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Pulmonology Coding:

Identify the Correct ICD-10-CM Codes for Cystic Fibrosis

Use 4th and 5th characters for CF with manifestations.

According to the Cystic Fibrosis Foundation, cystic fibrosis (CF) is a genetic disease that progresses over time, affecting the lungs, pancreas, and other organs. As a pulmonology coder, you’ll primarily see cases in your workflow of CF affecting the respiratory system.

Read on to learn more about the condition, how it is diagnosed, and how providers treat patients, so you can assign the correct codes.

Build Your Condition Knowledge

CF is inherited in an autosomal recessive pattern, which means that affected individuals have two defective copies of the gene – one from each parent. Individuals with only one copy are carriers but do not develop the disease. There are approximately 1,000 new CF diagnoses each year with more than 75 percent of patients diagnosed by 2 years of age. Currently, approximately 60 percent of patients with CF are 18 years or older.

At the cellular level, CF is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The CFTR protein is located in cells lining the lungs, pancreas, intestines, and sweat glands. When the CFTR protein malfunctions, it is unable to properly move chloride, a component of salt, to the cell surface to attract water. This disruption prevents water from being drawn into the mucus, resulting in thick, sticky secretions.

In the lungs, thick mucus clogs the bronchi and bronchioles, trapping bacteria and leading to infections, inflammation, and other complications.

Respiratory system CF signs and symptoms vary based on the severity of the disease and can include:

  • Salty-tasting skin
  • Persistent coughing, at times with phlegm
  • Frequent lung infections
  • Wheezing or shortness of breath
  • Nasal polyps
  • Chronic sinus infections

Determine Diagnostic Testing Codes

To confirm a clinical diagnosis of cystic fibrosis, healthcare professionals typically order diagnostic tests.

Physicians perform newborn heel blood stick testing to check for elevated levels of immunoreactive trypsinogen (IRT). If elevated, a sweat test is performed to measure salt and chloride in the sweat. Use 89230 (Sweat collection by iontophoresis) to report a sweat test.

Pulmonologists may perform DNA testing for CFTR gene mutations to evaluate for specific mutations in the CFTR gene. This can confirm a diagnosis, identify carriers, and help with family planning. The code selection depends on how extensive the analysis is.

Commonly used CPT® codes for CFTR gene mutation testing include:

  • 81220 (CFTR (cystic fibrosis transmembrane conductance regulator) (e.g., cystic fibrosis) gene analysis; common variants (e.g., ACMG/ACOG guidelines))
  • 81221  (… known familial variants)
  • 81222 (…duplication/deletion variants)
  • 81223 (… full gene sequence)

Providers may also perform other diagnostic testing such as additional blood tests, chest X-rays, CT scans, and pulmonary function tests like spirometry.

Use the Correct Diagnosis Codes

You’ll assign one of the following codes to report a screening for the condition:

  • Z13.228 (Encounter for screening for other metabolic disorders)
  • Z13.71(Encounter for nonprocreative screening for genetic disease carrier status)

Whereas you’ll use the following code for a newborn screening with abnormal findings:

  • P09.4 (Abnormal findings on neonatal screening for cystic fibrosis)

After the condition is confirmed, cystic fibrosis coding uses the E84.- (Cystic fibrosis) code category. This ICD-10-CM code category requires 4th and 5th characters to complete the codes.

The 4th character in the code represents manifestations, such as:

  • E84.0 (Cystic fibrosis with pulmonary manifestations)
  • E84.1- (Cystic fibrosis with intestinal manifestations)
  • E84.8 (Cystic fibrosis with other manifestations)

Important: Code E84.0 features a “Use additional code” instruction to identify any infectious organisms, which are coded in the B codes of the ICD-10-CM code set.

The 5th character designation only applies to one code — E84.1- — and it identifies the intestinal manifestation, distinguishing between meconium and other intestinal issues, such as the following:

  • E84.11 (Meconium ileus in cystic fibrosis)
  • E84.19 (Cystic fibrosis with other intestinal manifestations)

For patients with only one CFTR gene mutation who are identified as carriers through testing, you’ll assign the following diagnosis code:

  • Z14.1 (Cystic fibrosis carrier)

Know How to Report Therapy Services

Currently, no cure exists for CF, but treatment can lessen complications and improve the patient’s quality of life. Treatment goals are put in place to prevent and control lung infections, loosen and remove mucus from the lungs, prevent and treat intestinal blockages, and provide adequate nutrition.

Several medicinal options with specific benefits exist. Physicians can administer medicines that target gene changes and how the CFTR protein works — these are called CFTR modulators. Antibiotics help prevent infections and anti-inflammatories lessen swelling in the lung airways. Mucus-thinning medicines help the patient expel mucus to improve lung function. Bronchodilators help keep airways open by relaxing the muscles around the bronchial tubes. Pancreatic enzymes and acid-reducing medicines help the digestive tract use nutrients and work better. Other treatments may include:

  • Nasal surgery for polyps
  • Oxygen therapy
  • Noninvasive ventilation
  • Feeding tubes
  • Bowel surgeries for blockages and lung or liver transplants

Review Payer Guidance

Medicare coverage for CF-related testing, particularly genetic (CFTR) testing, and certain laboratory services, may be governed by Local Coverage Determinations (LCDs) by Medicare Administrative Contractors (MACs). Providers and coders will need to be diligent about reviewing payer policies to ensure coverage criteria and medical necessity are met.

Avoid These Common Coding Issues

CF involves a multisystem disease that affects respiratory and digestive systems with endocrine involvement. Insufficient documentation can affect coding including:

  • Failure to capture manifestations: This causes an increase in unspecified codes, such as E84.9 (Cystic fibrosis, unspecified). Documentation must identify all manifestations so the diagnosis can be coded completely and accurately.
  • Missing secondary diagnoses: CF is a systemic disease. A common error is only coding the acute condition (for example, pneumonia) while missing the underlying CF, or not documenting the infectious organism so it can be coded.
  • Confusing status vs. disease: Only use the Z code for carrier status. If the patient has an active diagnosis, use codes from E84.0-E84.9.

Consistent provider education and coder review can significantly reduce documentation gaps and improve long-term coding accuracy overall compliance.

Dawnelle Sager, CPC, CPMA, CPC-I, CRC, Professional Fee Coding & Compliance Auditor,
Pinnacle Enterprise Risk Consulting Services (PERCS)

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