Table 2 Germline variants detected in SMAD3 and SMAD4 in breast cancer
Gene | Exon | Variants | # Times (%) | RefSnp (rs) number | Case/Control | In silicoPrediction |
|---|---|---|---|---|---|---|
SMAD3 | 9 | IVS9+132A > T | 1 (0.25%) | Novel | Case | No effect |
SMAD3 | 7 | IVS6-132 C > T | 1 (0.18%) | Novel | Control | No effect |
| Â | 7 | IVS7+69 G > C | 4 (0.72%) | rs58056680 | Control | No effect |
| Â | 8 | IVS8-48 T > G | 4 (0.72%) | Novel | Control | No effect |
| Â | 8 | IVS8+161 C > T | 1 (0.18%) | Novel | Control | No effect |
| Â | 9 | IVS8-211 C > T | 1 (0.18%) | rs56264428 | Control | No effect |
| Â | 9 | IVS8-170 C > T | 1 (0.18%) | Novel | Control | No effect |
| Â | 9 | IVS8-55 A > G | 2 (0.36%) | rs28410524 | Control | Abolish branch site |
SMAD3 | 7 | IVS6-113 G > T | 7 (1.72%); 15 (2.11%) | rs2289791 | Case & Control | No effect |
| Â | 7 | IVS6-95 T > C | 4 (0.98%); 15 (2.11%) | rs2289790 | Case & Control | No effect |
| Â | 8 | IVS8+23 A > C | 2 (0.49%); 5 (0.70%) | rs55678244 | Case & Control | No effect |
SMAD4 | 9 | IVS9+118A > G | 1 (0.25%) | Novel | Case | No effect |
| Â | 10 | IVS10+41G > A | 1 (0.25%) | Novel | Case | No effect |
| Â | 10 | c.1350G > A/p.Gln450Gln | 1 (0.25%) | Novel | Case | Loss of ESE motifs |
| Â | 11 | IVS10-33T > A | 1 (0.25%) | Novel | Case | Cryptic branch site |
SMAD4 | 8 | IVS7-121 A > C | 1 (0.18%) | Novel | Control | No effect |
| Â | 8 | IVS8+44 T > C | 1 (0.18%) | rs28539779 | Control | No effect |
| Â | 9 | IVS9+43delTT | 1 (0.18%) | Novel | Control | No effect |
| Â | 9 | IVS9+68delGAA | 1 (0.18%) | Novel | Control | No effect |
| Â | 9 | IVS9+126 del7 | 1 (0.18%) | Novel | Control | Cryptic branch site |
SMAD4 | 11 | IVS10-52 A > T | 1 (0.18%) | Novel | Control | Cryptic donor |
| Â | 11 | c.1701A > G/p.Ile525Val | 1 (0.18%) | Novel | Control | No effect |
| Â | 11 | IVS11+53 A > G | 1 (0.18%) | Novel | Control | No effect |
SMAD4 | 8 | c.1214T > C/p.Phe362Phe | 1 (0.25%); 1 (0.18%) | rs1801250 | Case & Control | Loss of ESE motifs |
| Â | 8 | IVS8+109 A > G | 1 (0.25%); 3 (0.42%) | Novel | Case & Control | Cryptic donor |
| Â | 10 | IVS10+132delA | 3 (0.74%); 2 (0.28%) | Novel | Case & Control | No effect |
| Â | 11 | IVS11+11 C > T | 8 (1.96%); 11 (1.55%) | rs1163402 | Case & Control | No effect |