Table 1.
Bioinformatics analysis and RNA results of variants with impact on splicing of BRCA2 exons 19, 20, 23 and 24.
| Mutation (HGVS)a |
Bioinformatics analysisc | Splicing outcomed | RNA effect (HGVS)a |
Predicted protein effect (HGVS)a |
|---|---|---|---|---|
| Exons 19-20b | WT Minigene 19-20: N_Sp(99%) | |||
| c.8378G > A (ex19) | [-] ESE, [+] hnRNP-B | N_Sp/Ex19 skipping | r.[8378g > a, 8332_8487del] | p.[G2793E, Ile2778_Gln2829del] |
| c.8486A > T (ex19) | ↓score donor site/[-] SF2/ASF | Ex19 skipping | r.8332_8487del | p.Ile2778_Gln2829del |
| c.8487G > A (ex19) | ↓score donor site/[-] SF2/ASF | Ex19 skipping | r.8332_8487del | p.Ile2778_Gln2829del |
| c.8487+1G > A (ivs19) | [-] Donor site disruption. | Ex19 skipping | r.8332_8487del | p.Ile2778_Gln2829del |
| c.8487+3A > G (ivs19) | ↓score donor site. | Ex19 skipping | r.8332_8487del | p.Ile2778_Gln2829del |
| c.8488-2A > G (ivs19) | [-] Acceptor site | Intron retention/Ex20_12nt deletion/Ex20 skipping | r.[8487_8488ins8487+1_8488-1, 8488_8499del, r.8488_8632del] | p.[Gln2829fsX2, Trp2830_Lys2833del Trp2830LysfsX13] |
| c.8488-1G > A (ivs19) | [-] Acceptor site | Intron retention/Ex20_12nt deletion/Ex20 skipping | r.[8487_8488ins8487+1_8488-1, 8488_8499del, r.8488_8632del] | p.[Gln2829fsX2, Trp2830_Lys2833del Trp2830LysfsX13] |
| Exons 23-24b | WT Minigene 23-24: N_Sp (100%) | |||
| c.8954-3C > G (ivs22) | [+] Acceptor site 2-nt upstream | Ex23_2-nt insertion | r.8954-2_8954-1ins | p.Val2985GlufsX4 |
| c.8954-1_8955delinsAA (ivs22-ex23) | Disruption acceptor site | Ex23_51-nt deletion/Ex23 skipping/Ex23+24 skipping | r.[8954_9004del, 8954_9117del, 8954_9256del] | p.[Val2985_Thr3001del, Val2985GlyfsX3, p.Val2985_Thr3085del] |
| c.8969G > A (ex23) | [+] hnRNPA1; [+] hnRNP-B | N_Sp/Ex23_51-nt del | r.[8969g > a, 8954_9004del] | p.[W2990X, Val2985_Thr3001del] |
| c.9006A > T (ex23) | [-] SRp40; ↑score cryptic site | N_Sp/Ex23_51-nt del | r.[9006a > u, 8954_9004del] | p.[E3002D, Val2985_Thr3001del] |
| c.9076C > T (ex23) | [+] ESS | N_Sp/Ex23 skipping/Ex23+24 skipping | r.[9076c > u, 8954_9117del, 8954_9256del] | p.[Q3026X, Val2985GlyfsX3, Val2985_Thr3085del] |
| c.9117G > A (ex23) | [-] Donor site | Ex23 skipping/Ex23_51-nt del/Ex23+24 skipping | r.[8954_9117del, 8954_9004del, 8954_9256del] | p.[Val2985GlyfsX3, Val2985_Thr3001del, Val2985_Thr3085del] |
| c.9117+1G > T (ivs23) | [-] Donor site | Ex23 skipping | r.8954_9117del | p.Val2985GlyfsX3 |
| c.9117+1G > A (ivs23) | [-] Donor site | Ex23 skipping | r.8954_9117del | p.Val2985GlyfsX3 |
| c.9118-2A > G (ivs23) | [-] Acceptor site. Novel acceptor 7-nt downstream | Ex24_7-nt del/Ex24_24-nt del/Ex23+24 skipping | r.[9118_9124del, 9118_9141del, 8954_9256del] | p.[Val3040MetfsX20, Val3040_Gln3047del, Val2985_Thr3085del] |
| c.9248_9256+7del (ex24-ivs24) | [-] Donor site | Ex24 skipping/Ex24_43-nt del/Ex23+24 skipping | r.[9118_9256del, 9214_9256del, 8954_9256del] | p.[Val3040AspfsX18, Val3072AspfsX18, Val2985_Thr3085del |
| c.9256G > T (ex24) | [-] Donor site | Ex24 skipping/Ex23+24 skipping/Ex24_43-nt del/N_Sp | r.[9118_9256del, 8954_9256del, 9214_9256del,9256g > u] | p.[Val3040AspfsX18, Val2985_Thr3085del, Val3072AspfsX18, G3086X] |
| c.9256+1G > A (ivs24) | [-] Donor site | Ex24 skipping/Ex23+24 skipping/Ex24_43-nt del | r.[9118_9256del, 8954_9256del, 9214_9256del] | p.[Val3040AspfsX18, Val2985_Thr3085del, Val3072AspfsX18] |
aNomenclature of variants at DNA, RNA and protein levels follows the guidelines of the Human Genome Variation Society. bIntronic (ivs) or/and exonic (ex) location of each variant are indicated between brackets. cSummary of bioinformatics results with NNSPLICE and Human Splicing Finder. [-], disruption; [+], creation. ESE, Exonic Splicing Enhancer; ESS, Exonic Splicing Silencer; SF2/ASF and SRp40 are SR proteins that bind ESE/enhancer motifs; hnRNP proteins bind ESS/silencer motifs. dMajor isoforms are described. EX, exon; nt, nucleotide; del, deletion. Wild type minigene of exons 19 and 20 produced a minimal amount (1%) of exon 19 and exons 19+20 skipping. Variants with a relevant fraction of the wild type isoform are italicized (N_Sp: Normal Splicing). The relative proportions of each isoform are shown in Additional file 1, Figure S3.