ABCMdb

PMID: 17413420

Grangeia A, Sa R, Carvalho F, Martin J, Girodon E, Silva J, Ferraz L, Barros A, Sousa M
Molecular characterization of the cystic fibrosis transmembrane conductance regulator gene in congenital absence of the vas deferens.
Genet Med. 2007 Mar;9(3):163-72., [PubMed]

Sentences

No. Mutations Sentence Comment

14 ABCC7 p.Arg117His The most common CFTR mutations found in CAVD are T5 allele, deltaF508, and R117H, with the combination between the T5 allele and a severe CF mutation in the other allele being the main cause of CAVD.9 The polymorphic polythymidine locus (Tn) is located within the 3= splice acceptor site of intron 8 (IVS8 poly[T]n). Login to comment 80 ABCC7 p.Arg334Trp ABCC7 p.Ser1235Arg Patients with two detected mutations were mostly compound heterozygotes (38/42, 90.5%), whereas four patients (9.5%) were homozygotes for T5 allele (two cases), R334W, and S1235R (Table 2). Login to comment 82 ABCC7 p.Glu831* With the exception of one patient carrying two severe CF mutations (DeltaF508del/E831X), all other patients with two detected mutations (97.6%) had a mild missense/splicing site mutation in one of the alleles. Login to comment 85 ABCC7 p.Ser1235Arg ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr Three mutations were found as complex alleles (two or three sequence alterations associated in cis on the same allele), each in two patients, G576A-R668C, D443Y-G576A-R668C, and S1235R-T5 (one patient with T5 in homozygosity) (Table 2). Login to comment 86 ABCC7 p.Arg334Trp Three novel CFTR missense mutations were identified in three patientswithCBAVDwhowerecompoundheterozygotes.P439S was identified in a 34-year-old patient who carried a R334W mutation in the other chromosome. It results in a proline substitution by a serine at position 439, located in the nucleotide-binding domain (NBD) 1 of the CFTR protein. Login to comment 87 ABCC7 p.Val1108Leu V1108L was found in a 37-year-old patient who also carried the T5 allele. Login to comment 89 ABCC7 p.Glu1401Lys E1401K was found in a 37-year-old patient who carried a deltaF508 mutation in the other chromosome. It leads to the substitution of a glutamic acid by a lysine in (NBD) 2 at its carboxy-terminal side (Tables 1 and 2). Login to comment 93 ABCC7 p.Arg117His ABCC7 p.Arg334Trp ABCC7 p.Arg334Trp ABCC7 p.Asn1303Lys ABCC7 p.Gly542* ABCC7 p.Val754Met ABCC7 p.Glu831* ABCC7 p.Pro205Ser ABCC7 p.Leu206Trp ABCC7 p.Arg258Gly ABCC7 p.Ser1235Arg ABCC7 p.Leu1227Ser ABCC7 p.Asp614Gly ABCC7 p.Val562Ile ABCC7 p.Val1108Leu ABCC7 p.Glu1401Lys ABCC7 p.Pro1290Ser ABCC7 p.Pro439Ser DeltaF508 was the second most common mutation, representing 21 (23.3%) of total alleles, followed by R334W (6, Table 1 CFTR gene mutations and polymorphisms in patients with congenital absence of the vas deferens Mutation Location Nucleotide alteration Effect Method 1 CFTRdele2,3 Exons 2-3 Deletion of exons 2 and 3 Frameshift QFM-PCR 2 R117H Exon 4 G¡A at 482 AA substitution 31 mutation panel 3 P205S Exon 6a C¡T at 745 AA substitution DGGE/dHPLC 4 L206W Exon 6a T¡G at 749 AA substitution DGGE/dHPLC 5 R258G Exon 6b A¡G at 904 AA substitution DGGE/dHPLC 6 R334W Exon 7 C¡T at 1132 AA substitution 31 mutation panel 7 T5 allele Intron 8 Deletion of 2T at 1342-12 to -6 Aberrant splicing DGGE/DNA sequencing 8 P439S Exon 9 C¡T at 1447 AA substitution DGGE/dHPLC 9 D443Ya Exon 9 G¡T at 1459 AA substitution DGGE/dHPLC 10 I507del Exon 10 Deletion of 3 bp at 1648-1653 AA deletion 31 mutation panel 11 DeltaF508 Exon 10 Deletion of 3 bp at 1652-1655 AA deletion 31 mutation panel 12 G542X Exon 11 G¡T at 1756 Truncation 31 mutation panel 13 V562I Exon 12 G¡A at 1816 AA substitution DGGE/dHPLC 14 G576Aa Exon 12 G¡C at 1859 Aberrant splicing DGGE/dHPLC 15 D614G Exon 13 A¡G at 1973 AA substitution DGGE/dHPLC 16 R688Ca Exon 13 C¡T at 2134 AA substitution DGGE/dHPLC 17 V754M Exon 13 G¡A at 2392 AA substitution DGGE/dHPLC 18 E831X Exon 14a G¡T at 2623 Truncation DGGE/dHPLC 19 3272-26AϾG Intron 17a A¡G at 3272-26 Aberrant splicing DGGE/dHPLC 20 2789ϩ5G¡A Intron 14b G¡A at 2789ϩ5 Aberrant splicing 31 mutation panel 21 V1108L Exon 17b G¡C at 3454 AA substitution DGGE/dHPLC 22 L1227S Exon 19 T¡C at 3812 AA substitution DGGE/dHPLC 23 S1235R Exon 19 T¡G at 3837 AA substitution DGGE/dHPLC 24 P1290S Exon 20 C¡T at 4000 AA substitution DGGE/dHPLC 25 N1303K Exon 21 C¡G at 4041 AA substitution 31 mutation panel 26 E1401K Exon 23 G¡A at 4333 AA substitution DGGE/dHPLC Polymorphisms 1 TG repeats Intron 8 9-13 copies at 1342-12 to -35 Sequence variation DGGE/DNA sequencing 2 M470V Exon 10 A or G at 1540 Sequence variation DNA sequencing 3 125G/C Exon 1 G¡C at 125 Sequence variation DGGE/dHPLC 4 1001ϩ11T/C Intron 6b C¡4T at 1001ϩ11 Sequence variation DGGE/dHPLC 5 1716G/A Exon 10 G¡A at 1716 Sequence variation DGGE/dHPLC 6 1899-136T/G Intron 12 T¡G at 1899-136 Sequence variation DGGE/dHPLC 7 T854T Exon 14a T¡G at 2694 Sequence variation DGGE/dHPLC 8 3601-65C/A Intron 18 C¡A at 3601-65 Sequence variation DGGE/dHPLC 9 4521G/A Exon 24 G¡A at 4521 Sequence variation DGGE/dHPLC QFM-PCR, semiquantitative fluorescent multiplex polymerase chain reaction; bp, base pair; DGGE, denaturing gradient gel electrophoresis; dHPLC, denaturing high-performance liquid chromatography. Login to comment 94 ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr a Missense mutations linked on the same allele, G576A-R688C and D443Y-G576A-R688C, were present in two patients with CBAVD each. CFTR mutations: severe (bold); novel (italics). Login to comment 97 ABCC7 p.Arg117His ABCC7 p.Gly542* ABCC7 p.Pro205Ser ABCC7 p.Leu206Trp ABCC7 p.Ser1235Arg ABCC7 p.Arg668Cys ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr ABCC7 p.Asp614Gly The allelic frequency of the other mutations was 4.4% for R117H, G576A, and R668C, 3.3% for S1235R and 3272-26A¡G, and 2.2% for P205S, L206W, D443Y, G542X, D614G, and N1301K, whereas the remaining 12 mutations were present in single patients (Table 3). Login to comment 101 ABCC7 p.Arg117His ABCC7 p.Arg117His ABCC7 p.Arg117His ABCC7 p.Arg334Trp ABCC7 p.Arg334Trp ABCC7 p.Arg334Trp ABCC7 p.Arg334Trp ABCC7 p.Arg334Trp ABCC7 p.Asn1303Lys ABCC7 p.Asn1303Lys ABCC7 p.Gly542* ABCC7 p.Glu831* ABCC7 p.Pro205Ser ABCC7 p.Pro205Ser ABCC7 p.Leu206Trp ABCC7 p.Leu206Trp ABCC7 p.Arg258Gly ABCC7 p.Ser1235Arg ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr ABCC7 p.Asp443Tyr ABCC7 p.Leu1227Ser ABCC7 p.Asp614Gly ABCC7 p.Asp614Gly ABCC7 p.Val562Ile ABCC7 p.Val1108Leu ABCC7 p.Glu1401Lys ABCC7 p.Pro1290Ser ABCC7 p.Pro439Ser The missense M470V polymorphism was evaluated in all 45 pa- tientswithCAVD(Table2).TheallelicfrequencyoftheM470variant Table 2 CFTR genotypes identified in patients with congenital absence of the vas deferens CFTR mutation genotypes [(TG)mTn] genotype M470V Patients N % DeltaF508 (TG)10T9 (TG)12T5 M V 11 24.4 DeltaF508 (TG)10T9 (TG)11T5 M M 1 2.2 DeltaF508 R117H (TG)10T9 (TG)10T7 M M 2 4.4 G542X (TG)10T9 (TG)12T5 M V 2a 4.4 DeltaF508 R334W (TG)10T9 (TG)11T7 M V 1 2.2 DeltaF508 D443Y-G576A-R668C (TG)10T9 (TG)10T7 M M 1 2.2 DeltaF508 D614G (TG)10T9 (TG)11T7 M V 1 2.2 DeltaF508 E831X (TG)10T9 (TG)11T7 M V 1 2.2 DeltaF508 L1227S (TG)10T9 (TG)11T7 M M 1 2.2 DeltaF508 E1401K (TG)10T9 (TG)11T7 M V 1 2.2 I507del D614G (TG)11T7 (TG)10T7 M V 1 2.2 N1303K L206W (TG)10T9 (TG)9T9 M M 1 2.2 R117H P205S (TG)11T7 (TG)10T7 M V 1 2.2 R117H R334W (TG)10T7 (TG)11T7 M V 1 2.2 R334W P439S (TG)11T7 (TG)11T7 M V 1 2.2 R334W R334Wb (TG)11T7 (TG)11T7 V V 1 2.2 R334W V562I (TG)11T7 (TG)11T5 V M 1 2.2 D443Y-G576A-R668C 3272-26A¡G (TG)10T7 (TG)10T7 M M 1 2.2 G576A-R668C V754Mb (TG)10T7 (TG)11T7 M M 1 2.2 S1235R S1235Rb (TG)13T5 (TG)13T5 M M 1 2.2 2789ϩ5G¡A S1235Rb (TG)10T7 (TG)13T5 M M 1 2.2 3272-26A¡G P1290S (TG)11T7 (TG)10T7 M V 1 2.2 P205S (TG)11T7 (TG)12T5 V V 1 2.2 G576A-R668C b (TG)10T7 (TG)11T5 M M 1 2.2 V1108L b (TG)11T7 (TG)11T5 V M 1 2.2 N1303K (TG)10T9 (TG)12T5 M V 1 2.2 3272-26A¡G b (TG)10T7 (TG)12T5 M V 1 2.2 CFTRdele2,3 b (TG)11T7 (TG)13T5 V M 1 2.2 b (TG)11T5 (TG)12T5 M V 1 2.2 b (TG)13T5 (TG)12T5 M V 1 2.2 DeltaF508 - (TG)10T9 (TG)11T7 M V 1a 2.2 L206W -b (TG)9T9 (TG)11T7 M V 1 2.2 R258G -b (TG)11T7 (TG)11T7 V V 1 2.2 a CUAVD. Login to comment 110 ABCC7 p.Arg117His ABCC7 p.Arg334Trp ABCC7 p.Asn1303Lys ABCC7 p.Gly542* ABCC7 p.Val754Met ABCC7 p.Glu831* ABCC7 p.Pro205Ser ABCC7 p.Leu206Trp ABCC7 p.Arg258Gly ABCC7 p.Ser1235Arg ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr ABCC7 p.Leu1227Ser ABCC7 p.Asp614Gly ABCC7 p.Val562Ile ABCC7 p.Val1108Leu ABCC7 p.Glu1401Lys ABCC7 p.Pro1290Ser ABCC7 p.Pro439Ser Large Table 3 Allelic frequencies of CFTR mutations in patients with congenital absence of the vas deferens CBAVD CUAVD Total Patients 42 3 45 Alleles 84 6 90 Mutations N % N % N % 1 T5 allele 26a 31 2 33.3 28 31.1 2 DeltaF508 20 23.8 1 16.7 21 23.3 3 R334W 6a 7.1 0 0 6 6.7 4 R117H 4 4.8 0 0 4 4.4 5 G576A 4b 4.8 0 0 4 4.4 6 R688C 4b 4.8 0 0 4 4.4 7 S1235R 3a 3.6 0 0 3 3.3 8 3272-26A¡G 3 3.6 0 0 3 3.3 9 P205S 2 2.4 0 0 2 2.2 10 L206W 2 2.4 0 0 2 2.2 11 D443Y 2b 2.4 0 0 2 2.2 13 D614G 2 2.4 0 0 2 2.2 14 N1303K 2 2.4 0 0 2 2.2 12 G542X 0 0 2 33.3 2 2.2 15 R258G 1 1.2 0 0 1 1.1 16 P439S 1 1.2 0 0 1 1.1 17 I507del 1 1.2 0 0 1 1.1 18 V562I 1 1.2 0 0 1 1.1 19 V754M 1 1.2 0 0 1 1.1 20 E831X 1 1.2 0 0 1 1.1 21 2789ϩ5G¡A 1 1.2 0 0 1 1.1 22 V1108L 1 1.2 0 0 1 1.1 23 L1227S 1 1.2 0 0 1 1.1 24 P1290S 1 1.2 0 0 1 1.1 25 E1401K 1 1.2 0 0 1 1.1 26 CFTRdele2,3 1 1.2 0 0 1 1.1 CBAVD, congenital bilateral absence of the vas deferens; CUAVD, congenital unilateral absence of the vas deferens. Login to comment 112 ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr b Missense mutations linked on the same allele, G576A-R688C and D443Y-G576A-R688C, were present in two patients with CBAVD each. CFTR gene rearrangements are not detectable using conventional PCR-based screening techniques, because the amplification of a nondeleted allele masks the lack of a PCR product corresponding to the deletion site.21,22,24 This detected a CFTRdele2,3 (21 kb) deletion in a Ukrainian emigrant with CBAVD and heterozygous for the T5 allele. Login to comment 120 ABCC7 p.Arg334Trp Despite the high heterogeneity of the mutations found in Portuguese patients with CAVD, three were the most frequent mutations (T5, deltaF508, and R334W), being present in 37 of 45 cases (82%) with 61% (55/ 90) allelic frequency. Login to comment 123 ABCC7 p.Arg334Trp However, and contrary to all other studies, the third most frequent mutation was R334W, with 7% allelic frequency5,6,13,30,32-44 (Table 5). Login to comment 136 ABCC7 p.Glu831* Patients with CAVD carry CFTR genotypes composed of a severe and a mild mutation or two mild mutations.2,9 However, one Portuguese patient with CBAVD, without clinical manifestation of CF, was found to be a compound heterozygote for two severe CFTR mutations, deltaF508/E831X. Login to comment 137 ABCC7 p.Glu831* ABCC7 p.Glu831* ABCC7 p.Glu831* This genotype was previously associated with a CF phenotype, with pancreatic insufficiency.8 A Turkish patient with CBAVD was also reported to be a compound heterozygote for the same E831X mutation and the truncating mutation 1677delTA.35 It is possible that the association of the E831X mutation with a CF mutation confers an unusually mild phenotype, because the disease phenotype may be ameliorated through modulation of the CFTR genotype by external/internal factors or modifier genes.47 In addition, E831X mutation is located at the first nucleotide of exon 14a and may alter exon 14a splicing. Login to comment 139 ABCC7 p.Glu831* Therefore, E831X may not be considered as a classic severe mutation. Login to comment 140 ABCC7 p.Val1108Leu ABCC7 p.Glu1401Lys ABCC7 p.Pro439Ser Three novel missense mutations (E1401K, P439S, and V1108L), not detected in the general population or in patients with CF, were here first described in patients with CAVD. Login to comment 141 ABCC7 p.Arg334Trp ABCC7 p.Val1108Leu ABCC7 p.Glu1401Lys ABCC7 p.Pro439Ser Although the pathogenicity of these mutations is still being assessed by expression and functional in vitro studies, the combination of the amino acid substitutions with other mutations (deltaF508/E1401K, R334W/P439S, V1108L/T5) might be responsible for the CBAVD phenotype. Login to comment 142 ABCC7 p.Arg117His ABCC7 p.Arg334Trp ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr ABCC7 p.Asp443Tyr ABCC7 p.Asp443Tyr ABCC7 p.Glu1401Ala ABCC7 p.Glu1401* ABCC7 p.Glu1401Lys ABCC7 p.Pro439Ser ABCC7 p.Pro439Ser In fact, they occur in highly conserved regions of the CFTR protein, which share 100% amino acid sequence homology between species48 and affect the NBD1, NBD2, and transmembrane regions of the protein, which are known to regulate chloride conductance and permeability.49-51 P439S was previously reported in a child with CF with pancreatic insufficiency and mild lung disease, in association with the P439S/R688C genotype.52 The E1401K mutation occurs at a position in which other mutations, E1401X and E1401A, have been described in patients with CF with pancreatic insufficiency.8 Some difficulties in defining CF or CAVD-causing mutations were observed with some missense mutations.6,27 G576A and R668C have been found independently, in pairs, or combined with the D443Y mutation on the same chromosome in patients withaCF-relatedsyndrome.Inaccordancewithpreviousstudies, we expected that G576A and R668C were located in cis in two patients and combined with D443Y in the same chromosome in two patients.6,9,12 Although initially described as polymorphisms,27 they were later considered mild mutations associated with the CBAVD phenotype when combined in trans with the severedeltaF508mutation.53 However,ourpresentresultssuggest they might also cause the CAVD phenotype when associated with other mild CFTR mutations, because three of four patients carry- ingthesecomplexallelesharboredamildorverymildmutationin the other chromosome (D443Y-G576A-R668C/3272-26A¡G, Table 5 Comparative analysis of CFTR mutation allelic frequencies (%) in patients with congenital absence of the vas deferens Countries Patients T5 allele DeltaF508 R334W R117H References Argentina 36 NA 20.8 NA 5.6 43 Austria 22 NA 13.6 NA 9.1 44 Italy 12 8.3 29.2 NA 4.2 39 The Netherlands 21 9.5 19.0 NA 21.4 38 Germany 106 12.3 26.4 0.5 11.3 30 Greece 14 14.3 14.3 NA NA 32 France 800 16.3 21.8 NA 4.4 6 United States 92 17.9 21.2 NA 2.2 41 Canada 74 18.2 16.9 1.4 6.1 5 Turkey 51 19.6 2.9 NA NA 35 Brazil 17 20.6 11.7 NA 2.9 34 Spain 134 20.9 16.0 0.4 3.0 33 Iran 113 25.7 12.4 0.9 3.5 37 Egypt 16 43.7 6.2 NA NA 40 Taiwan 27 44.4 NA NA NA 42 Portugal 45 31.1 23.3 6.7 4.4 13, 36, PS NA, not available; PS, present study. Login to comment 143 ABCC7 p.Val754Met ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Arg668Cys ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Gly576Ala ABCC7 p.Asp443Tyr G576A-R668C/V754M, G576A-R668C/T5), and only one case was associated with a severe mutation (DeltaF508del/D443Y-G576A-R668C). Login to comment 144 ABCC7 p.Ser1235Arg ABCC7 p.Ser1235Arg In regard to the S1235R mutation, in this study it was found in homozygosity in one patient (2.2%) and in compound heterozygosity with a mild CFTR mutation (2789 ϩ 5G¡A/S1235R) in one patient (2.2%). Login to comment 145 ABCC7 p.Ser1235Arg In both cases, S1235R was in cis with the haplotype (TG)13T5. Login to comment 146 ABCC7 p.Ser1235Arg ABCC7 p.Ser1235Arg ABCC7 p.Ser1235Arg ABCC7 p.Ser1235Arg Homozygosity for the S1235R mutation is first described here, whereas compound heterozygosity between S1235R and another CFTR mutation (DeltaF508del) was previously described with a frequency of 0.08% in patients with variable CF phenotypic manifestations6 or of 0.12% to 0.98% in pa- tientswithCAVD.2,6 Althoughthereissomecontroversywhether T5 homozygosity explains the CAVD phenotype, the T5/T5 genotype was found with a frequency of 6.7% (Table 2), similar to that previously reported (1.1%-10.4%).2,5,30,33,35,37,41 Because the penetrance of the T5 allele might be increased when there is an association between the T5 allele and the (TG)13 tract, the combination of S1235R with (TG)13T5 in homozygosity or in compound heterozygosity with another CFTR mutation might be responsible for the CBAVD phenotype, although the primary pathogenic factor, the T5 allele or the S1235R mutation, remains to be evaluated. 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