Deleterious (C0)

Neutral

Neutral (−0.167)

Tolerated

Benign (0.201)

Prob. Not Deleterious

Disease (4,0.714)

 

(−0.156)

−0.056

(0.233)

I11

c.4186-22G > A

NA

NA

NA

NA

NA

NA

NA

NA

Not alter splicing site

11

c.2146 T > A

p.Ser716Arg

Prob. Deleterious

Neutral

Neutral (−1.673)

Tolerated

Benign (0.002)

Prob. Not Deleterious

Neutral (3,0.354)

 

(C65)

(−0.109)

(0.537)

(0.288)

11

c.2368 A > G

p.Thr790Ala

Prob. Deleterious

Neutral (−2)

Deleterious (−3.873)

Tolerated (0.059)

Prob. Damaging (0.926)

Prob. Deleterious

Disease (6,0.775)

 

(C55)

(0.419)

11

c.2876G > A

p.Arg959Lys

Prob. Deleterious

Neutral (−1)

Neutral (− 2.126)

Tolerated (0.081)

Prob. Damaging (0.0.81)

Prob. Deleterious

Disease (8,0.878)

 

(C25)

(0.448)

11

c.3083G > A

p.Arg1028His

Prob. Deleterious

Neutral

Neutral (0.117)

Tolerated (0.304)

Benign (0)

Prob. Not Deleterious

Disease (4,0.723)

 

(C25)

(−2.906)

(0.391)

11

c.3506A > C

p.Asp1169Ala

Prob. Deleterious

Neutral

Neutral (2.020)

Damaging

Benign (0.077)

Prob. Not Deleterious

Disease (2,0.580)

 

(C 65)

(−1.960)

(0.036)

(0.267)

11

c.3978 T > G

p.His1326Gln

Prob. Deleterious

Neutral

Neutral (−1.689)

Damaging

Benign (0.294)

Prob. Not Deleterious

Disease (4,0.708)

 

(C15)

(−1.918

(0.013)

(0.177)

11

c.4033G > A

p.Glu1345Lys

Prob. Deleterious

Neutral (−1.767)

Neutral (−0.754)

Damaging

Prob. Damaging (0.48)

Prob. Not Deleterious

Disease (6,0.799)

 

(C55)

(0.002)

(0.186)

BRCA2

I10

c.1909-37dup

NA

NA

NA

NA

NA

NA

NA

NA

MaxEnt

5.19 3.47 (−33.14%)

HSF:

73.17 72.04 (−1.54%)

I10

c.1909-33delA

NA

NA

NA

NA

NA

NA

NA

NA

GS:

6.5 7.0 (7.14%)

11

c.2147A > G

p.Gln716Arg

Prob. Not Deleterious (C0)

Neutral

Neutral

Tolerated

Benign

Neutral

Disease

 

(−1,58)

(−1.79)

(−0,12)

(0.001)

(0.111)

(4, 0.703)

11

c.2313A > T

p.Leu771Phe

Prob. Not Deleterious (C0)

Neutral

Deleterious

Damaging

Damaging

Neutral

Disease

 

(−2,078)

(−3,155)

(0.03)

1

(0.221)

(2, 0.588)

 

11

c.2386G > A

p.Asp796Asn

Prob. Not Deleterious (C0)

Neutral

Neutral

Damaging

Benign

Neutral

Disease

 

(−1.5)

(−1.678)

(0.01)

(0.031)

(0.18)

(6, 0.779)

 

11

c.2454 T > A

p.Asn818Lys

Prob. Not Deleterious (C0)

Neutral

Deleterious

Damaging

Benign

Neutral

Disease

 

(−1.1)

(−4.026)

(0.01)

(0.024)

(0.346)

(8, 0.916)

 

11

c.2574dup

p.Val859Ser*22

NA

NA

NA

Damaging

NA

NA

NA

 

11

c.3095A > T

p.Lys1032Ile

Prob. Not Deleterious (C0)

Neutral

Deleterious

Damaging

Prob. Damaging

Prob. Deleterious

Disease

 

(−2.6)

(−7.108)

0

(0.971)

(0.504)

(9, 0.929)

 
  1. Entries in boldface indicate likely deleterious mutations