CF Genetic Analysis Consortium NEWSLETTER #65-
1. Summary of new CF mutations and DNA sequence polymorphisms:
Name of Nucleotide Exon Consequence Institute Names of mutation change Contributors Q353H A->C at 1191 7 Gln->His at 353 Centre de Férec C, Quere Transfusion I, Verlingue C, Sanguine et de Raguenes O, Biogénétique, Audrezet M-P, Brest, France Mercier B (Dec 19) R334Q G->A at 1133 7 Arg->Gln at 334 same as above Férec et al. (Dec 19) 2752-1G->T G->T at 2752-1 intron splice mutation same as above Férec et al. 14a (Dec 19) R1066S C->A at 3328 17b Arg->Ser at 1066 same as above Férec et al. (Dec 19) Q290X C->T at 1000 6b Gln->Stop at 290 same as above Férec et al. (Feb 7) 306delTAGA deletion of 3 frameshift same as above Férec et al. TAGA from 306 (Feb 7) see Savov et al. below (Feb 1) H949R A->G at 2978 15 His->Arg at 949 same as above Férec et al. (Feb 14) 3499+6A->G A->G at 3499+6 intron splice mutation? same as above Férec et al. 17b (Feb 14) Note: The above mutations were found by DGGE and direct sequencing in Caucasian patients. Contact: Dr. Claude Férec; Address: Centre de Biogénétique, Centre de Transfusion Sanguine et de Biogénétique, 46 Rue Félix Le Dantec - B.P. 454 - 29275 BREST Cédex, France; Telephone: +33 188.8.131.52; FAX: +33 98.43.05.55 1811+18G->A G->A at intron splice mutation? University of Teng H, Cuppens 1811+18 11 Leuven, Belgium H, Cassiman J-J (Dec 20) Note: The above mutation was detected once among 60 unrelated Belgian CF chromosomes. This mutation creates a new potential splice acceptor site, but it has not been proven at the mRNA level at the moment. Contact: Harry Cuppens; Address: Center for Human Genetics, University of Leuven, Campus Gasthuisberg, Herestraat 49, B-3000 Leuven, Belgium Telephone: +32 16-34.58.60; FAX: +32 16-34.59.97; E-Mail: Harry=Cuppens%COM%CME@cc3.kuleuven.ac.be V562L G->C at 1816 12 Val->Leu at 562 Belfast City Hughes D, Hill Hospital, A, Graham (Jan 4) Northern Ireland G486X G->T at 1588 10 Glu->Stop at 486 same as above Hughes et al. (Jan 18) M1I G->T at 135 1 Met->Ile at codon same as above Hughes et al. 1 (Jan 18) S10R C->A at 160 1 Ser->Arg at codon same as above Hughes et al. 10 with R117H (Jan 18) Note: V562L was detected by DGGE analysis, followed by direct fluorescent sequencing. It was detected in one patient from 220 in Northern Ireland. The other CF allele is presently unknown. One nine-year old girl, PI, with moderate pulmonary disease carries G486X and [[Delta]]F508 on the other allele. M1I was previously reported by Axton and Brock (NL#61), but with a GA nucleotide change. This mutation was found in one nine-year old male, PI, with mild pulmonary disease. The other allele is [[Delta]]F508. S10R, a change of a neutral amino acid for a basic one, was found in one 4 year old boy, PI, with moderate pulmonary disease. R117H is also found on the S10R allele, with [[Delta]]F508 on the other chromosome. The latter 3 mutations were found once on 174 non-[[Delta]]F508 chromosomes. Contact: David Hughes; Address: Department of Medical Genetics, Floor A, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB Telephone: (0232) 329241; FAX: (0232) 236911 4005+121delTT deletion of intron mutation? Medical Faculty, Strmecki L, Vouk TT from 20 Inst. of K, Komel R (Jan 4005+121 Biochem., 5) Ljubljana Note: The above deletion was detected by SSCP analysis and identified by DNA sequencing of the PCR fragment cloned in pCR(TM) from TA Cloning Kit (Invitrogen). The deletion of two thymidines at the position 4005+121 results in the sequence polymorphism between positions 4005+121 and 4005+130 which is as follows: (+120) cttttttc (+128) instead of cttttttttc. The deletion was detected in one Slovenian CF chromosome. The investigators are uncertain of the status of 4005+121delTT, because it was found in a non-[[Delta]]F508 CF chromosome of a one-year old CF patient (pancreatic insufficient and presenting until now moderate lung disease) in which the 3905insT was identified. The other CF chromosome was found to be [[Delta]]F508. The 4005+121delTT was confirmed to be present in the non-[[Delta]]F508 chromosome of the patient's mother. Contact: Prof.dr. Radovan Komel ; Address: Institute of Biochemistry, Medical Faculty, Vrazov trg2, 61000 Ljubljana, Slovenia; Telephone: (+386 61) 312 357; FAX: (+386 61) 132 0016 3556insAGTA insertion of 18 frame shift Instituto Duarte A, AGTA after Nacional de Lavinha J, position 3556 Saúde, Lisboe, Barreto C, Lopes Portugal B (Jan 10) M1137R T->G at 3542 18 Met->Arg at 1137 same as above Duarte et al. (Jan 10) Note: 3556insAGTA results in a duplication of the preceding sequence (AGTAAGTA) and introduced a frameshift which creates a stop codon 15 codons downstream. This mutation has been found once in 59 non-[[Delta]]F508 CF chromosomes from the Portuguese population, associated with haplotype A. The patient carries the [[Delta]]F508 mutation on the other chromosome and presents a severe form of CF. 3556insAGTA was found neither in 28 normal chromosomes nor in 31 [[Delta]]F508 CF chromosomes. The M1137R mutation has been found once in 59 non-[[Delta]]F508 chromosomes from the Portuguese population, associated with haplotype C. The patient carries the F1052V mutation on the other chromosome and presents a mild form of CF. M1137R was found neither in 28 normal chromosomes nor in 31 [[Delta]]F508 CF chromosomes. Contact: Ângela Duarte; Address: Departmento de Genética Humana, Instituto Nacional de Saúde, Av. Padre Cruz, 1699 Lisboe Codex, Portugal; Telephone: 351.1.7585129; FAX: 351.1.7590441 2751G->A G->A at 2751 14a splice mutation? University of Wagner K, Petek Graz, Austria E (Jan 20) Note: The above mutation was detected after DGGE and subsequent sequencing with Sequenase 2.0. The nucleotide change was detected once in 200 non-[[Delta]]F508 chromosomes screened by DGGE. The mutation has been inherited from his mother and the second mutation, 457TAT->G is from his father. The male patient was born in April 1992 and the investigators do not have any clinical information. Contact: Dr. Klaus Wagner; Address: University of Graz, Institute of Medical Biology & Human Genetics, Harrachgasse 21/8, A-8010 Graz, Austria; Telephone: +43 316 380 4116; FAX: +43 316 32 55 66; e-mail: email@example.com 3459delA deletion of A 17b frameshift St. Mary's Wallace A, at 3495 Hospital, Tassabehji M Manchester, (Jan 27) England Note: The above mutation was detected by SSCP/heteroduplex analysis and was observed only once in a panel of English CF patients. Contact: Andrew Wallace; Address: Regional Molecular Genetics Laboratory, Department of Medical Genetics, St. Mary's Hospital, Hathersage Road, Manchester M13 0JH; Telephone: 061-276-6129/6122; FAX: 061-274-3159 1924del7 deletion of 7 13 frameshift Instituto Orozco L, bp (AAACTA) Nacional de Villarreal T, from 1924 Pediatria, Lezana JL, Mexico and The Zielenski J, Hospital for Markiewicz D, Sick Children, Tsui L-C (Jan 30) Toronto, Canada 2055del9->A complex 13 frameshift same as above Orozco et al. deletion of 9 (Jan 30) bp CTCAAAACT->A at 2055 Note: 1924del7 was detected by SSCP. The deletion removes the only restriction site for MaeI in the PCR fragment amplified from 13i-5 and 13i-3A primers. The mutation was found in one Mexican (Mestee) CF patient .Patient : [[Delta]]F508/1924del7; sweat Cl-, 102 mEq/L; pancreatic insufficiency (PI); moderate lung disease. 2055del9->A was detected by SSCP. The deletion removes restriction site for Alu I. The mutation was found in two Mexican (Mestee) CF patients. Patient #1: [[Delta]]F508/2055del9->A; sweat Cl-, 117 mEq/L; pancreatic insufficiency (PI); moderate-severe lung disease. Patient #2: 2055del9->A/unknown; sweat Cl-, 112 mEq/L; pancreatic insufficiency (PI); moderate lung disease. Contact: Julian Zielenski; Address: Department of Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, M5G 1X8 CANADA; Telephone: (416) 813 6365 FAX: (416) 813 4931; E-Mail: firstname.lastname@example.org. S50P T->C at 280 2 Ser->Pro at codon Institut de Casals T, 50 Recerca Gimenez J, Ramos Oncologica, MD, Barcelona, Spain Nunes V, Estivill X (Jan 31) 741C/T C or T at 741 6a no change same as above Casals et al. (Jan 31) 296+128G/C G or C at intron polymorphism same as above Casals et al. 296+128 3 (Jan 31) 2751+3A->G A->G at 2751+3 intron splice mutation? same as above Casals T, Ramos 14a (CBAVD) MD,Gimenez J, Nunes V, Estivill X (Mar 22) F1074L T->A at 3354 17b Phe->Leu at 1074 same as above Casals et al. (Mar 22) Note: Abnormal pattern in SSCA exon 2 was observed for I50T. Direct sequence of the sample allowed us to detect this new mutation. Mutation was observed in a Spanish man with CBAVD, carrying DE115 in the other chromosome. 741C/T was observed by direct sequencing after detection of an abnormal SSCA pattern. This variation in the coding region of exon 6a removes a site for MboI. 296+128G/C was observed by direct sequencing after detection of an abnormal SSCA pattern. Abnormal DGGE pattern in exon 14a was detected for 2751+3A->G. Direct sequence of the sample allowed us to detect this new mutation. Mutation was observed in a Spanish man with CBAVD, carrying [[Delta]]F508 and allele 5T intron 8. Screening in 154 CF and 110 Normal chromosomes has been negative. F1074L was observed by direct sequencing after detection of an abnormal DGGE pattern in exon 17b. CF patient with unknown mutation in the other chromosome, presented lung involvement and PI. Contact: Virginia Nunes / Teresa Casals; Address: Institut de Recerca Oncologica, Hospital Duran i Reynols, Autovia de Castelldefels km. 2.7, Hospitalet, 08907 Barcelona, Catalunya, Spain; Telephone: (34-3) 335 71 52; FAX: (34-3) 263 22 51; E-Mail: email@example.com 306delTAGA deletion of 3 frameshift Bulgarian Savov A, TAGA from 306 Institute, Angelicheva D, Sofia, Bulgaria Jordanova A, Kremensky I, Kalaydjieva L (Feb 1) Note: The above mutation was identified by SSCP and direct sequencing of a Bulgarian patient. Contact: Ivo Kremensky; Address: Bulgarian Institute-Laboratory of Molecular Pathology, Zdrave 2, Sofia 1431, Bulgaria; Telephone and FAX: +3592 650198; E-Mail: Ivo.Kremensky@infolink.infotel.bg M265R T->G at 926 6b Met->Arg at 265 Royal Manchester Schwarz M, Children's Haworth A, Hospital, England Malone G (Feb 6) Y569D T->G at 1837 12 Tyr->Asp at 569 same as above Malone G, Schwarz M, Haworth A (Feb 14) 3423delC deletion of C 17b frameshift same as above Kay E, Malone G, at 3423 Haworth A, Schwarz M, Robertson E (Mar 15) Note: M265R was detected by SSCP and identified by direct DNA sequencing. This mutation was detected in an obligate carrier of CF, whose daughter died at 1 day old with meconium ileus. The child is inferred to have been a compound heterozygote of [[Delta]]F508 and M265R since her father is a carrier of [[Delta]]F508. M265R was found only once in 50 non[[Delta]]F508 chromosome screened. Y569D was identified by direct DNA sequencing. The mutation was found in three Pakistani patients, presumed to be unrelated; all were from consanguineous partnerships and all homozygous for the mutation. 60 non-[[Delta]]F508 chromosomes, of which 12 were Pakistani in origin, were negative for Y569D. Contact: Martin Schwarz; Address: Regional Molecular Genetics Laboratory, Royal Manchester Children's Hospitals, Hospital Road, Pendlebury, Manchester M27 4HA; Telephone: 0161-794 4696; FAX: 0617272328 3196del54 deletion of 17a deletion of 18 aa Institut de Desgeorges M, 54 bp from from codon 1022 Biologie Carles S, 3196 Montpellier, Tuffery S, France Claustres M, Ramsay M (Feb 9) 3196del54 was found by DGGE in a black CF patient from South Africa. Contact: Pr. Mirreille Claustres; Address: Laboratoire de Biochemie Génétique, Institut de Biologie, 34060 Montpellier CEDEX, France; Telephone: ***** ; FAX: 33 67 60 11 81 A141D C->A at 554 4 Ala->Asp Hôpitaux Robert Gouya L, Pascaud Debré, Paris, O, Elion J, France Denamur E (Feb 15) The above mutation was identified by DGGE and sequencing (direct sequencing and sequencing after cloning) in an Algerian CF patient, with the other mutation being N1303K. Contact: Laurent Gouya; Address: Laboratoire de Biochemie Génétique, Hôpitaux Robert Debré, 48, Bd Sérurier, 75019 Paris; Telephone: (1) 40.03.20.00; FAX: (1) 40.03.20.20 L375F A->C at 1257 8 Leu->Phe at 375 Universite de Jézéquel P (Mar Rennes I, France 13) The above mutation was detected by DGGE and identified by direct sequencing using two different sequencing kits (both strands) in a patient with CUAVD. This mutation creates an MboII restriction site. This patient was also found to carry G551D. Contact: P Jézéquel/Y.E. le Gall; Address: Départment de Biochimie et Biologie Molecularie, Universite de Rennes I, 2 Avenue du Professeur Léon Bernard, 35043 Rennes Cédex, France; Telephone: 184.108.40.206.20; FAX: 220.127.116.11.98; E-Mail: firstname.lastname@example.org
2. C Férec noted that the change Q353H in exon 7 is a sequence polymorphism on the basis of family analysis.
3. I apologize for the delay in getting this issue of newsletter ready. It is partly due to the new formatting. As we discussed at the last consortium meeting, we should try to reduce the page number of our newsletter. Some investigators have already taken advantage of the electronic mailing system and sent their report by e-mail. Some have followed the suggested reporting format. The majority are still using the old style, however. I have tried to preserve the content of the letter in the "Note" field. Please let me know if you like the new format. I have also spent some time in setting up an electronic database (see next section).
4. As agreed at the last Consortium meeting in Montreal, I would try to implement an electronic database for our mutation and polymorphism tables which is publicly accessible. As an experiment, I have posted a "home page" of the Cystic Fibrosis Genetic Analysis Consortium accessible through World Wide Web. To make the files less cumbersome, I have put the summary tables into different files. The format is similar to the present tables. In the future, I intend to divide the tables further to exons and domains, and perhaps even graphic displays, but it will probably take me some time to do it. For those who have INTERNET access, please try to see if you can view the data by calling <http://18.104.22.168/>. The number is a temporary one for this experiment. If successful, it will be replaced by something more permanent later.
Please drop me note by e-mail <email@example.com> that you have seen it and give me any suggestions regarding future improvements.