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Table 1 BRCA1 isoforms identified by long-range PCR and nanopore sequencing

From: Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events

Isoform designation RNA Size of isoform (bp) Number of MinION reads In-frame/out-of-frame Deleted protein domain(s)a Previously described by Colombo et al. [9]b
Δ11q r.788_4096del 3898 31 In-frame Yes
Δ9,10,11q r.548_670del + r.788_4096del 3775 27 In-frame Yes
Full length 7207 17 In-frame Yes
Δ10-17 r.594_5074del 2726 14 Out-of-frame BCRT No
Δ9,11q r.548_593del + r.788_4096del 3852 10 Out-of-frame Yes
11Δ3110 r.788_3897del 4093 8 In-frame Yes
Δ1Aq,9,10,11q,12-15,16p r.-25_-20del + r.548_670del + r.788_4804 3061 7 In-frame No
Δ14 r.4358_4484del 7080 6 Out-of-frame Yes
Δ10,11,17 r.594_ 4096del + r.4987_5074del 3616 5 In-frame BCRT No
Δ1Aq,11Δ3110,Δ14p,15-17 r.-25_-20del + r.788_3897del + r.4358_4360del + r.4485_ 5074del 3498 5 Out-of-frame BCRT No
Δ9,10 r.548_670del 7084 5 In-frame Yes
Δ1Aq,5q,11q,14,21 r.-25_-20del + r.191_212del + r.788_4096del + r.4358_4484del + r.5278_5332del 3688 5 Out-of-frame RING No
Δ3 r.81_134del 7153 5 Out-of-frame RING Yes
Δ9,10,14 r.548_670del + r.4358_4484del 6957 3 Out-of-frame No
Δ3-23 r.81_ 5467del 1820 3 Out-of-frame RING, BCRT No
Δ2,9,10,11q,21 r.-19_80del + r.548_670del + r.788_4096del + r.74421_74422ins74421 + 873_74421 + 1001 3676 3 Out-of-frame (loss of coding start site) RING No
Δ9-11 r.548_4096del 3658 3 In-frame Yes
Δ2,9,10,11Δ3110,Δ14,20,22 r.-19_80del + r.548_670del + r.788_3897del + r.4358_4484del + r.5194_5277del + r.5333_5406del 3586 3 Out-of-frame (loss of coding start site) RING, BCRT No
Δ11q,21 r.788_4096del + r.5278_5332del 3843 3 Out-of-frame BCRT No
Δ11 r.671_4096del 3781 2 In-frame Yes
Δ3,11Δ3110 r.81_134del + r.788_3897del 4039 1 Out-of-frame RING No
Δ9,10,21 r.548_670del + r.5278_5332del 7029 1 Out-of-frame BCRT No
Δ21 r.5278_5332del 7152 1 Out-of-frame BCRT Yes
Δ3,9,10,11q r.81_134del + r.548_670del + r.788_4096del 3721 1 Out-of-frame RING No
Δ15-17 r.4485_ 5074del 6617 1 Out-of-frame BCRT Yes
11Δ3110,14,20-22 r.788_3897del + r.4358_4484del + r.5194_ 5406del 3753 1 Out-of-frame BCRT No
Δ8,11 r.442_547 + r.671_4096del 3675 1 Out-of-frame No
11Δ3110,Δ14 r.788_3897del + r.4358_4484del 3966 1 Out-of-frame No
Δ11q,19,20 r.788_4096del + r.5153_5193_ + r.5194_5277del 3773 1 Out-of-frame BCRT No
Δ5,9,10,11q r.135 _212del + r.548_670del + r.788_4096del 3697 1 In-frame RING No
Δ3,9 r.81_134del + r.548_593del 7107 1 Out-of-frame RING No
11Δ3110,Δ21,23 r.788_3897del + r.5278_5332del + r.5407_5467del 3977 1 Out-of-frame BCRT No
  1. bp base pairs, BRCT BRCA1 C-terminal domain, RING RING finger domain, Δ whole or partial exon skipping, partial intron retention
  2. aOnly clinically important BRCA1 protein domains are shown (ENIGMA BRCA1/2 Gene Variant Classification Criteria, Version 2.5 29 June 2017, https://enigmaconsortium.org/library/general-documents/). Position of amino acid residues denoting BRCA1 protein domains are as follows: RING, 1–101 and BCRT, 1651–1863
  3. bNovel isoforms that are created entirely from previously identified partial or whole exon skipping events are shown in bold