Table 1. BRCA1, BRCA2 and RAD51C splicing variants carried by patients used in the current study showing detection of aberrant splices.
| Gene | Transcript | Type | Site | Descriptiona | Frequency in controls (ExAC) | Major effect on splicing observed by RT-PCR | References | Percentage of junction reads detected by RNA-Seqb Patients/mean controls |
|---|---|---|---|---|---|---|---|---|
| BRCA1 | NM_007294 | SNV | Ex 15 | c.4675G>C p.Glu1559Gln | — | Δ15q (r.4665_4675del) p.Gln1556Glyfs*14 Δ15 (r.4485_4675del) p.Ser1496Glyfs*14 | This study Supplementary Figure S5 | 13.4/0.16% (Δ15q) 1.3/0.15% (Δ15) |
| BRCA2 | NM_000059 | SNV | Int 1 | c.39−1G>A p.? | — | Δ2 (r.39_67del) p.0 Δ2,3 (r.39_316del) p.0 | This study Supplementary Figure S5 | 20.9%/not detected 4.8%/not detected |
| BRCA2 | NM_000059 | Indel | Ex 3 | c.156_157insAluc p.? | — | Δ3 (r.68_316del) p.Asp23_Leu105del | 37 | 46/1.2% |
| BRCA2 | NM_000059 | SNV | Int 5 | c.475+3 A>G p.? | — | Δ5 (r.426_475del) p.Pro143Glyfs*23 | This study Supplementary Figure S5 | 94/2.5% |
| BRCA2 | NM_000059 | SNV | Ex 17 | c.7975 A>G p.Arg2659Gly | — | Δ17 (r.7806_7976del) p.Ala2603_Arg2659del | 38 | 3%/not detected |
| BRCA2 | NM_000059 | SNV | Int 25 | c.9501+3 A>T p.? | 0.0001486 | Δ25 (r.9257_9501del) p.Gly3086Glufs*3 | 23 | 2.6%/not detected |
| RAD51C | NM_058216 | SNV | Int 4 | c.706−2 A>G p.? | 0.00002471 | Δ5 (r.706_837del) p.Arg237_Val280del | 11 | 29.2/0.03% |
| RAD51C | NM_058216 | Indel | Int 8 | c.1026+5_1026+7del p.? | — | Δ8 (r.966_1026del) p.Arg322Serfs*22 | 11 | 17.9/0.08% |
Abbreviations: ExAC, Exome Aggregation Consortium; HGVS, Human Genome Variation Society; LCL, lymphoblastoid cell line; RNA-Seq, RNA sequencing; RT-PCR, reverse transcription PCR; SNV, single-nucleotide variation.
All the experimental data on splicing presented were obtained from LCLs by using RT-PCR and RNA-Seq. For an alternative junction, the percentage of junction reads was calculated and compared with the mean of the negative controls as described in Patients and Methods.
Variant nomenclature according to HGVS recommendations, nucleotide position was numbered with +1 corresponding to the A of the ATG of the translation initiation codon.
The numerator shows percentage observed in the sample carrying the variant; the denominator shows mean percentage observed in the negative controls.
Variant corresponding to the Portuguese founder mutation c.156_157insAP003441.3:g.105088_105370.