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Table 1 Sequence variants identified in the BRCA1 gene

From: Prevalance of BRCA1 and BRCA2 mutations in familial breast cancer patients in Lebanon

Nucleotide Change AA change Number of patients Clinical Relevance (BIC) Variation class§ Polyphen SIFT Align GVGD
Missense variations
250 G > T C44F* 2 Unknown 5 +++ Not tolerated Class 65
543 C > G P142A* 1 Not reported Not reported ++ Not tolerated Class 0
585 C > A L156I 1 Not reported 3 + Not tolerated Class 0
655A > G Y179C† 2 Unknown 1 +++ Not tolerated Class 45
1186A > G Q356R 19 Unknown 1 +++ Not tolerated Class 0
1575 T > C F486L† 2 Unknown 1 + Tolerated Class 0
1767A > C N550H† 2 Unknown 1 ++ Not tolerated Class 0
2196 G > A D693N 11 No effect 1 + Not tolerated Class 0
2577A > G K820E 1 Unknown 1 + Tolerated Class 0
2731 C > T P871L 47 No effect 1 + Tolerated Class 0
3232A > G E1038G 44 No effect 1 + Not tolerated Class 0
3238 G > A S1040N 2 Unknown 1 + Tolerated Class 0
3646 T > A V1176I 1 Unknown Not reported + Tolerated Class 0
3667A > G K1183R 43 No effect 1 + Tolerated Class 0
4755 G > A D1546N 1 Unknown 1 + Tolerated Class 0
4773 T > C Y1552H 1 Not reported 3 ++ Tolerated Class 0
4956A > G S1613G 45 No effect 1 + Not tolerated Class 0
5075 G > A M1652I 2 Unknown 1 + Tolerated Class 0
Nonsense mutations
5563 G > A W1815X 2 Deleterious 5    
Synonyms
1964 T > C S615S 2 Not reported Not reported    
2201 C > T S694S 47 No effect 1    
2430 T > C L771L 45 No effect 1    
4427 T > C S1436S 44 Unknown 1    
5306 G > C L1729L 1 Not reported Not reported    
UTRs and Intronic variations
66-67delTA 5’-UTR 29 Not reported Not reported    
IVS2-91A > G   1 Not reported Not reported    
IVS5 + 45 T > A   1 Not reported Not reported    
IVS6 + 55 G > A   2 Not reported 3    
IVS7 + 15delTTC   6 Not reported Not reported    
IVS7-34 C > T   17 No effect 1    
IVS8-58delT   10 No effect 1    
IVS11 + 106 G > A   64 Not reported Not reported    
IVS13 + 117 G > A   8 Unknown Not reported    
IVS14-63 C > G   25 Not reported Not reported    
IVS18 + 66 G > A   44 No effect 1    
IVS19-26 G > A   2 Not reported Not reported    
IVS22 + 68 T > C   1 Unknown 3    
c.5711 + 36 C > G 3’-UTR 1 Not reported Not reported    
  1. † Missense considered deleterious when associated.
  2. *Missense considered deleterious.
  3. Polyphen: +++ Variant predicted to be probably damaging, ++ Variant predicted to be possibly damaging, + Variant predicted to be benign.
  4. UMD-BRCA1/2: 1 Variant considered neutral, 2 Variant considered likely-neutral, 3 Variant considered unclassified, 4 Variant considered likely-causal, 5 Variant considered causal.
  5. § in the UMD-BRCA1 database (http://www.umd.be/BRCA1/) (12) using classification system in five classes (13).