Final Diagnosis -- Cyctic Fibrosis



CF is the most common severe autosomal recessive disorder of the Caucasian population with a prevalence estimate of 1 in 2500 to 3300 live births. Since the identification of the CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene in 1989, over 1900 mutations have been identified and updated at (

Impaired function of the CFTR gene leads to defective chloride ion transport in a number of epithelial organs. Hence, CF is characterized by viscous mucus in the lungs with involvement of digestive and reproductive systems as well as sweat glands (excess salt loss). Pulmonary disease is the critical factor in prognosis/survival, but both pancreatic-sufficient and insufficient forms exist. Recurrent and persistent pulmonary infections are common and lead over time to respiratory failure. Pancreatic insufficiency occurs in 85% of affected individuals. Neonatal meconium ileus occurs in 10% to 20% of newborns with CF. Other manifestations may include chronic sinusitis, nasal polyps, liver disease, pancreatitis and congenital absence of the vas deferens. The overall average survival of CF patients, including those with milder presentation, is now ~35 years. Treatment for CF patients is palliative and includes control of infections, clearance of mucus in the lung and improvement of nutrition through pancreatic enzyme replacement.

CFTR mutations

There were initially four classes of CFTR mutations1,2,12,16 described on the basis of defects in protein production and function. These have been expanded to six classes recently. Mutations are situated throughout the entire coding region of the CFTR, to include the nucleotide binding (NBD) and regulatory (R) domains, as well as in the promoter region.

Class 1- defective protein production, Ex: G542X and R553X
Class II- defective protein processing, Ex: ?F508 mutation
Class III - defective regulation, Ex: G551D
Class IV - defective conduction, Ex: R117H
Class V -defective synthesis - abnormal splicing13
Class VI- affecting protein stability 3,4.
AS previously noted, these mutations result in defective cAMP-regulated chloride- secretion by epithelial cells of the sweat gland, airway, pancreas, and intestine.

Severe & Mild Mutations

Of the various clinical symptoms of CF only the pancreatic function has been shown to correlate well with CFTR genotype. Pulmonary disease is usually highly variable, even among sibs who have identical mutations. Severe mutations (i.e. Class I, II or III) where there is absence of functional CFTR correlate well with pancreatic insufficiency (>95% cases), liver disease (3-5% of patients), young age at diagnosis (usually <1 year), high sweat chloride levels (>80 meq/l) and meconium ileus (?20% of cases). 'Mild' mutations (i.e. Class IV, V, VI) which may still produce a small amount of functional CFTR are generally associated with pancreatic sufficiency (70-80% cases), a later age at diagnosis (usually >10 years), lower sweat chloride levels, no meconium ileus and milder pulmonary disease.

F508 & Other Common Mutations

A single mutation, F508del (a 3-nucleotide deletion that removes the phenylalanine residue at position 508 of CFTR, results in mis-folding of the CFTR protein and mislocalisation of the mature protein), and accounts for about 70% of CF chromosomes worldwide. The majority of other CFTR mutations seen with any frequency are relatively rare with four other mutations (G542X, N1303K, G551D and W1282X) having overall frequencies above 1% in the mixed Caucasian population. Certain 'founder' mutations are seen at higher frequencies in specific ethnic groups.


The R117H mutation is a Class IV mild mutation present in 0.3% of the Caucasian population can result in a wide variety of clinical outcomes depending on what other genetic variations are present.

Poly-T tract and the TG tract

Two regions in intron 8 of the CFTR gene, the Poly-T tract and the TG tract, have been demonstrated to impact CFTR function by aberrant splicing of exon 914,15. The Poly-T tract in the splice acceptor region occurs in 3 forms: 5T, 7T, and 9T. Bboth 7T and 9T alleles are considered polymorphic variants, but 5T alleles are considered variably penetrant mutations thought to decrease the efficiency of intron 8 splicing. Similarly, a region of dinucleotide repeats (the TG tract) located adjacent to the poly-T tract comes in 3 lengths called TG11, TG12, and TG13. and identified at the intron 8 - exon 9 junction. A longer TG tract (12 or 13) in conjunction with a shorter poly T tract (5T) has the strongest adverse effect on proper intron 8 splicing with resultant reduced expression CFTR mRNA containing exon 97,17. Up to 92% of CFTR mRNA transcripts can lack exon 9 without causing overt CF6.

The phenotypic consequences of the R117H mutation have been shown to be modulated in cis by the 5/7/9T polypyrimidine tract in intron 8 such that R117H/7T is associated with milder forms of CF such as CBAVD while R117H/5T alleles are may be associated with classic CF5. The 5T allele by itself has also been associated with male infertility due to CBAVD, with or without mild or atypical symptoms of CF. There is no known clinical significance of 5T in females. The penetrance of 5T effects is variable, and it is difficult to predict the clinical significance of the 5T variant.

This table is adapted from Moskowitz SM, Chmiel JF, Sternen DL, Cheng E, Cutting GR (Updated [19 February 2008]). CFTR-Related Disorders In: GeneReviews at GeneTests: Medical Genetics Information Resource (database online). Copyright, University of Washington, Seattle. 1997-2008. Available at

  1. Patterns reflect dominant effect of "milder" alleles in compound heterozygotes. Classic alleles generally refer to Class I-III mutations; mild alleles refer to Class IV-V mutations exclusive of R117H and 5T alleles.
  2. It is based on risk after testing for the ACMG recommended panel of mutations.

The patient described in this web case falls into the third group down in table 1 and appears to have non-classic cystic fibrosis.

Indications for Testing

Diagnostic Testing: for individuals showing classic or non-classic symptoms of cystic fibrosis, as well as atypical forms and infants with meconium ileus, also congenital bilateral absence of the vas deferens (CBAVD) in males.

Carrier Testing: in partners of individuals with a confirmed CFTR mutation or positive family history for CF, partners of CBAVD males, general population of reproductive couples, premarital population, to assist in selection of a mate, gamete donors.

Preimplantation/Prenatal Testing: positive family history, couples with a 1 in 4 risk (each carries a CFTR mutation), echogenic bowel in a fetus during second trimester, follow-up testing after newborn screening.

CF Screening Panel

Prepregnancy or premarital carrier screening of the mixed Caucasian population was recommend by an NIH consensus development conference in the late 1990s. In October of 2001, ACOG and ACMG recommended a panel of 25 mutations with 0.1% or greater frequency in CF patients worldwide for such screening. The panel was revised downward to 23 mutations after several years of experience (see below).11 These mutations With account for 94.04% to 88.29% of detectable mutations for individuals of mixed Caucasian background undergoing screening for CF.

ACMG's Other Recommendations on CF testing:

  1. CF carrier screening should be offered to non-Jewish Caucasians and Ashkenazi Jews, and made available to other ethnic groups who should be informed of their detection rate.
  2. Preconception testing should be encouraged whenever possible, although testing often occurs in the prenatal setting.
  3. The 5/7/9T variant is excluded from routine carrier screens but is tested on a reflex basis for carriers heterozygous for the R117H mutation. The 5/7/9T variant should be included in diagnostic panels to distinguish the genotypes of R117H associated with CF from those associated with CBAVD and as a potential pathogenic mutation for CBAVD.
  4. For R117H/5T positive heterozygotes, testing of parents is recommended to determine the cis/trans inheritance of R117H and the 5T variant . For diagnostic testing, and particularly for testing for CBAVD in males with infertility, it is recommended that the intron 8 variant be included in the testing panel.
  5. An extended panethnic mutation panel may be appropriate for certain diagnostic testing purposes but it is not currently recommended by ACMG for routine carrier screening of reproductive couples8.
  6. The composition of any extended panel should be determined based on frequency of the mutation within the target population. An extended panel would look for mutations below the 0.1% frequency worldwide and expand its scope to the population of service. Additional mutations of >0.1% frequency in the U.S. population that laboratories may wish to consider adding to the minimum panel have been recently described9.

Standards and Guidelines of Reports on CF testing8

  1. Reports should include all information described in the ACMG Standards and Guidelines for Clinical Genetics Laboratories (
  2. CF reports should include the reported ethnicity of the patient and the indication for testing (i.e., carrier test, no family history, etc.) as well as the mutations tested and method of testing.
  3. The best current estimates of residual risks for the major ethnic groups after testing negative with the standard mutation panel should be included.
  4. Labs should include clear interpretation of the patient result as homozygous for a mutation (predicted affected with CF), a compound heterozygote (predicted affected with CF), heterozygous carrier (interpretation depends on whether this is carrier testing or diagnostic testing) or negative (interpretation depends on whether this is carrier testing, presence or absence of family history or diagnostic).
  5. All positive results for diagnostic tests or for positive/positive couple screening results should state that genetic counseling is indicated and testing is appropriate for at-risk family members. When sequential carrier testing is done, a positive result on one partner should include the recommendation of testing the other partner and at-risk family members.


  1. Welsh, M., Ramsey, B. W., Accurso, F. & Cutting, G. R. 2001. Cystic Fibrosis. In The Molecular and Metabolic Basis of Inherited Disease (ed. A. B.CL Scriver, W. S.Sly & D.Valle), pp. 5121-5188. McGraw-Hill, New York .
  2. Zielenski, J. & Tsui, L. C. 1995. Cystic fibrosis: genotypic and phenotypic variations. Annu Rev Genet 29, 777-807.
  3. Zielenski, J. 2000. Genotype and phenotype in cystic fibrosis. Respiration 67, 117-33.
  4. Haardt, M., Benharouga, M., Lechardeur, D., Kartner, N. & Lukacs, G. L. 1999. C-terminal truncations destabilize the cystic fibrosis transmembrane conductance regulator without impairing its biogenesis. A novel class of mutation. J Biol Chem 274, 21873-7.
  5. Kiesewetter S, Macek M Jr, Davis C, Curristin SM, Chu CS, Graham C, Shrimpton AE, Cahsman SM, Tsui LC, Mickle J, Amos J, Highsmith WE, Shuber A, Witt DR, Crystal RG, Cutting GR. A mutation in CFTR produces different phenotypes depending on chromosomal background. Nat Genet 1993;5:274-278.
  6. Chu, C. S., Trapnell, B. C., Murtagh, J. J., Moss, J. Jr., Dalemans, W. Jallat, S., Mercenier, A., Pavirani, A., Lecocq, J. P., Cutting, G. R. & et al 1991. Variable deletion of exon 9 coding sequences in cystic fibrosis transmembrane conductance regulator gene mRNA transcripts in normal bronchial epithelium. Embo J 10, 1355-63.
  7. Cuppens H, Lin W, Jaspers M, Costes B, Teng H, Vankeerberghen A, Jorissen M, Droogmans G, Reynaert I, Goossens M, Nilius B, Cassiman JJ. Polyvariant mutant cystic fibrosis transmembrane conductance regulator genes. The polymorphic (Tg)m locus explains the partial penetrance of the T5 polymorphism as a disease mutation. J Clin Invest. 1998;101:487-96.
  8. Grody WW, Cutting GR, Klinger KW, Richards CS, Watson MS, Desnick RJ: Subcommittee on Cystic Fibrosis Screening, Accreditation of Genetic Services Committee, ACMG. American College of Medical Genetics. Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Genet Med 2001;3:149-154.
  9. Heim RA, Sugarman EA, Allitto, BA. Improved detection of cystic fibrosis mutations in the heterogeneous U.S. population using an expanded, pan-ethnic mutation panel. Genet Med 2001;3:168-176.
  10. Moskowitz SM, Chmiel JF, Sternen DL, Cheng E, Cutting GR. CFTR-Related Disorders. 2001 Mar 26 [updated 2008 Feb 19]. In: Pagon RA, Bird TD, Dolan CR,Stephens K, editors. GeneReviews [Internet]. Seattle (WA): University ofWashington, Seattle; 1993-. Available from
  11. Watson MS, Cutting GR, Desnick RJ, Driscoll DA, Klinger K, Mennuti M, Palomaki GE, Popovich BW, Pratt VM, Rohlfs EM, Strom CM, Richards CS, Witt DR, Grody WW. Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Genet Med. 2004; 6: 387-91.
  12. 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
  13. Rowntree, R. K. and Harris, A. (2003), The Phenotypic Consequences of CFTR Mutations. Annals of Human Genetics, 67: 471-485. doi: 10.1046/j.1469-1809.2003.00028.x
  14. Rave-Harel N, Kerem E, Nissim-Rafinia M, Madjar I, Goshen R, Augarten A, Rahat A, Hurwitz A, Darvasi A, Kerem B. The molecular basis of partial penetrance of splicing mutations in cystic fibrosis. Am J Hum Genet. 1997 Jan;60(1):87-94.
  15. Niksic M, Romano M, Buratti E, Pagani F, Baralle FE. Functional analysis of cis-acting elements regulating the alternative splicing of human CFTR exon 9. Hum Mol Genet. 1999 Dec;8(13):2339-49.
  16. Tsui LC. The spectrum of cystic fibrosis mutations. Trends Genet. 1992 Nov;8(11):392-8. Review.
  17. Groman JD, Meyer ME, Wilmott RW, Zeitlin PL, Cutting GR. Variant cystic fibrosis phenotypes in the absence of CFTR mutations. N Engl J Med. 2002;347:401

Contributed by Arivarasan Karunamurthy, MD. and Jeffrey A. Kant, MD, PhD

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