ABCMdb

PMID: 25085279

Davit-Spraul A, Oliveira C, Gonzales E, Gaignard P, Therond P, Jacquemin E
Liver transcript analysis reveals aberrant splicing due to silent and intronic variations in the ABCB11 gene.
Mol Genet Metab. 2014 Nov;113(3):225-9. doi: 10.1016/j.ymgme.2014.07.006. Epub 2014 Jul 15., [PubMed]

Sentences

No. Mutations Sentence Comment

41 ABCB11 p.Arg1153Cys Briefly, patient 1 is compound heterozygous for the missense mutation p.Arg1153Cys and the intronic substitution c.3213+4ANG. Login to comment 42 ABCB11 p.Gly982Arg Patient 2 is compound heterozygous for the missense mutation p.Gly982Arg and the silent substitution of unknown significance c.3003ANG (p.Arg1001Arg) in exon 23. Login to comment 43 ABCB11 p.Gly1003Glu Patient 3 is compound heterozygous for the non-sense mutation p.Tyr1041X and the missense mutation p.Gly1003Glu. Login to comment 44 ABCB11 p.Gly982Arg Patient 4 is compound heterozygous for the non-sense mutation p.Tyr354X and the missense mutation p.Gly982Arg. Login to comment 45 ABCB11 p.Arg1128Cys Patient 5 is homozygous for the missense mutation p.Arg1128Cys that has been reported to induce mild exon skipping in minigene construct [7]. Login to comment 48 ABCB11 p.Val444Ala ABCB11 p.Met677Val Byrne et al. [7] showed that the silent variants p.Gly319Gly and p.Ala1028Ala had respectively a mild and a severe exon skipping effect while p.Phe90Phe, p.Val444Ala, and p.Met677Val variants had no effect on splicing. Login to comment 71 ABCB11 p.Arg1153Cys ABCB11 p.Gly982Arg ABCB11 p.Gly982Arg ABCB11 p.Arg1128Cys ABCB11 p.Gly1003Glu Maternal allele Paternal allele Patient 1 c.3213+4ANG p.Val444Ala&#b0; p.Arg1153Cys p.Val444Ala&#b0; Patient 2 p.Gly982Arg p.Val444Ala&#b0; p.Phe90Phe&#b0; c.3003ANG (silent p.Arg1001) Patient 3 p.Gly1003Glu p.Val444Ala&#b0; p.Ala1028Ala** p.Tyr1041X p.Val444Ala&#b0; Patient 4 p.Tyr354X p.Gly319Gly* p.Met677Val&#b0; p.Ala1028Ala** c.389+8GNA p.Gly982Arg Patient 5 p.Arg1128Cys* p.Val444Ala&#b0; p.Met677Val&#b0; p.Thr1086Thr p.Arg1128Cys p.Val444Ala&#b0; p.Met677Val&#b0; p.Thr1086Thr In bold: disease-causing mutation. In italic: common variation. Login to comment 72 ABCB11 p.Val444Ala ABCB11 p.Met677Val ABCB11 p.Arg1128Cys Some variants were previously studied in minigene system [7] and predicted the following consequences: &#b0;no effect: p.Phe90Phe (rs4148777); p.Met677Val (rs11568364); p.Val444Ala (rs2287322); *mild exon skipping: p.Gly319Gly (rs7563233); p.Arg1128Cys (disease-causing mutation); **severe exon skipping: p.Ala1028Ala (rs497692). Login to comment 78 ABCB11 p.Val444Ala ESE Finder predicted modifications of ESE pattern (gain and/or loss) for most variants while RESCUE-ESE predicted loss of ESE for only 3 variants (c.3003ANG, p.Gly319Gly, p.Val444Ala). Login to comment 79 ABCB11 p.Arg1128Cys The missense disease-causing mutation p.Arg1128Cys was only predicted to disrupt a SC35 binding site. Login to comment 86 ABCB11 p.Val444Ala ABCB11 p.Met677Val ABCB11 p.Arg1128Cys Table 3 ABCB11 exonic variations. Modification Location SSF NNSplice MaxEntScan HSF ESE Finder RESCUE-ESE Observed consequence on cDNA WT 3'ss N MUT 3'ss or WT 5'ss N MUT 5'ss WT N MUT c.3003ANG p.Arg1001Arg 54 nt from 5' ss 90.6 N 90.6 Creation of a cryptic donor 54 bp upstream scored 84.8 0.99 N 0.99 Creation of a cryptic donor 54 bp upstream scored 0.98 10.07 N 10.07 Creation of a cryptic donor 54 bp upstream scored 10 96.9 N 96.9 Creation of a cryptic donor 54 bp upstream scored 89.3 Loss: SRp55 Gain: 2 SF2/ ASF SRp40: 3.28 N 5.66 (72.5%) Loss 2 ESE Use of the cryptic 5'ss p.Tyr1002_Arg1019del c.3382CNT p.Arg1128Cys 30 nt from 5' ss 82.7 N 82.7 0.97 N 0.97 8.15 N 8.15 91.3 N 91.3 Loss: SC35 None found No change detected c.270TNC p.Phe90Phe In middle exon None found None found No change detected c.957ANG p.Gly319Gly 58 nt from 3' ss 95.9 N 95.9 0.98 N 0.98 8.61 N 8.61 94.4 N 94.4 SC35: 3.46 N 3.82 (+10%) Loss 2 ESE No change detected c.1331TNC p.Val444Ala 29 nt from 3' ss 92.9 N 92.9 0.99 N 0.99 12.39 N 12.39 94.7 N 94.7 SC35: 3.23 N 3.8 (+17%) Loss 1 ESE No change detected c.2029ANG p.Met677Val 46 nt from 5' ss 93.9 N 93.9 1.00 N 1.00 10.22 N 10.22 97.0 N 97.0 Loss: SRp40 Gain: SF2/ ASF None found No change detected c.3084ANG p.Ala1028Ala 27 nt from 3' ss 87.9 N 87.9 0.86 N 0.96 9.34 N 9.34 89.2 N 89.2 SRp55: 2.93 N 3.54 (+20%) SRp40: 2.86 N 4.30 (+50%) Loss 1 ESE No change detected c.3258ANG p.Thr1086Thr 44 nt from 3' ss 81.1 N 81.1 0.97 N 0.97 10.90 N 10.90 91.0 N 91.0 Gain SRp55 SRp55: 4.55 N 5.16 (-13%) None found No change detected In bold: disease-causing mutation. In italics: common variation. WT, wild type; MUT, mutant; ss, splice site; SRp, serine/arginine-rich protein, a family of conserved splicing factors. Login to comment 97 ABCB11 p.Val444Ala ABCB11 p.Met677Val In accordance to in silico predictions and minigene system's results, no splice defect due to the p.Phe90Phe, p.Val444Ala and p.Met677Val polymorphic variants was observed. Login to comment 98 ABCB11 p.Arg1128Cys Transcripts of RT-PCR and sequencing analysis did not reveal abnormal splicing due to the other common (p.Gly319Gly, p.Ala1028Ala) or disease-causing (p.Arg1128Cys) variations identified in patients (Fig. 2). Login to comment 127 ABCB11 p.Arg1128Cys A - Amplified fragments (G, H and I) from patient 5 harboring homozygous p.Arg1128Cys on exon 25 (fragment G). Login to comment 128 ABCB11 p.Arg1128Cys Fragment G showed only one band at the expected size indicating that p.Arg1128Cys variant does not induce exon 25 skipping. Login to comment 130 ABCB11 p.Met677Val Patient 4 (P4) harbored heterozygous variants p.Gly319Gly on exon 10 (fragment C), p.Met677Val on exon 17 (fragment E) and p.Ala1028Ala on exon 24 (fragment G). Login to comment 134 ABCB11 p.Met677Val ABCB11 p.Arg1128Cys Among those identified in the five PFIC2 patients, Byrne et al. [7] reported that some variants (p.Met677Val, p.Phe90Phe) had no effect on splicing while others affected splicing either mildly (p.Gly319Gly, p.Arg1128Cys), or severely (p.Ala1028Ala). Login to comment