ABCMdb

PMID: 16786510

Niel F, Legendre M, Bienvenu T, Bieth E, Lalau G, Sermet I, Bondeux D, Boukari R, Derelle J, Levy P, Ruszniewski P, Martin J, Costa C, Goossens M, Girodon E
A new large CFTR rearrangement illustrates the importance of searching for complex alleles.
Hum Mutat. 2006 Jul;27(7):716-7., [PubMed]

Sentences

No. Mutations Sentence Comment

1 ABCC7 p.Val754Met A New Large CFTR Rearrangement Illustrates the Importance of Searching for Complex Alleles F Niel1 , M Legendre1 , T Bienvenu2 , E Bieth3 , G Lalau4 , I Sermet5 , D Bondeux6 , R Boukari7 , J Derelle8 , P Levy9 , P Ruszniewski9 , J Martin1 , C Costa1 , M Goossens1 , and E Girodon1* 1 Service de Biochimie-Génétique, Hôpital Henri Mondor AP-HP, Créteil, France; 2 Service de Biochimie-Génétique, Hôpital Cochin AP-HP, Paris, France; 3 Laboratoire de Génétique Médicale, Hôpital Purpan, Toulouse, France; 4 Laboratoire de Biochimie et Biologie Moléculaire, Hôpital Calmette, Lille, France; 5 Service de Pédiatrie, Hôpital Necker-Enfants-Malades AP-HP, Paris, France; 6 Département de Pédiatrie, Hôpital Porte Madeleine, Orléans, France; 7 Service de Pédiatrie, Hôpital Noureddine El Atassi, Alger, Algérie; 8 Médecine Infantile, Hôpital d`Enfants, Vandoeuvre-les Nancy, France; 9 Service de Gastro-Entérologie, Hôpital Beaujon AP-HP, Clichy, France *Correspondence to: Emmanuelle Girodon, Service de Biochimie-Génétique, Hôpital Henri Mondor AP-HP, Créteil, France, Tel.: 33 1 49 81 28 57; Fax: 33 1 49 81 28 42; E-mail: Emmanuelle.Girodon@im3.inserm.fr Communicated by Richard G.H. Cotton The p.Val754Met variant, described in 1996 in a CF patient, has been considered a CF mutation. Login to comment 2 ABCC7 p.Val754Met However, biochemical aspects, results of functional studies and, finally, the identification of a complex deletion removing exons 3 to 10 and 14b to 16 in cis of p.Val754Met in a CF patient, argue against a strong deleterious effect. Login to comment 3 ABCC7 p.Val754Met An inventory through the French CF network of patients carrying p.Val754Met led to the registration of seven patients (CF: n=4; idiopathic chronic pancreatitis: n=3) and six healthy individuals, all heterozygous for the variation. Login to comment 7 ABCC7 p.Val754Met ABCC7 p.Val754Met [Phe508del]+[Val754Met] genotype was found in a healthy individual, bring further arguments against the association of p.Val754Met with CF. Login to comment 8 ABCC7 p.Val754Met We thus suggest looking for a possible complex allele whenever p.Val754Met is detected and considering it neutral regarding genetic counseling when found in isolation. Login to comment 9 ABCC7 p.Val754Met (c) 2006 Wiley-Liss, Inc. KEY WORDS: CFTR; ABCC7; CF; cystic fibrosis; gene rearrangement; complex deletion; complex allele; p.Val754Met INTRODUCTION Cystic fibrosis (CF; MIM# 219700) is one of the most common autosomal recessive hereditary diseases in the Caucasian population. Login to comment 12 ABCC7 p.Leu997Phe Of these, some have been described as polymorphisms because they were identified in the non CF allele of CF patients` parents, but also seem to be involved in moderate forms of CF or syndromes of late onset, such as the 1342-12(T)5 or IVS8(T)5 variant (c.1210-12(T)5 according to the approved nomenclature, www.hgvs.org/mutnomen/) (Chillon et al., 1995a; Costes et al., 1995; Pignatti et al., 1996; Wang et al., 2000), p.Leu997Phe (Pignatti et al., 1995; Girodon et al., 1997), 1716A>G (c.1584A>G according to the approved nomenclature) (Cuppens and Cassiman, 1995). Login to comment 13 ABCC7 p.Ile148Thr Conversely, other mutations were initially reported as mutations because they were identified in CF patients, but are now reclassified as polymorphisms, as is the case for p.Ile148Thr (Rohlfs et al., 2002; Claustres et al., 2004). Login to comment 15 ABCC7 p.Val754Met The p.Val754Met variant (2392G>A or c.2260G>A according to the approved nomenclature), first described by A.Wallace in 1996 in a CF patient (www.genet.sickkids.on.ca/cftr) and subsequently identified in other CF patients, has therefore been considered a CF mutation. Login to comment 18 ABCC7 p.Val754Met ABCC7 p.Val754Met However, there have been several lines of evidence against a strong deleterious effect of p.Val754Met: 1) the conservative nature of the Val>Met substitution; 2) the presence of a Met residue in place of Val in some species and the benign nature of the substitution predicted by the SIFT® and Polyphen® softwares; 3) results of functional studies which suggest that residue Val754 does not belong to the functional "R" domain (Chen et al., 2000); 4) finally, the recent identification by semi-quantitative fluorescent multiplex PCR of a complex deletion, CFTRdele3_10,14b_16, removing exons 3 to 10 and 14b to16 in cis of p.Val754Met in a CF patient (Niel et al., 2004). Login to comment 19 ABCC7 p.Val754Met The aim of this study was to determine whether we should still consider p.Val754Met as a possible disease-associated mutation or reclassify it as a neutral polymorphism. Login to comment 20 ABCC7 p.Val754Met We thus made an inventory of patients and individuals with p.Val754Met, screened for the complex deletion and for other possible CFTR anomalies, and studied the associated CFTR haplotypes. Login to comment 21 ABCC7 p.Val754Met Here, we gather lines of evidence that p.Val754Met should be no longer considered as a CF mutation. Login to comment 22 ABCC7 p.Val754Met PATIENTS AND METHODS Patients and controls Thirteen patients and individuals from diverse origins and all heterozygous for the p.Val754Met variant, were registered from the French CF network of molecular genetics laboratories (Table 1): seven patients (four having CF and three presenting with idiopathic chronic pancreatitis) and six healthy individuals (an infant, three partners of CF carriers, a CF patient`s relative and a mother of a fetus with bowel anomalies). Login to comment 33 ABCC7 p.Asn1303Lys ABCC7 p.Val754Met ABCC7 p.Val754Met ABCC7 p.Val754Met ABCC7 p.Phe311Leu Phenotype and genotype data of patients/individuals carrying the p.Val754Met variation Patient Phenotype Origin Allele 1 Allele 2 CFTR haplotype linked to p.Val754Met c p.Val754Met b CFTRdele3_10, 14b_16 b 1a CF Kabylia + + 1812-1G>A (c.1680-1G>A) 22; del; del; 7; 17 2 CF Northwestern France + + 3659delC (c.3528delC) 22; del; del; 7; 17 3 CF Algeria + + p.Asn1303Lys 22; del; del; 7; 17 4 CF Turkey + + p.Phe508del 22; del; del; 7; 17 5 Chronic pancreatitis Portugal + - but p.Phe311Leu p.Phe508del 22; 23; 10-9; 7; 17 6 Chronic pancreatitis Not known + - IVS8(TG)12(T)5 (c.1210-34(TG)12(T)5) 21 or 23; 16; 107; 7; 17 7 Chronic pancreatitis Northern France + - IVS8(TG)11(T)5 (c.1210-34(TG)11(T)5) 22; 23; 10-9; 7; 17 8 healthy Southwestern France + - p.Phe508del 22; 23; 10-9; 7; 17 9 healthy Northern France + - Wild 22; 23; 10-9; 7; 17 10 healthy Northern France + - Wild 22; 16 or 21; 109; 7; 17 11 healthy Northern France + - Wild 22; 23; 10-9; 7; 17 12 healthy Turkey + - Wild 22; 23; 10-9; 7; 17 13 healthy France + - Wild 22; 23; 10-9; 7; 17 The recommendations for mutation nomenclature (www.hgvs.org/mutnomen/) were used to name CFTR gene sequence variations at the protein level. For variations described at the nucleotide level, the A of the ATG translation start codon was numbered as +133 in accordance with the current CFTR gene numbering based on cDNA sequence (GenBank NM_000492.2) and on the CF mutation database. These variations were also given in parentheses following the approved nomenclature format (A of the ATG translation start codon as +1, "c." Login to comment 36 ABCC7 p.Val754Met b "+" and "-" refer to the presence or absence of p.Val754Met and CFTRdele3_10,14b_16. Login to comment 39 ABCC7 p.Val754Met Phenotype data of patients carrying the p.Val754Met variation Patient Age at diagnosis Current age Gender Pulmonary outcome Pancreatic status Other Sweat testa 1 9 y Deceased at 14 y F Severe PI 150 2 birth (neonatal screening) 6 y M Severe PI 80 3 1 y 11 y M Severe PI Failure to thrive 120-150 4 birth (neonatal screening) 17 m M Severe PI 104-107 5 16 y 17 y M None PS Minor epilepsy Nd 6 60 y 62 y F None PS Lymphoid hemopathy Nd 7 adulthood Deceased at 37 y M None PS Severe, complicated, Crohn`s disease; alcoholism Nd y: years; m: months; F: female; M: male; PI: pancreatic insufficiency; PS: pancreatic sufficiency; Nd: not done. Login to comment 41 ABCC7 p.Val754Met The frequency of the p.Val754Met variant in the general population has been estimated low in European populations, below 0.17%, as it was found neither among 191 healthy European individuals (Bombieri et al., 2000) nor among 115 healthy French individuals (Girodon et al., 2002). Login to comment 42 ABCC7 p.Val754Met As two of our patients carrying p.Val754Met were of Arab origin and one was Turkish, we studied another control population of 116 healthy individuals from Arab (mostly Northern African) or Turkish extraction, who were referred to our laboratory for carrier screening (56 partners of CF carriers and 60 parents of fetuses with bowel anomalies but not affected with CF). Login to comment 48 ABCC7 p.Val754Met Extensive CFTR gene analyses were performed in the patients / individuals carrying p.Val754Met: (i) screening for frequent mutations using diverse commercial assays; (ii) scanning of the 27 exons and their boundaries using denaturing gradient gel electrophoresis (DGGE) (Fanen et al., 1992; Costes et al., 1993) or denaturing high pressure liquid phase chromatography (DHPLC) (Le Marechal et al., 2001), followed by sequencing to characterize the variants; (iii) screening for the intronic splicing 1811+1.6kbA>G mutation (c.1679+1634A>G) (Chillon et al., 1995b); (iv) screening for large CFTR rearrangements using a semi-quantitative fluorescent multiplex PCR (QFM-PCR) assay recently developed in our laboratory and which enabled the detection of 20% of the rearrangements among previously unidentified alleles in CF patients (Niel et al., 2004). Login to comment 49 ABCC7 p.Val754Met The healthy subjects tested for genetic counseling purposes were screened for frequent mutations (CF OLA assay, Abbott, Rungis, France, www.abbott.com) and for other mutations according to their geographical or ethnic background (Claustres et al., 2000; Kilinc et al., 2002), including DHPLC analysis of exon 13 where p.Val754Met is located. Login to comment 50 ABCC7 p.Val754Met CFTR haplotype analysis To determine the haplotypes associated with p.Val754Met in isolation and in cis with the complex deletion, five intragenic multiallelic markers were studied: IVS1(CA) [185+10167(CA)17_26] ([c.53+10167(CA)17_26]); IVS8(CA) [1342-307(GT)14_24] ([c.1210-307(GT)14_24]); IVS8(TG)m(T)n [1342-34(TG)9_13(T)5_9] ([c.1210-34(TG)9_13(T)5_9]); IVS17b(TA) [3499+200(TA)7_57] ([c.3367+200(TA)7_57]) and IVS17b(CA) [3499+428(CA)11_19] ([c.3367+428(CA)11_19]). Login to comment 55 ABCC7 p.Val754Met RESULTS Among the 13 patients / individuals carrying p.Val754Met, only the four patients affected with classical CF carried the complex deletion (Fig. Login to comment 57 ABCC7 p.Val754Met In all these cases, p.Val754Met was in cis of the deletion. Login to comment 59 ABCC7 p.Phe311Leu Patient #5, already heterozygous for p.Phe508del, was found to carry the known p.Phe311Leu CF mutation. Login to comment 60 ABCC7 p.Val754Met In case #8, the healthy infant carried p.Phe508del and p.Val754Met in trans, but not the deletion. Login to comment 61 ABCC7 p.Val754Met Chronic pancreatitis patients #6 and 7 carried the IVS8(T)5 variant, albeit linked to different (TG) repeats, but we could not confirm that it was in trans of p.Val754Met. Login to comment 70 ABCC7 p.Val754Met Analysis of five intragenic CFTR microsatellites in the patients / individuals carrying p.Val754Met and their families evidenced the same haplotype linked to the complex allele, [IVS1(CA)22; IVS17b(TA)7; IVS17b(CA)17], extended to IVS8(CA)23 and IVS8(TG)10(T)9 in cases 8, 11 and 12 (Table 1). Login to comment 71 ABCC7 p.Val754Met The same haplotype could be linked to p.Val754Met also in cases #5, 7, 9 and 13, despite the absence of a segregation study. Login to comment 73 ABCC7 p.Val754Met Among the 116 healthy subjects, one carried p.Val754Met (allele frequency: 0.43%) and was thus included in our series (case #12). Login to comment 74 ABCC7 p.Val754Met She was the mother of a fetus with an echogenic bowel, who was not affected with CF and did not inherit p.Val754Met. Login to comment 80 ABCC7 p.Val754Met DISCUSSION An inventory of patients / individuals carrying the p.Val754Met variation through the French CF network of molecular genetics laboratories (dealing with around 10,000 samples for CFTR gene studies per year), led to the registration of 13 patients / individuals. Login to comment 83 ABCC7 p.Val754Met ABCC7 p.Val754Met Cases #1-5 and 8 with compound heterozygosity for p.Val754Met and a severe mutation (Table 1) are particularly informative and bring further arguments against considering p.Val754Met as a CF-causing mutation. Login to comment 84 ABCC7 p.Val754Met The four CF patients carried the complex deletion in cis with p.Val754Met. Login to comment 86 ABCC7 p.Phe311Leu [Phe508del]+[Phe311Leu] compound heterozygous, though no family study could be performed in this case, as this genotype has already been described in CF (www.genet.sickkids.on.ca/cftr). Login to comment 87 ABCC7 p.Val754Met ABCC7 p.Val754Met ABCC7 p.Phe311Leu We also hypothesize that p.Val754Met is in cis with p.Phe311Leu rather than with p.Phe508del, because of the putative frequent haplotype linked to p.Phe508del, [IVS1(CA)22; IVS8(CA)23; IVS8(TG)10(T)9; IVS17b(TA)31; IVS17b(CA)13], the other haplotype being identical to that found in other p.Val754Met alleles (Table 1). Login to comment 89 ABCC7 p.Phe311Leu [Phe508del]+[Phe311Leu] compound heterozygous genotype, no other CF symptom was observed in this patient, and the family declined any further clinical and molecular investigation at present towards assessment of CFTR dysfunction. Login to comment 91 ABCC7 p.Val754Met The infant in case #8 carried p.Phe508del and p.Val754Met in trans but neither the deletion nor any other detectable CFTR mutation. Login to comment 94 ABCC7 p.Val754Met Later on, the counseling was more reassuring because of the complex deletion identified in cis of p.Val754Met in the meanwhile in patient #1, and the pregnancy was finally continued to term. Login to comment 95 ABCC7 p.Val754Met A mild detrimental effect of p.Val754Met cannot be however definitely excluded, and this case is worth clinical follow-up. Login to comment 96 ABCC7 p.Val754Met Also, it is not possible to definitely rule out a role of p.Val754Met in the pathogenesis of chronic pancreatitis or other CFTR related diseases. Login to comment 98 ABCC7 p.Val754Met However, segregation analysis could not be performed in the families of patients #6 and 7 to determine whether p.Val754Met was in cis or trans of the IVS8(T)5 variant, because of the clinical context (age of patient #6 and decease of patient #7) and the limited value of genetic counseling in these cases. Login to comment 99 ABCC7 p.Val754Met Analysis of the literature evidenced other descriptions of p.Val754Met at the heterozygous state, but which are of no further help in considering whether the variant is deleterious or not: in a German patient with idiopathic chronic pancreatitis (Weiss et al., 2005) and in a patient from Spain with unexplained disseminated bronchiectasis (Casals et al., 2004). Login to comment 101 ABCC7 p.Arg668Cys ABCC7 p.Gly576Ala [Gly576Ala; Arg668Cys] (Grangeia et al., personal communication). Login to comment 103 ABCC7 p.Val754Met It is noteworthy that, while we found p.Val754Met in patients from diverse origins, two patients carrying the deletion were of Arab extraction and one was from Turkey, a cosmopolitan country including European, Middle Eastern and Arab populations. Login to comment 105 ABCC7 p.Val754Met ABCC7 p.Val754Met The frequency of p.Val754Met in the Caucasian general population appears to be weak: although we could register five unrelated healthy French individuals for this study, p.Val754Met was not found among 191 healthy European individuals (Bombieri et al., 2000) nor among 115 healthy French individuals (Girodon et al., 2002) (allele frequency: below 0.17%). Login to comment 107 ABCC7 p.Val754Met Determination of haplotypes linked to p.Val754Met in cis with the deletion or in isolation demonstrated the same haplotype in the four CF patients, consisting of three microsatellites, and extended to five sites in three healthy individuals. Login to comment 108 ABCC7 p.Val754Met The same haplotype may be linked to p.Val754Met in four other cases despite the absence of segregation study, while different alleles have been found in two cases (#6 and 10). Login to comment 109 ABCC7 p.Val754Met These results, together with the fact that p.Val754Met is located at a CpG dinucleotide and has been found in patients from diverse geographical origins, suggest a possible recurrent event. Login to comment 110 ABCC7 p.Val754Met We however hypothesize a founding effect for the complex deletion occurring on a p.Val754Met background, possibly in an Arab population. Login to comment 119 ABCC7 p.Val754Met In conclusion, while a mild detrimental effect of p.Val754Met could not be definitely ruled out, there are now strong lines of evidence against a severe deleterious effect and its association with CF. Login to comment 120 ABCC7 p.Val754Met This has notable implications for genetic counseling: whenever p.Val754Met is identified, we suggest looking for a possible complex allele, in particular associating the CFTRdele3_10,14b_16 deletion. Login to comment 123 ABCC7 p.Val754Met When p.Val754Met is in isolation in non CF patients or healthy individuals, counseling can be reassuring with regard to its transmission in offspring. Login to comment 124 ABCC7 p.Val754Met Also, the search for p.Val754Met should not be recommended in their relatives. Login to comment