CFTR: The Gene Associated with Cystic Fibrosis

Approximate gene location is based on Chromosome 7 map from NCBI Entrez Map Viewer.

Official Gene Symbol: CFTR

Name of Gene Product: cystic fibrosis transmembrane conductance regulator

Locus: 7q31.2 - The CFTR gene is found in region q31.2 on the long (q) arm of human chromosome 7.

Gene Structure: The normal allelic variant for this gene is about 250,000 base pairs (bp) long and contains 27 exons.

mRNA: The intron-free mRNA transcript for the CFTR gene is 6129 bp long. See the NCBI sequence record NM_000492 to access the mRNA sequence data.

Coding Sequence (CDS): 4443 bp within the mRNA code for the amino acid sequence of the gene's protein product.

Protein Size: The CFTR protein is 1480 amino acids long and has a molecular weight of 168,173 Da. See the annotated CFTR protein sequence record in Swiss-Prot.

Protein Function: The normal CFTR protein product is a chloride channel protein found in membranes of cells that line passageways of the lungs, liver, pancreas, intestines, reproductive tract, and skin. CFTR is also involved in the regulation of other transport pathways.

Associated Disorders: Defective versions of this protein, caused by CFTR gene mutations, can lead to the development of cystic fibrosis (CF) and congenital bilateral aplasia of the vas deferens (CBAVD).

Figure 1: Diagram depicting the five domains of the CFTR membrane protein (Sheppard 1999).

Protein Structure

CFTR is a type of protein classified as an ABC (ATP-binding cassette) transporter or traffic ATPase. These proteins transport molecules such as sugars, peptides, inorganic phosphate, chloride, and metal cations across the cellular membrane. CFTR transports chloride ions (Cl^-) ions across the membranes of cells in the lungs, liver, pancreas, digestive tract, reproductive tract, and skin.

The structure of the complete CFTR protein has not yet been experimentally determined. This is because membrane proteins, such as CFTR, with substantial hydrophobic ("water-fearing") regions are extremely difficult to crystallize, and X-ray crystallography can only be carried out on protein crystals.

By comparing the CFTR protein sequence with that of other known ABC transporters, models depicting the structure of CFTR have been proposed. See Figure 1. CFTR is made up of five domains: two membrane-spanning domains (MSD1 and MSD2) that form the chloride ion channel, two nucleotide-binding domains (NBD1 and NBD2) that bind and hydrolyze ATP (adenosine triphosphate), and a regulatory (R) domain. Delta F508, the most common CF-causing mutation, occurs in the DNA sequence that codes for the first nucleotide-binding domain (NBD1).

Figure 2: Theoretical Model of NBD1. PDB ID 1NBD as viewed in Protein Explorer http://proteinexplorer.org

While most ABC transporters consist of four domains (two membrane-spanning and two nucleotide-binding domains), CFTR is the only one known to possess a regulatory domain. Modification of the regulatory domain, either through the addition or removal of chemical phosphate groups, has been shown to regulate the movement of chloride ions across the membrane.

Although there are no structures of the entire CFTR protein in the Protein Data Bank (PDB), an international archive of molecular structure data, a structure for a similar ABC transporter is available from the PDB. In September 2001, the journal Science published an article on the X-ray structure of a CFTR-related ABC protein (Msba)caseydk1 in E. coli. The PDB ID for this protein is IJSQ. PDB also contains a structure based on the theoretical model of the first nucleotide-binding domain (NBD1). PDB ID for this entry is 1NBD. See Figure 2. In addition, PDB contains synthetic peptide structures (25 to 26 amino acids long) of NBD1's alpha helical region containing the delta F508 mutation. PDB IDs for structures of these peptides are 1CKW, 1CKX, 1CKY, and 1CKZ.

Common Disease Causing Mutation

About 70% of mutations observed in CF patients result from deletion of three base pairs in CFTR's nucleotide sequence. This deletion causes loss of the amino acid phenylalanine located at position 508 in the protein; therefore, this mutation is referred to as delta F508 or F508. See Figure 3.

Figure 3: The deltaF508 deletion is the most common cause of cystic fibrosis. The isoleucine (Ile) at amino acid position 507 remains unchanged because both ATC and ATT code for isoleucine

With normal CFTR, once the protein is synthesized, it is transported to the endoplasmic reticulum (ER) and Golgi apparatus for additional processing before being integrated into the cell membrane. When a CFTR protein with the delta F508 mutation reaches the ER, the quality-control mechanism of this cellular component recognizes that the protein is folded incorrectly and marks the defective protein for degradation. As a result, delta F508 never reaches the cell membrane.

People who are homozygous for delta F508 mutation tend to have the most severe symptoms of cystic fibrosis due to critical loss of chloride ion transport. This upsets the sodium and chloride ion balance needed to maintain the normal, thin mucus layer that is easily removed by cilia lining the lungs and other organs. The sodium and chloride ion imbalance creates a thick, sticky mucus layer that cannot be removed by cilia and traps bacteria, resulting in chronic infections. While the mechanism that leads to lung damage is not fully understood, lung disease is the leading cause of morbidity and mortality among CF patients.

Factors That Affect the Disease Phenotype

Because CF is an autosomal recessive genetic disorder, an individual must have two copies of a mutated CFTR gene to express the disease phenotype. Someone with one normal, functional copy of the CFTR gene and one mutated copy would just be a carrier of the disorder, and would not display typical CF symptoms. It is important to note that just because two people might have the same two copies of the mutated CFTR gene, each may experience very different symptoms. This is because the development of a disorder such as CF is greatly influenced by environmental factors and genetic factors other than CFTR .

According to the Cystic Fibrosis Mutation Database maintained by the Hospital for Sick Children in Toronto, Ontario, more than 900 mutations are known in the CFTR gene. Different CFTR mutations result in different disease phenotypes. Some may have little or no effect on CFTR function, and some may result in milder forms of disease. For example, one study in the Netherlands indicated that CF patients who had one copy of delta F508 deletion and one of A455E mutation generally expressed a milder form of pulmonary disease than those who were homozygous delta F508.

The presence of variant forms of genes other than CFTR can also affect disease phenotype. Meconium ileus (MI), a severe intestinal obstruction, is observed in 15% to 20% of babies born with cystic fibrosis. No CFTR gene mutations have been associated with MI. A 1999 study has shown that cystic fibrosis modifier 1 (CFM1), a modifier gene located on chromosome 19, may determine MI susceptibility.

For more information about cystic fibrosis see the Disorder Profile.

Additional CFTR Resources

Records from Different Bioinformatics Databases

OMIM entry for CFTR (MIM No 602421)

OMIM entry for Cystic Fibrosis (MIM No 219700)

NCBI LocusLink entry for CFTR

GeneCard for CFTR

GENATLAS - To access the CFTR record enter CFTR into the "Symbol Name" search box and click "find" to submit your search.

CFTR Nucleotide Sequence

NCBI mRNA Reference Sequence (NM_000492) - cDNA sequence derived from the mRNA transcript of the CFTR gene.

CFTR Genomic DNA Sequence -This sequence provided by the Cystic Fibrosis Mutation Database includes segments of noncoding DNA and exons broken down into codons and corresponding amino acids. Links to the GenBank record for each exon are also provided.

CFTR Protein Sequence

CFTR_HUMAN - Annotated protein sequence record from Swiss-Prot that provides descriptions of the protein's domains, amino acid sequence variations, secondary structure, and more.

NCBI Protein Reference Sequence (NP_000483)

CFTR Protein Structure

1CKW and 1CKZ - PDB entries for synthetic peptide structures based on CFTR's delta F508 region. These peptides (25 amino acids long) contain the Phe 508 deletion.

1CKX and 1CKY - PDB entries for synthetic peptide structures based on CFTR's delta F508 region. These peptides (26 amino acids long) contain the Phe 508 residue.

1NBD - PDB entry for the theoretical model of CFTR's first nucleotide binding domain. As of July 1, 2002, theoretical models are only available for download from the PDB FTP site and are no longer included in the main PDB archive.

CFTR Mutation Resources

Cystic Fibrosis Mutation Database - This database of CFTR gene mutations is maintained by the Hospital for Sick Children in Toronto, Ontario. Researchers at this hospital discovered the gene that causes cystic fibrosis.

Human Gene Mutation Database Entry for CFTR

Researchers

Learn more about some of the scientists involved in the discovery of the cystic fibrosis gene.

Francis S. Collins, M. D., Ph. D. - Director of the National Institute for Human Genome Research

John R. Riordan, Ph. D. - Research scientist with the Mayo Clinic Scottsdale

Lap-Chee Tsui, Ph. D. - Research Scientist with the Department of Genetics at the Research Institute of The Hospital for Sick Children, Toronto

Other CFTR Researchers

Michael J. Welsh - Howard Hughes Medical Institute (HHMI) investigator who researches ion channel structure and function in cystic fibrosis and mechanosensation.

CF Researchers & Laboratories - A list maintained by Jeffrey Wine, PhD of the Cystic Fibrosis Research Laboratory, Stanford University.

Other CFTR Resources

Oxford University GeneMedicine - Click on cystic fibrosis in the navigation bar on the left for CF pathogenesis, gene discovery, and therapies as well as animations and interactive guides to protein sequence, structure, and function.

Cystic Fibrosis - An animated, introductory overview to what causes cystic fibrosis from Your Genes, Your Health of the Dolan DNA Learning Center.

Stalking a Lethal Gene - This section of Blazing a Genetic Trail, a report produced by HHMI, describes CF gene discovery, treatments, and testing.

Articles Reporting CFTR Gene Identification

B. Kerem, J. M. Rommens, J. A. Buchanan, D. Markiewicz, T. K. Cox, A. Chakravarti, M. Buchwald, and L.C. Tsui. "Identification of the Cystic Fibrosis Gene: Genetic Analysis." Science 245 (4922): 1073-80 (Sept. 8, 1989). PMID: 2570460

J. R. Riordan, J. M. Rommens, B. Kerem, N. Alon, R. Rozmahel, Z. Grzelczak, J. Zielenski, S. Lok, N. Plavsic, J. L. Chou, M. L. Drumm, M. C. Iannuzzi, F. S. Collins, and L. C. Tsui. "Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA." Science 245 (4922): 1066-73 (Sept. 8, 1989). PMID: 2475911 (Source for GenBank CFTR mRNA sequence record M28668.)

J. M. Rommens, M. C. Iannuzzi, B. Kerem, M. L. Drumm, G. Melmer, M. Dean, R. Rozmahel, J. L. Cole, D. Kennedy, N. Hidaka, M. Zsiga, M. Buchwald, J. R. Riordan, L. C. Tsui, and F. S. Collins. "Identification of the Cystic Fibrosis Gene: Chromosome Walking and Jumping." Science 245 (4922): 1059-65 (Sept. 8, 1989). PMID: 2772657

References

K. H. Gan et al. 1995. "A Cystic Fibrosis Mutation Associated with Mild Lung Disease." New England Journal of Medicine 333 (2): 95-99.

Online Mendelian Inheritance in Man, OMIM (TM). Johns Hopkins University, Baltimore, MD. MIM No. 602421. Record created: March 7, 1998. Record last updated: July 14, 2003. Last accessed: August 20, 2003. <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM>

D. N. Sheppard, and M. J. Welsh. 1999. "Structure and Function of the CFTR Chloride Channel." Physiological Review 79 (1 Suppl): S23-45.

M. J. Welsh and A. E. Smith. 1995. "Cystic Fibrosis." Scientific American 273 (6): 52-59.

J. Zielenski et al. 1991. "Genomic DNA Sequence of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Gene." Genomics 10 (1): 214-28.

J. Zielenski et al. 1999. "Detection of a Cystic Fibrosis Modifier Locus for Meconium Ileus on Human Chromosome 19q13." Nature Genetics 22 (2): 128-129.