Invitae Cystic Fibrosis Test


Test description

The Invitae Cystic Fibrosis Test analyzes the CFTR gene, which is associated with the conditions cystic fibrosis (CF) and congenital absence of the vas deferens (CAVD). Pathogenic variants in the CFTR gene inhibit the function of chloride channels across cell membranes. This disrupts the ability of the cells to regulate the flow of water and chloride ions, resulting in a thick mucus clogging airways and organs such as the pancreas and intestine.

Genetic testing for CF is particularly useful because of the strong genotypic/phenotypic correlations in this gene. The combination of specific variants may correlate to specific expected outcomes for the patient.

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Primary panel (1 gene)


CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C>T (also known as 3849+10kbC>T), c.1210-34TG[12]T[5] (also known as T5TG12), c.1210-34TG[11]T[5] (also known as T5TG11), and c.1679+1634A>G.

Add-on chronic pancreatitis genes (4 genes)

CFTR is also associated with an increased risk of chronic pancreatitis (CP), a condition that results in irreversible morphological changes and impairment of both exocrine and endocrine functions. If clinically indicated, clinicians can include additional genes associated with chronic pancreatitis at no additional charge.


  • Cystic fibrosis (CF)
  • Congenital absence of the vas deferens (CAVD)

Clinical subtypes:

  • Congenital absence of the vas deferens (CAVD) — abnormal development of the vas deferens, leading to male infertility; approximately 80% of men with CAVD have at least one identifiable mutation in CFTR
  • Cystic fibrosis-related diabetes mellitus (CFRDM) — individuals with CF who experience insulin deficiency and who may or may not be insulin deficient

Cystic fibrosis (CF) is a complex multisystemic disorder caused by the buildup of thick, viscous secretions on the lining (epithelia) of many different organ systems, which damages organ function over time. Affected individuals often present with pulmonary symptoms, including lower airway inflammation, recurrent pulmonary infections, airway damage, and the buildup of scar tissue in the lungs (lung fibrosis). Pulmonary failure used to be a common cause of childhood morbidity, but with improved preventive treatment, individuals with CF now frequently live into adulthood.

Individuals with CF may also present with digestive problems associated with the pancreas and the intestine. The reduced production of insulin and digestive enzymes by the pancreas (pancreatic insufficiency) can lead to nutritional deficiencies. In infants with CF, excess mucus production in the intestine can cause a blockage called meconium ileus.

Both CF and congenital absence of the vas deferens (CAVD) are caused by pathogenic variants in the gene CFTR. CAVD is a disorder that occurs in males; the tubes that carry sperm out of the testes (vas deferens) develop abnormally. Without the assistance of reproductive technology, this disorder results in male infertility. CAVD is sometimes observed in males with CF, though it can also occur independently.

CFTR is the only gene known to be associated with the CFTR-related disorders—cystic fibrosis (CF) and congenital absence of the vas deferens (CAVD). Sequencing identifies more than 98% of CFTR pathogenic variants.

CF and CAVD are inherited in an autosomal recessive pattern.

CF is considered to have incomplete penetrance and variable expression. Genotypic/phenotypic correlations have been well studied and account for much of this variability.

In the United States, cystic fibrosis occurs most frequently in the Caucasian population, with an incidence of 1 in 2,500 to 1 in 3,500 newborns. CF is less common in other ethnic groups, occurring in approximately 1 in 15,000 to 1 in 17,000 African Americans and 1 in 31,000 Asian Americans.

Testing a seemingly unaffected individual can identify asymptomatic carriers who may be at risk of having a child with CF. Molecular testing can also help distinguish CAVD from a mild form of CF.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Assay notes

CFTR: Analysis includes the polymorphic TG/T tract within intron 10 as well as known promoter, 5’ UTR, 3’UTR, and intronic HGMD variants (including, but not limited to, c.3718-2477C>T, also known as 3849+10kbC>T and c.3717+12191C>T in the literature). Variants in these regions will be interpreted and only reported if classified as likely pathogenic or pathogenic. Polymorphisms and uncertain variants will be reported upon request.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
CASR NM_000388.3
CFTR* NM_000492.3
CTRC NM_007272.2
PRSS1 NM_002769.4
SPINK1 NM_003122.4

CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C>T (also known as 3849+10kbC>T), c.1210-34TG[12]T[5] (also known as T5TG12), c.1210-34TG[11]T[5] (also known as T5TG11), and c.1679+1634A>G.