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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