ABCMdb

ABCC7 p.Asp565Gly

ClinVar:	c.1694A>G , p.Asp565Gly ? , not provided
CF databases:	c.1694A>G , p.Asp565Gly (CFTR1) ? , Additional consequence: splicing mutation (mRNA analysis proves that mutation causes exon 12 skipping)
Predicted by SNAP2:	A: D (71%), C: D (66%), E: D (59%), F: D (80%), G: D (75%), H: D (75%), I: D (80%), K: N (53%), L: D (85%), M: D (80%), N: D (59%), P: D (85%), Q: N (72%), R: D (75%), S: D (63%), T: D (66%), V: D (75%), W: D (85%), Y: D (80%),
Predicted by PROVEAN:	A: D, C: D, E: N, F: D, G: D, H: N, I: D, K: N, L: D, M: D, N: N, P: D, Q: N, R: N, S: D, T: D, V: D, W: D, Y: D,

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[hide] CFTR gene mutations--including three novel nucleot... Hum Genet. 2001 Mar;108(3):216-21. Tzetis M, Efthymiadou A, Strofalis S, Psychou P, Dimakou A, Pouliou E, Doudounakis S, Kanavakis E
CFTR gene mutations--including three novel nucleotide substitutions--and haplotype background in patients with asthma, disseminated bronchiectasis and chronic obstructive pulmonary disease.
Hum Genet. 2001 Mar;108(3):216-21., [PMID:11354633]

Abstract [show]
In order to investigate the incidence of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations and unclassified variants in chronic pulmonary disease in children and adults, we studied 20 patients with asthma, 19 with disseminated bronchiectasis (DB) of unknown aetiology, and 12 patients with chronic obstructive pulmonary disease (COPD), and compared the results to 52 subjects from the general Greek population. Analysis of the whole coding region of the CFTR gene and its flanking intronic regions revealed that the proportion of CFTR mutations was 45% in asthma (P<0.05), 26.3% in DB (P>0.05), 16.7% in COPD (P>0.05), compared to 15.4% in the general population. Seventeen different molecular defects involved in disease predisposition were identified in 16 patients. Three potentially disease-causing mutations, T388 M, M1R and V11I, are novel, found so far only in three asthma patients. The hyperactive M470 allele was found more frequently in COPD patients (frequency 70.8%, P<0.01) than in the controls. The study of the TGmTnM470 V polyvariant CFTR allele revealed the presence of CFTR function-modulating haplotypes TG13/T5/M470, TG11/T5/M470, TG12/T5/V470 and TG12/T7, combined with M470 or V470, in six asthma patients, four DB patients (P<0.01), and two COPD patients (P<0.05). These results confirm the involvement of the CFTR gene in asthma, DB and possibly in COPD.

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50 Mutation D565G had previously been reported in a CBAVD patient (Kanavakis et al. 1998). Login to comment
60 of CFTR gene IVS8-(T)n IVS8-(TG)m M470 V tested cases mutationa Asthma 20 1 L997F, T338Mb 9/7 10/12 M/V 1 Y301C 7/7 11/11 V/V 1 M1Rb, V11Ib 7/7 12/10 M/M 1 I148T/- 9/9 10/10 M/V 1 L997F/- 9/9 11/9 M/V 1 R297Q/- 5/5 13/11 M/M 1 R297Q/- 7/7 11/11 V/V 1 R75Q/- 7/7 11/11 V/V 1 A120T/ 5/7 11/11 V/V 1 -/- 7/7 11/12 M/V 1 -/- 7/9 11/11 M/M 2 -/- 7/7 12/10 M/V 7 -/- 7/7 11/11 V/V DB 19 1 F508del, I1027T 9/9 10/10 M/M 1 D565G, R668C 7/7 11/11 M/V 1 T896I/- 7/7 11/10 M/V 1 I148T/- 7/9 11/10 M/V 1 F508del/S977F 5/9 12/10 M/V 1 -/- 7/9 12/10 V/V 1 -/- 7/9 10/10 M/V 1 -/- 7/7 11/12 M/M 2 -/- 7/7 11/10 1 M/V, 1 V/V 2 -/- 7/7 12/10 1 V/V, 1 M/M 3 -/- 7/9 11/10 1 M/M, 2 V/V 4 -/- 7/7 11/11 1 V/V, 3 M/V COPD 12 1 F1052 V/- 7/7 11/10 M/V 1 S1235R/- 7/9 12/10 M/M 1 -/- 5/5 11/12 M/V 1 -/- 7/9 10/10 M/M 2 -/- 7/9 11/10 1 M/M,1 M/V 3 -/- 7/7 11/10 M/V 3 -/- 7/7 11/11 1 M/V, 2 M/M Controls 52 1 F508del/- 7/9 10/10 M/M 1 F1052 V/- 5/7 10/11 M/V 1 F1052 V/- 7/7 11/11 M/M 1 R668C, D565G/- 7/7 11/11 M/M 1 R688C, D565G/- 7/7 11/10 M/V 1 R75Q/- 7/7 11/11 V/V 1 R297Q/- 7/7 11/10 M/V 1 L997F/- 7/9 10/10 M/V 1 -/- 7/7 10/10 M/V 1 -/- 7/9 10/10 M/M 1 -/- 7/9 12/10 M/M 4 -/- 7/9 11/10 1 M/M, 1 V/V, M/V 15 -/- 7/7 11/10 13 M/V, 2 V/V 22 -/- 7/7 11/11 18 V/V, 3 M/V, 1 M/M been found that affect the same codon, of which M1 K affects the same nucleotide (T>A) (Cystic Fibrosis Genetic Analysis Consortium website). Login to comment
72 The proportion of CFTR alleles in each group is expressed as c/d (e), where c indicates the number of alleles with the genotype indicated at left, d indicates the number of total alleles examined in each group and e represents the percentage aMutation name according to the Cystic Fibrosis Genetic Analysis Consortium bNovel mutations, reported for the first time in this study Mutationa Control Pulmonary disease patients Greek CF population patients (PS; PI) (n=52) Asthma DB COPD (n=426) (n=20) (n=19) (n=12) R75Q (356 G/A, exon 3) 1 (0.96%) 1 (2.5%) - - 1 (0.1%) R668C (2134 C/T, exon 13) 2 (1.9%) - 1 (2.6%) - 1 (0.1%) L997F (3123 G>C, exon 17a) 1 (0.96%) 2 (5%) - - - F508del 1 (0.96%) - 2 (5.3%) - 465 (54.6%) D565G (A>G at 1825, exon 12) 2 (1.9%) - 1 (2.6%) - 1 (0.1%) F1052 V (T>G at 3286, exon 17b) 2 (1.9%) - - 1 (4.2%) 1 (0.1%) R297Q (G>A at 1022, exon 7) 1 (0.96%) 2 (5%) - - - Y301C (A>G at 1034, exon 7) - 1 (2.5%) - - - I148T (T>C at 575, exon 4) - 2 (5%) - - 1 (0.1%) T388Mb (C>T at 1295, exon 8) - 1 (2.5%) - - - M1Rb (T>G at 134, exon 1) - 1 (2.5%) - - - V11Ib (G>A at 163, exon 1) - 1 (2.5%) - - - I1027T (3212 T/C, exon 17a) - - 1 (2.6%) - 1 (0.1%) T896I (C>T at 2819, exon 15) - - 1 (2.6%) - - S977F (C>T at 3062, exon 16) - - 1 (2.6%) - - A120T (G>A at 490, exon 4) - 1 (2.5%) - - - S1235R (T>G at 3837, exon 19) - - - 1 (4.2%) - Table 3 Frequency of M470 and (TG)mTn alleles in pulmonary disease patients and controls (DB disseminated bronchiectasis, COPD chronic obstructive pulmonary disease, n number of cases, ND not detected) Clinical status Allele M470 TG11/T7 TG10/T7 TG12/T7 TG10/T9 TG11/T5 TG12/T5 TG13/T5 Asthmaa (n=20) 13 (32.5%) 23 (57.5%) 3 (7.5%) 5 (12.5%) 3 (7.5%) 2 (5%) ND 1 (2.5%) DB (n=19) 17 (44.7) 18 (47.4%) 6 (15.8%) 4 (10.5%) 9 (23.7%) ND 1 (2.6%) ND COPD (n=12) 17 (70.8) 12 (50%) 5 (20.8%) 1 (4.2%) 4 (16.7%) 1 (4.2%) 1 (4.2%) ND Controls (n=52) 37 (35.5%) 71 (68.%) 23 (22.1%) 1 (0.96%) 6 (5.8%) 1 (0.96%) ND ND aAlleles TG11/T9 (2) and TG9/T9 (1) also detected alleles, P<0.01) were both found more frequently in patients with COPD. Login to comment
81 Two patients had two mutations each (F508del and I1027T; D565G and R668C). Login to comment
83 Mutation D565G is a novel Greek mutation previously reported by us in a CBAVD patient (Kanavakis et al. 1998). Login to comment

[hide] Qualitative and quantitative analysis of mRNA asso... Hum Genet. 2001 Dec;109(6):592-601. Epub 2001 Nov 6. Tzetis M, Efthymiadou A, Doudounakis S, Kanavakis E
Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621+3A-->G, 2751+2T-->A, 296+1G-->C, 1717-9T-->C-D565G) and one nonsense mutation (E822X) in the CFTR gene.
Hum Genet. 2001 Dec;109(6):592-601. Epub 2001 Nov 6., [PMID:11810271]

Abstract [show]
The effects of four splicing mutations and one nonsense mutation on cystic fibrosis transmembrane conductance regulator ( CFTR) gene expression were investigated by reverse transcription-polymerase chain reaction analysis of mRNA extracted from nasal epithelial cells harvested from patients harbouring the mutations. We studied four subjects with 621+3A-->G, two with 2751+2T-->A, one with 296+1G-->C, two with 1717-9T-->C-D565G and seven with E822X and compared the results with CFTR mRNA from normal subjects. Our results showed that mutations 621+3A-->G, 2751+2T-->A, and 296+1G-->C, which disrupt the 5' splice donor sites of introns 4, 14a, and 2, respectively, and 1717-9T-->C-D565G, which possibly disrupts the exonic splicing enhancer sequences of exon 12 (owing to the missense mutation in cis), lead to the production of aberrantly spliced mRNA in nasal epithelial cells. Three of the splicing mutations (621+3A-->G, 2751+2T-->A, and 296+1G-->C) result in severe deficiency of normal CFTR mRNA and severe phenotype in the patients. This information is especially useful for mutation 621+3A-->G, which is found in other populations as well, and was initially reported as a polymorphism. The complex allele 1717-9T-->C-D565G results in aberrant splicing of CFTR mRNA with production of transcripts lacking exon 12 (major product), with minor amounts of transcripts revealing joint exon 11 and 12 skipping. Nonsense mutation E822X results in a severe reduction in mRNA levels to about 6% of wild type. Patients with the mutation have a severe clinical phenotype, with both the pancreatic and the pulmonary function affected.

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1 We studied four subjects with 621+3A→G, two with 2751+2T→A, one with 296+1G→C, two with 1717-9T→C-D565G and seven with E822X and compared the results with CFTR mRNA from normal subjects. Login to comment
2 Our results showed that mutations 621+3A→G, 2751+2T→A, and 296+1G→C, which disrupt the 5` splice donor sites of introns 4, 14a, and 2, respectively, and 1717-9T→C-D565G, which possibly disrupts the exonic splicing enhancer sequences of exon 12 (owing to the missense mutation in cis), lead to the production of aberrantly spliced mRNA in nasal epithelial cells. Login to comment
5 The complex allele 1717-9T→C-D565G results in aberrant splicing of CFTR mRNA with production of transcripts lacking exon 12 (major product), with minor amounts of transcripts revealing joint exon 11 and 12 skipping. Login to comment
19 Ultimately, however, all the disease-causing mutations result in defective cAMP-regulated Cl-secretion by epithelial cells, though for various reasons, namely defective pro- Maria Tzetis · Alexandra Efthymiadou · Stavros Doudounakis · Emmanuel Kanavakis Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621+3A→G, 2751+2T→A, 296+1G→C, 1717-9T→C-D565G) and one nonsense mutation (E822X) in the CFTR gene Hum Genet (2001) 109:592-601 DOI 10.1007/s00439-001-0631-0 Received: 18 June 2001 / Accepted: 13 September 2001 / Published online: 6 November 2001 ORIGINAL INVESTIGATION M. Tzetis · A. Efthymiadou · E. Kanavakis (✉) Department of Medical Genetics, Athens University, "Aghia Sophia" Children`s Hospital, Thivon & Livadias, Athens, 11527, Greece e-mail: ekanavak@cc.uoa.gr, Tel.: +30-1-7467460, Fax: +30-1-7795553 S. Doudounakis Cystic Fibrosis Unit, "Aghia Sophia" Children`s Hospital, Athens, Greece (c) Springer-Verlag 2001 tein production (class I), defective protein processing (class II), defective regulation (class III), defective conduction (class IV), or defective synthesis (class V) (Welsh and Smith 1993; Zielenski and Tsui 1995). Login to comment
30 We have investigated three putative splicing mutations, 621+3A→G, 2751+2T→A, 296+1G→C, which disrupt the 5` splice donor sites of introns 4, 14a, and 2, respectively, and the complex allele 1717-9T→C-D565G, which should disrupt the 3` acceptor splice site of intron 10 and possibly cause skipping of exon 12 owing to missense mutation D565G. Login to comment
36 Patients and controls Nasal epithelial cells were collected from four subjects with 621+3A→G (all compound heterozygotes), two with 2751+2T→A (one compound heterozygote and one carrier), one with 296+1G→C, two with 1717-9T→C-D565G (both only carriers), and seven with E822X (three compound heterozygotes, two homozygotes, and two carriers). Login to comment
37 A patient with the 621+1G→T mutation and one with the 1898+1G→T were also studied for the appropriate cDNA fragment and the results were compared with those of mutations 621+3A→G and D565G, respectively. Login to comment
59 593 594 Table1Genotype/phenotypeoftheCFTRpatientsa DevelopmentPulmonaryfunctionCFTRgenotypeAge (yrs) SexAgeat diagnosis Sweattest (mEq/l) Meconium ileusHeight (%-ile) Weight (%-ile) Pancreatic status FEV1 (%) FVC (%) Other Bacterial pathogens Other clinical features F508del/621+3AÆÆÆÆG6FBirth108.5Yes<50%>50%PI10398-Sa,Klebsiella- F508del/621+3AÆÆÆÆG7M2mos93.6No>10%~25%PI131132-Sa,Hi,Sa- 1898+1GÆÆÆÆT/621+3AÆÆÆÆG18F3mos82.1No>97%<90%PI7370Bronchi- ectasis Sa,PaDiabetes W1282X/621+3AÆÆÆÆG2F8mos100.9No<75%>75%PI---Hi,Psputida- F508del/2751+2TÆÆÆÆA5MBirth85.7Yes75%75%PI---Sa,Pa- 3120+1GÆA/296+1GÆÆÆÆC33M27yrs93.1No>75%~50%PI133128-Pa- 1717-9TÆÆÆÆC-D565G/Nb 7F5yrs41.4No??PS? Login to comment
91 C Sequencing results of alternatively spliced transcript (253 bp), lacking all of exon 4 1717-9T→C-D565G cDNA from nasal epithelial cells of two heterozygotes with 1717-9T→C-D565G, two controls, and a patient with the 1898+1G→T mutation was amplified with primers F2/B21 spanning exons 10 to 13. Login to comment
100 Discussion Analysis of CFTR mRNA from nasal epithelial cells, which are the cells biologically relevant to the disease process in CF, shows that mutations 621+3A→G, 2751+2T→A, 296+1G→C, and double allele 1717-9T→C-D565G result in the production of aberrantly spliced mRNA transcripts and that nonsense mutation E822X results in severe reduction of CFTR mRNA. Login to comment
111 The reduc- 598 Fig.3A-D mRNA results for mutations 296+1G→C and 1717-9T→C-D565G. Login to comment
113 A mRNA RT-PCR products analysed by 2% agarose gel electrophoresis. M, Marker lane, phiX174/HaeIII DNA; lane 1: normal control; lane 2: sample with mutation 296+1G→T. B mRNA RT-PCR products analysed by 2% agarose gel electrophoresis. M, Marker lane, phiX174/HaeIII DNA; lanes 1 and 2: samples with double allele 1717-9T→C-D565G; lane 3: sample with mutation 1898+1G→T; lane 4: normal control. Login to comment
129 Two aberrantly spliced transcripts were produced by double allele 1717-9T→C-D565G (mRNA transcripts lacking exon 12 as a major product and a minor aberrant transcript lacking both exons 11 and 12), while mutation 1818+1G→T produced aberrant transcripts lacking exon 12 only. Login to comment
133 However, the high percentage of aberrant transcripts produced lacking exon 12, comparable to those produced from the 1818+1G→T, which is a true splicing mutation, could be the result of D565G (A→G@1826). Login to comment
141 Further studies are needed in order to confirm the effect of D565G mutation on such sequences in exon 12. Login to comment
147 In conclusion, the splicing mutations (621+3A→G, 2751+2T→A, 296+1G→C, and 1717-9T→C-D565G) all lead to the production of alternatively spliced CFTR transcripts. Login to comment

[hide] Multiplex sequence variation detection throughout ... Mol Hum Reprod. 2002 Sep;8(9):880-6. Vrettou C, Tzetis M, Traeger-Synodinos J, Palmer G, Kanavakis E
Multiplex sequence variation detection throughout the CFTR gene appropriate for preimplantation genetic diagnosis in populations with heterogeneity of cystic fibrosis mutations.
Mol Hum Reprod. 2002 Sep;8(9):880-6., [PMID:12200467]

Abstract [show]
Cystic fibrosis (CF) is one of the most important genetic diseases requiring prevention programmes. Preimplantation genetic diagnosis (PGD) represents an alternative to prenatal diagnosis, and is especially appropriate for couples with an unsuccessful reproductive history. For clinical application, protocols must be optimized to minimize PCR failure, allelic drop-out (ADO) and contamination, while simultaneously detecting a wide spectrum of CF genotypes. We have developed a flexible multiplex PCR protocol allowing analysis of sequence variations in any combination amongst seven CFTR gene exons (4, 10, 11, 13 in two parts, 14b, 17b and 21) by nested PCR and denaturing gradient gel electrophoresis analysis, along with analysis of a fluorescently labelled intragenic microsatellite (IVS8CA). The experiments were carried out on 390 single lymphocytes from three CF patients, one heterozygote and one non-CF individual. PCR efficiency of the exons ranged from 90 to 100%, and ADO from 0 to 3.8%. IVS8CA was co-amplified with a PCR efficiency of 92.4 and 10.8% ADO. The present method overcomes the need for separate assays for each CFTR gene mutation. Additionally, it facilitates analysis of any informative linked polymorphic sequence variation (within the seven exons) along with analysis of a microsatellite, which is useful (when informative) for minimizing misdiagnosis and/or indirect diagnosis. This method proved robust and flexible for diagnosing diverse CF genotype combinations in single cells.

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24 cells PCR ADO/total polymorphism (length bp) amplified product (%) cells (%) Patient 1 F508del 25 (196) 10 50 47 (94.0) 0/47 (0) 621 ϩ 1G→T 23 (192) 4 48 (96.0) 1/48 (2.1) Patient 2 N1303K 25 (196) 21 85 80 (94.1) 3/80 (3.8) 2789 ϩ 5G→A 18 (182) 14b 85 (100) 2/85 (2.4) Patient 3 E822X 17 (180) 13 part b 80 72 (90.0) 1/72 (1.4) F1052V 18 (182) 17b 75 (93.8) 2/75 (2.6) Heterozygotea 1719-9T→C 17 (180) 11 75 75 (100.0) 0/75 (0) R668C 13 part a Normal allele 18 (182) 74 (98.7) 1/74 (1.4) Microsatellite 290 268 (92.4) 29/268 (10.8) IVS8CA aIndividual heterozygote for D565G mutation in exon 12 (not included in assay) had two polymorphisms in cis to D565G (1719-9T→C in exon 11 and R668C in exon 13 part a), which were also in cis with 17 CA repeats in IVS8. Login to comment

[hide] New type of disease causing mutations: the example... Hum Mol Genet. 2003 May 15;12(10):1111-20. Pagani F, Stuani C, Tzetis M, Kanavakis E, Efthymiadou A, Doudounakis S, Casals T, Baralle FE
New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12.
Hum Mol Genet. 2003 May 15;12(10):1111-20., 2003-05-15 [PMID:12719375]

Abstract [show]
The increase in genome scanning data, derived from clinical genetics practice, is producing a wealth of information on human sequence variability. The critical issue is to identify if a given nucleotide change results in a benign polymorphism or a disease-causing mutation. We have focused on one specific gene expression step, pre-mRNA processing, where we can functionally define the effect of nucleotide changes and in turn the patient's mutation can shed light on the basic pre mRNA splicing mechanisms. Our results show that several nucleotide changes in CFTR exon 12 induce a variable extent of exon skipping that leads to reduced levels of normal transcripts. This is the case in both natural mutations D565G and G576A (the latter having previously considered a neutral polymorphism) and several site-directed silent substitutions. We demonstrate here that this phenomenon is due to the interference with a new regulatory element that we have named composite exonic regulatory element of splicing (CERES). The effect of single nucleotide substitutions at CERES cannot be predicted by neither SR matrices nor enhancer identification. The recognition and characterization of splicing abnormalities, caused by exon sequence variations at CERES elements, may represent a frequent disease-causing mechanism that also relates to the phenotypic variability. Our results indicate that even the most benign looking polymorphism in an exon cannot be ignored as it may affect the splicing process. Hence, appropriate functional splicing assays should be included in genotype screenings to distinguish between polymorphisms and pathogenic mutations.

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4 This is the case in both natural mutations D565G and G576A (the latter having previously considered a neutral polymorphism) and several site-directed silent substitutions. Login to comment
29 This is the case for two interesting and enigmatic missense mutations, D565G and G576A. Login to comment
30 The D565G mutation was previously reported in a young subject during a screening program and suspected of inducing exon skipping (19). Login to comment
38 Mutations inducing exon skipping include both missense D565G and G576A mutants and several neutral substitutions. Login to comment
40 RESULTS D565G and G576A missense mutations cause CFTR exon 12 skipping in vivo We evaluated, in nasal epithelial cells, the pattern of CFTR exon 12 splicing in both normal subjects and heterozygous individuals with D565G and G576A alleles. Login to comment
41 The missense D565G mutation was detected in seven Greek subjects, always in cis with the common polymorphism R668C (2134C/T) in exon 13 (Table 1). Login to comment
46 Two PCR`s were set up for the nasal epithelial cell cDNA derived from each of the D565G and G576A heterozygotes and from heterozygous controls for R668C, using the common F3 forward primer in exon 11 and each of the two allele specific primers of exon 13 (Fig. 1A). Login to comment
48 In heterozygous individuals the 668C allele carrying the mutations D565G or G576A clearly showed a significantly lower proportion of normal transcripts containing exon 12 than the 668R allele (Fig. 1B, lanes 7-20). Login to comment
53 This analysis showed that the mutant D565G and G576A alleles produced about 40 and 22% of exon inclusion, respectively (Table 1). Login to comment
54 These results indicate that, in nasal epithelial cells, the D565G and G576A missense mutations cause a splicing defect affecting the recognition of CFTR exon 12. Login to comment
55 Defective CFTR exon 12 recognition in hybrid minigenes containing D565G and G576A missense mutations In order to study in more detail the splicing regulation of CFTR exon 12 we have developed a faithful splicing assay that mimics the in vivo situation. Login to comment
61 Allele-specific PCR transcript analysis F3/668R F3/668C Subjects with D565G mutation 89.7Æ 5.9 40Æ 8.3a Subject with G576A mutation 88Æ 3 22Æ 4b Normal controls (heterozygotes for polymorphism R668C) 91.7Æ 5.1 89.3Æ 8.1 Data from six subjects with the D565G mutation, one patient with the G576A mutation and four controls are calculated from the experimental proportions of CFTR exon 12 inclusion adjusted according to the graph shown in Figure 1C. Login to comment
63 a Transcripts containing exon 12 derived from the D565G allele. b Transcripts containing exon 12 derived from the G576A allele. Login to comment
65 RT-PCR allele-specific amplification experiments in D565G and G576A carriers. Login to comment
67 The position of the missense substitutions (D565G and G576A) in exon 12 and of the C668R polymorphic variant in exon 13 is indicated. Login to comment
70 The D565G and G576A carriers presented the missense mutation in cis with the 668C variant. Login to comment
72 RNA extracted from nasal epithelial cells from R688C heterozygous controls (lanes 1-6), from D565G carriers (lanes 7-18) and from the G576A carrier (lanes 19-20), was reverse transcribed and amplified with F3/668C primers (even-numbered lanes) and with F3/668R primers (odd-numbered lanes). Login to comment
89 We then studied the pattern of splicing of a minigene with the missense mutations D565G, G576A and Y577F, the latter associated to classical CF. Login to comment
90 The D565G showed about 35% of normal transcripts containing exon 12 (Fig. 2C). Login to comment
93 This indicates that, unlike G565A and D565G, the disease-causing effect of Y577F cannot be attributed to a splicing abnormality but rather to a protein defect. Login to comment
94 These results indicate that the two missense D565G and G576A mutations associated with non-classical CF induce variable proportion of exon 12 skipping, with G576A most severely affected. Login to comment
97 To evaluate their role in CFTR exon 12 we transfected normal and the three D565G, G576A and Y577F minigenes in different cell lines (Fig. 3A). Login to comment
98 For each cell line tested, the three variants cause comparable changes in splicing efficiency, with D565G and G576A inducing exon skipping and Y577F exon inclusion. Login to comment
118 In WTB, D565G and G576A, overexpression of any of the two splicing factors caused an increase in CFTR exon 12 skipping. Login to comment
119 The amount of normal transcript containing the exon 12 were reduced in WTB (40-51%), very low in D565G (7-12%) and virtually absent in the G576A mutant (Fig. 3B). Login to comment
121 These results indicate that, in the presence of high concentration of inhibitory splicing factors, the D565G and G576A missense mutations produce very low levels of normal CFTR transcripts. Login to comment
124 A total number of 26 hybrid minigenes were analysed containing site-directed mutations at two target sequences of the exon: the AAGATGC sequence at the 50 end from position 12 to 18, which includes D565G at position 15, and a central GGATAC sequence from position 47 to 52 which contains G576A and Y577F of position 48 and 51, respectively (Fig. 4). Login to comment
156 The mild CF phenotypes of the D565G and G576A patients may be explained considering that the variant CFTR protein is functional and that the defect is the consequence of exon 12 skipping induced by the nucleotide change. Login to comment
162 Thus, according to tissue concentration of regulatory splicing factors, and their variations from individual to individual, the D565G and G576A may produce different quantities of mRNAs lacking the exon leading to phenotype variability. Login to comment
187 MATERIALS AND METHODS Patients and DNA mutation analysis Nasal epithelial cells were collected from six individuals carriers of mutation D565G (A>G at 1826 in CFTR cDNA), from one CBAVD patient with G576A and from four non-CF control individuals heterozygotes for the polymorphism R668C. Login to comment
189 Clinical data and CFTR genotypes of all the D565G and G576A carriers are shown in Table 2. Login to comment
193 The phase of linkage for missense mutations D565G and G556A and polymorphism R668C was deduced from family studies and confirmed by sequencing of allele specific cDNAs. Login to comment
225 Data on individual carriers of D565G and G576A mutations Patient code CFTR genotypea Age (years) Sex Reason for CF testing Sweat test (mEq/l) Pancreatic status 1PM D565G/À 16 F Nasal polyposis, Sa 65, 70 PS 2DF D565G 7 1717À9T>C/À 7 F Recurrent episodes of pneumonia 41.4 PS 3MA D565G/À Adult M Carrier status nt nt 4KA D565G/À Adult F Carrier status nt nt 5KP D565G/À Adult M Carrier status nt nt 6PRA D565G/À Adult F Carrier status nt nt 7ORAb D565G/À Adult M CBAVD <40 PS 8 G576A/À Adult M Testicular azoospermia nt nt PS, pancreatic sufficiency; Sa, Staphylococcus; nt, non-tested; CBAVD, congenital bilateral absence of vas deferens. Login to comment

[hide] The phenotypic consequences of CFTR mutations. Ann Hum Genet. 2003 Sep;67(Pt 5):471-85. Rowntree RK, Harris A
The phenotypic consequences of CFTR mutations.
Ann Hum Genet. 2003 Sep;67(Pt 5):471-85., [PMID:12940920]

Abstract [show]
Cystic fibrosis is a common autosomal recessive disorder that primarily affects the epithelial cells in the intestine, respiratory system, pancreas, gall bladder and sweat glands. Over one thousand mutations have currently been identified in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene that are associated with CF disease. There have been many studies on the correlation of the CFTR genotype and CF disease phenotype; however, this relationship is still not well understood. A connection between CFTR genotype and disease manifested in the pancreas has been well described, but pulmonary disease appears to be highly variable even between individuals with the same genotype. This review describes the current classification of CFTR mutation classes and resulting CF disease phenotypes. Complex disease alleles and modifier genes are discussed along with alternative disorders, such as disseminated bronchiectasis and pancreatitis, which are also thought to result from CFTR mutations.

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132 Additionally, point mutations that are assumed to be single nucleotide polymorphisms (SNPs) play a role in CF disease by interfering with splicing signals (see aberrant splicing of exon 9) and causing mis-splicing of the gene, such as 1717-9T → C-D565G in exon 12 (Tzetis et al. 2001), as reviewed by Cartegni et al. 2002. Login to comment

[hide] Restoration of the cystic fibrosis transmembrane c... EMBO Rep. 2004 Nov;5(11):1071-7. Nissim-Rafinia M, Aviram M, Randell SH, Shushi L, Ozeri E, Chiba-Falek O, Eidelman O, Pollard HB, Yankaskas JR, Kerem B
Restoration of the cystic fibrosis transmembrane conductance regulator function by splicing modulation.
EMBO Rep. 2004 Nov;5(11):1071-7., [PMID:15472711]

Abstract [show]
A significant fraction of disease-causing mutations affects pre-mRNA splicing. These mutations can generate both aberrant and correct transcripts, the level of which varies among different patients. An inverse correlation was found between this level and disease severity, suggesting a role for splicing regulation as a genetic modifier. Overexpression of splicing factors increased the level of correctly spliced RNA, transcribed from minigenes carrying disease-causing splicing mutations. However, whether this increase could restore the protein function was unknown. Here, we demonstrate that overexpression of Htra2-beta1 and SC35 increases the level of normal cystic fibrosis transmembrane conductance regulator (CFTR) transcripts in cystic-fibrosis-derived epithelial cells carrying the 3849+10 kb C --> T splicing mutation. This led to activation of the CFTR channel and restoration of its function. Restoration was also obtained by sodium butyrate, a histone deacetylase inhibitor, known to upregulate the expression of splicing factors. These results highlight the therapeutic potential of splicing modulation for genetic diseases caused by splicing mutations.

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13 The second group includes mutations that generate both aberrantly and correctly spliced transcripts (such as 3849 þ 10 kb C-T, 3272À26 A-G, IVS8-5T, D565G and G576A), the level of which varies among patients and among organs of the same patient (Ramalho et al, 2002; Pagani et al, 2003; reviewed in Nissim-Rafinia & Kerem, 2002). Login to comment

[hide] Pharmacological induction of CFTR function in pati... Pediatr Pulmonol. 2005 Sep;40(3):183-96. Kerem E
Pharmacological induction of CFTR function in patients with cystic fibrosis: mutation-specific therapy.
Pediatr Pulmonol. 2005 Sep;40(3):183-96., [PMID:15880796]

Abstract [show]
CFTR mutations cause defects of CFTR protein production and function by different molecular mechanisms. Mutations can be classified according to the mechanisms by which they disrupt CFTR function. This understanding of the different molecular mechanisms of CFTR dysfunction provides the scientific basis for the development of targeted drugs for mutation-specific therapy of cystic fibrosis (CF). Class I mutations are nonsense mutations that result in the presence of a premature stop codon that leads to the production of unstable mRNA, or the release from the ribosome of a short, truncated protein that is not functional. Aminoglycoside antibiotics can suppress premature termination codons by disrupting translational fidelity and allowing the incorporation of an amino acid, thus permitting translation to continue to the normal termination of the transcript. Class II mutations cause impairment of CFTR processing and folding in the Golgi. As a result, the mutant CFTR is retained in the endoplasmic reticulum (ER) and eventually targeted for degradation by the quality control mechanisms. Chemical and molecular chaperones such as sodium-4-phenylbutyrate can stabilize protein structure, and allow it to escape from degradation in the ER and be transported to the cell membrane. Class III mutations disrupt the function of the regulatory domain. CFTR is resistant to phosphorylation or adenosine tri-phosphate (ATP) binding. CFTR activators such as alkylxanthines (CPX) and the flavonoid genistein can overcome affected ATP binding through direct binding to a nucleotide binding fold. In patients carrying class IV mutations, phosphorylation of CFTR results in reduced chloride transport. Increases in the overall cell surface content of these mutants might overcome the relative reduction in conductance. Alternatively, restoring native chloride pore characteristics pharmacologically might be effective. Activators of CFTR at the plasma membrane may function by promoting CFTR phosphorylation, by blocking CFTR dephosphorylation, by interacting directly with CFTR, and/or by modulation of CFTR protein-protein interactions. Class V mutations affect the splicing machinery and generate both aberrantly and correctly spliced transcripts, the levels of which vary among different patients and among different organs of the same patient. Splicing factors that promote exon inclusion or factors that promote exon skipping can promote increases of correctly spliced transcripts, depending on the molecular defect. Inconsistent results were reported regarding the required level of corrected or mutated CFTR that had to be reached in order to achieve normal function.

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58 C-D565G II DF508 D1507 S549R S549I S549N S549R S945D S945L H1054D G1061R L1065P R1066C R1066M L1077P H1085R N1303K G85E III G551D S492F V520F R553G R560T R560S Y569D IV R117H, R117C, R117P, R117L D1152H, L88S, G91R, E92K, Q98R, P205S, L206W, L227R, F311L, G314E, R334W, R334Q, I336K, T338I, L346P, R347C, R347H, R347L, R347P, L927P, R1070W, R1070Q V 3849 þ 10 kb C ! Login to comment
59 T, 1811 þ 1.6 kb A >G, 3272 À 26A !G, IVS8-5T, D565G, G576A, c4006 À 1 G À> A, 2789 þ 5 G > A 1 Included are mutations that have been studied in RNA/protein level or having enough experimental data to suggest their molecular mechanism. Login to comment
234 CLASS V MUTATIONS: REDUCED NUMBER OF ACTIVE CFTR This group includes mutations which generate both aberrantly and correctly spliced transcripts (such as 3849 þ 10 kb C -> T, 3272 À 26 A -> G, IVS8-5T, D565G, and G576A), the levels of which vary among different patients and among different organs of the same patient.85-89 These patients often have a relatively mild phenotype, yet with variable disease expression, from minimal lung disease, pancreatic sufficiency, and male fertility to relatively severe disease with multiorgan involvement.88,89 This variable disease expression is inversely correlated with the level of correctly spliced transcripts, such that lower levels are associated with a severe disease, while higher levels are associated with a milder phenotype. Login to comment

[hide] Genetics of idiopathic disseminated bronchiectasis... Semin Respir Crit Care Med. 2003 Apr;24(2):179-84. Luisetti M, Pignatti PF
Genetics of idiopathic disseminated bronchiectasis.
Semin Respir Crit Care Med. 2003 Apr;24(2):179-84., [PMID:16088537]

Abstract [show]
Bronchiectasis is an abnormal dilation of bronchi, consequent to the destruction of their walls. It is included in the category of obstructive pulmonary diseases, along with chronic obstructive pulmonary disease (COPD), asthma, and cystic fibrosis. In approximately 50% of cases, bronchiectasis is associated with underlying conditions; in the remainder, known causes are not ascertainable (idiopathic bronchiectasis). A search for genetic determinants of this phenotype, with the cystic fibrosis gene as a candidate, has been performed by three independent groups. The results of this search agreed on the association of bronchiectasis with cystic fibrosis gene mutations and polymorphisms. The cystic fibrosis gene is also associated with bronchiectasis due to rheumatoid arthritis and allergic bronchopulmonary aspergillosis. A few other genes have been investigated in idiopathic bronchiectasis, with negative results. Idiopathic bronchiectasis is, therefore, to be considered as an obstructive multifactorial disorder belonging to the category of cystic fibrosis monosymptomatic diseases (or CFTR-opathies), whose pathogenesis is influenced by environmental factors and other undetermined genes.

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42 Greek M/F 11/12 5/16 na Mean age (yrs) 53 Ϯ 15 53 Ϯ 14 na CFTR gene 1 G576A-R668C/L997F 1 ⌬F508/D192N 1 ⌬F508,I1027T mutation 1 ⌬F508/L997F 1 ⌬I507/3849 + 10kb C → T 1 D565G, R668C 1 ⌬F508/- 1 ⌬F508/3849 + 10kb C → T 1 T896I/- 1 R1066C/- 1 H949Y/T1220I 1 I148T/- 1 3667ins4/- 1 ⌬F508/- 1 ⌬F508/S977F 1 R75Q/- 1 2183AA→G 1 M1137V/- 1 L997F/- IVS8-5T 5 5/7 1 5/9 1 5/5 CFTR, cystic fibrosis transmembrane conductance regulator; na, not available. Login to comment

[hide] Contribution of the CFTR gene, the pancreatic secr... Clin Genet. 2007 May;71(5):451-7. Tzetis M, Kaliakatsos M, Fotoulaki M, Papatheodorou A, Doudounakis S, Tsezou A, Makrythanasis P, Kanavakis E, Nousia-Arvanitakis S
Contribution of the CFTR gene, the pancreatic secretory trypsin inhibitor gene (SPINK1) and the cationic trypsinogen gene (PRSS1) to the etiology of recurrent pancreatitis.
Clin Genet. 2007 May;71(5):451-7., [PMID:17489851]

Abstract [show]
Acute recurrent/chronic pancreatitis (CP) is a complex multigenic disease. This is a case-control study consisting of 25 Greek patients with CP and a control population of 236 healthy Greek subjects. The whole coding area and neighboring intronic regions of the three genes were screened. Seventeen of 25 patients (68%) had mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene: nine compound heterozygotes with either mild or severe mutations and eight heterozygotes. Four patients (16%) carried CFTR-modulating haplotypes V470-TG11-T5 and V470-TG12-T7. All were negative for PRSS1 gene mutations, while variants c.486C/T and c.738C/T were found in nine patients each, three homozygotes for the minor alleles. Two carried SPINK1 gene mutation p.N34S, one being transheterozygote with CFTR mutation p.F1052V. The promoter variant -253T>C was found in four individuals (one homozygous for the minor allele), all four being transheterozygotes with mutations in the CFTR gene as well. Finally two carried c.272C/T in the 3' untranslated region, one being a p.N34S carrier as well. In total, 80% (20/25) of patients had a molecular defect in one or both of the CFTR and SPINK1 genes, suggesting that mutations/variants in the CFTR plus or minus mutations in the SPINK1, but not the PRSS1 gene, may confer a high risk for recurrent pancreatitis.

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93 a Additional mutations found in the controls: p.R1162L (1.66%), p.D565G (0.47%), p.A120T (0.47%) and 0.24% each for p.R297Q, p.L997F, p.E826K, p.I807M, p.S495Y and p.C491S. Login to comment

[hide] Is CFTR 621+3 A>G a cystic fibrosis causing mutati... J Hum Genet. 2010 Jan;55(1):23-6. Epub 2009 Nov 6. Forzan M, Salviati L, Pertegato V, Casarin A, Bruson A, Trevisson E, Di Gianantonio E, Clementi M
Is CFTR 621+3 A>G a cystic fibrosis causing mutation?
J Hum Genet. 2010 Jan;55(1):23-6. Epub 2009 Nov 6., [PMID:19893581]

Abstract [show]
The 621+3 A>G variant of the CFTR gene was initially detected in four Greek patients with a severe form of cystic fibrosis, and it is reported to impair CFTR mRNA splicing. We present three lines of evidence that argue against the pathogenicity of this variant. First, its allelic frequency in the Italian population was 0.4%. Even considering the lowest value in the confidence interval we would expect 10% of Italian CF patients to be heterozygotes for this variant, whereas it has been reported only in one patient (0.04% of Italian CF patients). Second, expression of the 621+3 A>G variant in HeLa cells using a hybrid minigene showed that 39.5+/-1.1% of transcripts were correctly spliced, indicating that its effects on mRNA splicing are similar to those of the CFTR intron 8 5T variant, associated with congenital bilateral absence of vas deferens (CBAVD), but not with CF. Third, we have identified an asymptomatic individual who harbored the 621+3 A>G variant in trans with the Q552X mutation. Because 621+3 A>G is often included in population-screening programs, this information is critical to provide adequate counseling to patients. Further work should be aimed at investigating whether this variant may have a role in CBAVD or atypical CF.

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103 4 Tzetis, M., Efthymiadou, A., Doudounakis, S. & Kanavakis, E. Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621+3A4G, 2751+2T-4A, 296+1G-4C, 1717-9T-4C-D565G) and one nonsense mutation (E822X) in the CFTR gene. Login to comment

[hide] Cystic fibrosis mutation screening in CBAVD patien... Mol Hum Reprod. 1998 Apr;4(4):333-7. Kanavakis E, Tzetis M, Antoniadi T, Pistofidis G, Milligos S, Kattamis C
Cystic fibrosis mutation screening in CBAVD patients and men with obstructive azoospermia or severe oligozoospermia.
Mol Hum Reprod. 1998 Apr;4(4):333-7., [PMID:9620832]

Abstract [show]
Congenital bilateral absence of the vas deferens (CBAVD) found in otherwise healthy infertile males, is associated with a high incidence of mutated cystic fibrosis transmembrane conductance regulator (CFTR) alleles, and is considered a genital form of cystic fibrosis (CF). The CF gene may also be involved in the aetiology of male infertility in cases other than CBAVD. The present study was undertaken to test the involvement of CFTR gene mutations in 14 CBAVD males and additionally in cases of male infertility caused by obstructive azoospermia (n = 10) and severe oligozoospermia (n = 3). The entire coding region of the CFTR gene was analysed using denaturing gradient gel electrophoresis (DGGE). The three allele (5T, 7T, 9T) polymorphic tract of thymidines in intron 8 (IVS8-polyT) of which the 5T allele acts as a mild mutation, causing reduced levels of normal CFTR mRNA due to deletion of exon 9, was also analysed. Of the 14 CBAVD cases, four (28.6%) were found to have mutations in both copies of the CFTR gene, six (42.8%) had one CFTR mutation, and in the remaining four (28.6%) no CFTR mutations were found. Of the 10 cases with obstructive azoospermia, three (30%) had one CFTR mutation and in the remaining seven (70%) no mutations were found. None of the three severe oligozoospermia cases carried a CFTR mutation. The frequency of the IVS8(5T) allele was 14.3% (4/28) for the CBAVD cases and 5% (1/20) for the obstructive azoospermia cases, none of the severe oligozoospermia males carried the IVS8-5(5T) allele. The data indicate that while there is a strong association between male infertility caused by CBAVD and mutations in the CFTR gene, cases of obstructive azoospermia without CBAVD also seem to be associated with CFTR gene mutations.

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55 Results The analysis of the entire coding sequence identified 12 different molecular defects including ∆F508, and two are novel defects (D565G and 2790-8CϾG) (Table I). Login to comment
56 Of the two novel mutations, one was identified in a CBAVD case and is a missence mutation D565G, the other is a possible splicing defect 2790-8CϾG and was detected in a male with obstructive azoospermia. Login to comment
64 Cystic fibrosis transmembrane conductance regulator (CFTR), PolyT genotypes and clinical data of men with congenital bilateral absence of the vas deferens (CBAVD, n ϭ 14), obstructive azoospermia (ObsA, n ϭ 10) and oligozoospermia (n ϭ 3) Patients Sweat chloride CFTR IVS8-polyT Other clinical (mEq/l) mutations alleles features Two mutations detected MS1 (CBAVD) 107.7 ∆F508/M1I 5T/9T Recurrent bronchitis MS6 (CBAVD) 74.5 ∆F508/711ϩ3AϾG 9T/7T Chronic cough MS19 (CBAVD) 51 W496X/F1052V 9T/9T MS24 (CBAVD) Ͻ40 D565G/R668C 7T/7T One mutation detected MS5 (CBAVD) Ͻ40 3272-26AϾG/- 7T/7T MS12 (CBAVD) Ͻ40 ∆F508/- 9T/7T MS14 (CBAVD) Ͻ40 ∆F508/- 9T/5T MS15 (CBAVD) 57.7 L732X/- 7T/5T Dehydration/recurrent bronchitis MS16 (CBAVD) Ͻ40 711ϩ3AϾG/- 7T/5T MS20 (CBAVD) Ͻ40 4010delTAT/- 7T/7T MS18 (ObsA) 48 ∆F508/- 5T/9T MS11 (ObsA) Ͻ40 R75Q/- 7T/7T MS23 (ObsA) Ͻ40 2790-8CϾG/- 7T/7T No mutation detected MS7 (CBAVD) Ͻ40 -/- 7T/7T MS10 (CBAVD) Ͻ40 -/- 7T/7T MS21 (CBAVD) Ͻ40 -/- 7T/9T MS28 (CBAVD) Ͻ40 -/- 7T/7T MS2 (ObsA) 54.2 -/- 7T/7T MS8 (ObsA) Ͻ40 -/- 7T/7T MS17 (ObsA) 50 -/- 7T/7T MS22 (ObsA) Ͻ40 -/- 7T/9T MS25 (ObsA) Ͻ40 -/- 7T/7T MS26 (ObsA) Ͻ40 - / - 7T/7T MS27 (ObsA) Ͻ40 -/- 7T/7T MS3 (oligozoospermia) 50 -/- 7T/7T MS4 (oligozoospermia) Ͻ40 -/- 7T/7T MS13 (oligozoospermia) Ͻ40 -/- 7T/7T Table II. Login to comment
81 No mutation, except for ∆F508, was prevalent in individuals in this study and all of the mutations found in the CBAVD patients, except for the novel D565G and mutation R668C, have also been found in Greek CF patients (Tzetis et al., 1977). Login to comment
82 The novel missence mutation D565G has not been detected in Ͼ250 CF chromosomes, nor in Ͼ100 non-CF chromosomes that we have examined. Login to comment
83 The substitution produced by mutation D565G involves a change of a positively charged for a polar uncharged amino acid in exon 12 of the gene. Login to comment

[hide] The role of common single-nucleotide polymorphisms... Hum Mutat. 2004 Aug;24(2):120-9. Steiner B, Truninger K, Sanz J, Schaller A, Gallati S
The role of common single-nucleotide polymorphisms on exon 9 and exon 12 skipping in nonmutated CFTR alleles.
Hum Mutat. 2004 Aug;24(2):120-9., [PMID:15241793]

Abstract [show]
Classic cystic fibrosis (CF) is caused by two loss-of-function mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, whereas patients with nonclassic CF have at least one copy of a mutant gene that retains partial function of the CFTR protein. In addition, there are several other phenotypes associated with CFTR gene mutations, such as idiopathic chronic pancreatitis. In CFTR-associated disorders and in nonclassic CF, often only one CFTR mutation or no CFTR mutations can be detected. In this study, we screened 23 patients with CFTR-associated disorders for CFTR mutations by complete gene testing and quantitative transcript analysis. Mutations were found in 10 patients. In cells from respiratory epithelium, we detected aberrant splicing of CFTR mRNA in all investigated individuals. We observed a highly significant association between the presence of coding single-nucleotide polymorphisms (coding SNPs, or cSNPs) and increased skipping of exon 9 and 12. This association was found both in patients and in normal individuals carrying the same cSNPs. The cSNPs c.1540A>G, c.2694T>G, and c.4521G>A may have affected pre-mRNA splicing by changing regulatory sequence motifs of exonic splice enhancers, leading to lower amounts of normal transcripts. The analysis of CFTR exons indicated that less frequent and weak exonic splicing enhancer (ESE) motifs make exon 12 vulnerable to skipping. The number of splice variants in individuals with cSNPs was similar to previously reported values for the T5 allele, suggesting that cSNPs may enhance susceptibility to CFTR related diseases. In addition, cSNPs may be responsible for variation in the phenotypic expression of CFTR mutations. Quantitative approaches rather than conventional genomic analysis are required to interpret the role of cSNPs.

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184 Sequence variations (i.e., p.D565G and p.G576A) in the newly identified composite exonic regulatory element of splicing (CERES) of exon 12 [Pagani et al., 2003b] were excluded by SSCP and sequence analysis. Login to comment

[hide] Quantitative methods for the analysis of CFTR tran... J Cyst Fibros. 2004 Aug;3 Suppl 2:17-23. Amaral MD, Clarke LA, Ramalho AS, Beck S, Broackes-Carter F, Rowntree R, Mouchel N, Williams SH, Harris A, Tzetis M, Steiner B, Sanz J, Gallati S, Nissim-Rafinifa M, Kerem B, Hefferon T, Cutting GR, Goina E, Pagani F
Quantitative methods for the analysis of CFTR transcripts/splicing variants.
J Cyst Fibros. 2004 Aug;3 Suppl 2:17-23., [PMID:15463919]

Abstract [show]
In cystic fibrosis (CF), transcript analysis and quantification are important for diagnosis, prognosis and also as surrogate markers for some therapies including gene therapy. Classical RNA-based methods require significant expression levels in target samples for appropriate analysis, thus PCR-based methods are evolving towards reliable quantification. Various protocols for the quantitative analysis of CFTR transcripts (including those resulting from splicing variants) are described and discussed here.

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164 D565G, G576A and Y577Y induce exon skipping, while Y577F increases the percentage of exon 12 inclusion. Login to comment
169 In particular, two missense mutations, D565G and G576A (previously considered a neutral polymorphism), showed no clear association with loss of protein function or disease phenotype. Login to comment
173 D565G and G576A induce variable levels of exon 12 skipping, thus reducing levels of normal transcripts. Login to comment

[hide] Atypical 5' splice sites cause CFTR exon 9 to be v... Am J Hum Genet. 2002 Aug;71(2):294-303. Epub 2002 Jun 13. Hefferon TW, Broackes-Carter FC, Harris A, Cutting GR
Atypical 5' splice sites cause CFTR exon 9 to be vulnerable to skipping.
Am J Hum Genet. 2002 Aug;71(2):294-303. Epub 2002 Jun 13., [PMID:12068373]

Abstract [show]
The molecular basis of the skipping of constitutive exons in many messenger RNAs is not fully understood. A well-studied example is exon 9 of the human cystic fibrosis transmembrane conductance regulator gene (CFTR), in which an abbreviated polypyrimidine tract between the branch point A and the 3' splice site is associated with increased exon skipping and disease. However, many exons, both in CFTR and in other genes and have short polypyrimidine tracts in their 3' splice sites, yet they are not skipped. Inspection of the 5' splice sites immediately up- and downstream of exon 9 revealed deviations from consensus sequence, so we hypothesized that this exon may be inherently vulnerable to skipping. To test this idea, we constructed a CFTR minigene and replicated exon 9 skipping associated with the length of the polypyrimidine tract upstream of exon 9. We then mutated the flanking 5' splice sites and determined the effect on exon skipping. Conversion of the upstream 5' splice site to consensus by replacing a pyrimidine at position +3 with a purine resulted in increased exon skipping. In contrast, conversion of the downstream 5' splice site to consensus by insertion of an adenine at position +4 resulted in a substantial reduction in exon 9 skipping, regardless of whether the upstream 5' splice site was consensus or not. These results suggested that the native downstream 5' splice site plays an important role in CFTR exon 9 skipping, a hypothesis that was supported by data from sheep and mouse genomes. Although CFTR exon 9 in sheep is preceded by a long polypyrimidine tract (Y(14)), it skips exon 9 in vivo and has a nonconsensus downstream 5' splice site identical to that in humans. On the other hand, CFTR exon 9 in mice is preceded by a short polypyrimidine tract (Y(5)) but is not skipped in vivo. Its downstream 5' splice site differs from that in humans by a 2-nt insertion, which, when introduced into the human CFTR minigene, abolished exon 9 skipping. Taken together, these observations place renewed emphasis on deviations at 5' splice sites in nucleotides other than the invariant GT, particularly when such changes are found in conjunction with other altered splicing sequences, such as a shortened polypyrimidine tract. Thus, careful inspection of entire 5' splice sites may identify constitutive exons that are vulnerable to skipping.

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237 Hum Mol Genet 6:85-90 Tzetis M, Efthymiadou A, Doudounakis S, Kanavakis E (2001) Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621ϩ3ArG, 2751ϩ2TrA, 296ϩ1GrC, 1717-9TrC- D565G) and one nonsense mutation (E822X) in the CFTR gene. Login to comment
238 Hum Mol Genet 6:85-90 Tzetis M, Efthymiadou A, Doudounakis S, Kanavakis E (2001) Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621af9;3ArG, 2751af9;2TrA, 296af9;1GrC, 1717afa;9TrCafa; D565G) and one nonsense mutation (E822X) in the CFTR gene. Login to comment

[hide] Biosynthesis of cystic fibrosis transmembrane cond... Int J Biochem Cell Biol. 2014 Jul;52:26-38. doi: 10.1016/j.biocel.2014.03.020. Epub 2014 Mar 28. Pranke IM, Sermet-Gaudelus I
Biosynthesis of cystic fibrosis transmembrane conductance regulator.
Int J Biochem Cell Biol. 2014 Jul;52:26-38. doi: 10.1016/j.biocel.2014.03.020. Epub 2014 Mar 28., [PMID:24685677]

Abstract [show]
The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated chloride (Cl(-)) channel. Mutations of its gene lead to the disease of cystis fibrosis (CF) among which the most common is the deletion of phenylalanine at position 508 (Phe508del). CFTR is a multi-domain glycoprotein whose biosynthesis, maturation and functioning as an anion channel involve multi-level post-translational modifications of CFTR molecules and complex folding processes to reach its native, tertiary conformation. Only 20-40% of the nascent chains achieve folded conformation, while the remaining molecules are targeted for degradation by endoplasmic reticulum, lysosomes, or autophagy. A large number of mutations causing CF impair processing of CFTR. Growing knowledge of CFTR biosynthesis has enabled understanding the cellular basis of CF and has brought to light various potential targets for novel, promising therapies.

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1376 These splicing mutations (e.g. 3849 + 10 kb C ࢐ T, 3272-26 A ࢐ G, IVS8-5T, D565G and G576A) lead to variable levels of correctly spliced transcripts among different patients and among different organs of the same patient. Login to comment

[hide] Comparative ex vivo, in vitro and in silico analys... J Cyst Fibros. 2015 Feb 27. pii: S1569-1993(15)00039-9. doi: 10.1016/j.jcf.2015.02.002. Ramalho AS, Clarke LA, Sousa M, Felicio V, Barreto C, Lopes C, Amaral MD
Comparative ex vivo, in vitro and in silico analyses of a CFTR splicing mutation: Importance of functional studies to establish disease liability of mutations.
J Cyst Fibros. 2015 Feb 27. pii: S1569-1993(15)00039-9. doi: 10.1016/j.jcf.2015.02.002., [PMID:25735457]

Abstract [show]
The Cystic Fibrosis p.Ile1234Val missense mutation actually creates a new dual splicing site possibly used either as a new acceptor or donor. Here, we aimed to test the accuracy of in silico predictions by comparing them with in vitro and ex vivo functional analyses of this mutation for an accurate CF diagnosis/prognosis. To this end, we applied a new in vitro strategy using a CFTR mini-gene which includes the complete CFTR coding sequence plus intron 22 (short version) which allows the assessment of alternatively spliced mRNA levels as well as the properties of the resulting abnormal CFTR protein regarding processing, intracellular localization and function. Our data demonstrate that p.Ile1234Val leads to usage of the alternative splicing donor (but not acceptor) resulting in alternative CFTR transcripts lacking 18nts of exon 22 which produce a truncated CFTR protein with residual Cl- channel function. These results recapitulate data from native tissues of a CF patient. In conclusion, the existing in silico prediction models have limited application and ex vivo functional assessment of mutation effects should be made. Alternatively the in vitro strategy adopted here can be applied to assess the disease liability of mutations for an accurate CF diagnosis/prognosis.

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31 Indeed, it was demonstrated that several CFTR missense mutations also alter splicing, e.g., p.Asp565Gly and p.Gly576Ala [20], p.Asp648Val and p.Thr665Ser [21] as well as p.Gly893Gly (c.2811 G N T) [22]. Login to comment