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Surfactant Deficiency via the ABCA3 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
ABCA3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11045ABCA381479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Fang Xu, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Surfactant deficiency is a severe respiratory disorder due to dysfunction in the production or function of pulmonary surfactants. Surfactant is a lipid and protein mixture lining the lung tissue that lowers alveolar surface tension and prevents atelectasis during expiration. Loss of surfactant function results in alveoli collapse following expiration leading to shortness of breath and impaired oxygen delivery. In severe forms, respiratory failure occurs shortly after birth with infants requiring mechanical ventilation and lung transplantation for survival (Nogee et al. 2000. PubMed ID: 10712351; Tredano et al. 2003. PubMed ID: 12784301). Pathogenic variants in the ABCA3, SFTPB, SFTPC, and NKX2-1 genes have been reported to be causative for surfactant deficiency with patients with SFTPB-related surfactant deficiency being the most severely affected. Genetic testing is helpful in the differential diagnosis of ABCA3-related surfactant deficiency from other surfactant deficiencies, respiratory infections, cardiac disorders with obstructed pulmonary venous return, and other respiratory distress syndromes (Hamvas 2006. PubMed ID: 17142157).


Surfactant dysfunction may be inherited in an autosomal dominant manner through pathogenic variants in the SFTPC and NKX2-1 genes or an autosomal recessive manner through pathogenic variants in the ABCA3 or SFTPB genes (Hamvas 2006. PubMed ID: 17142157). To date over 150 different causative variants have been reported in the ABCA3 gene. Missense changes occurring throughout the gene account for greater than 75% of the reported causative variants (Shulenin et al. 2004. PubMed ID: 15044640; Garmany et al. 2008. PubMed ID: 18317237). Nonsense, splice site, insertions/deletions, and gross deletions have also been reported in a minority of cases (Shulenin et al. 2004. PubMed ID: 15044640; Garmany et al. 2008. PubMed ID: 18317237). The ABCA3 gene encodes an ATP-binding cassette transporter which is expressed in alveolar type II cells and is involved in pulmonary surfactant metabolism and lamellar biogenesis. Failure of ABCA3 function results in reduced surface tension at air-liquid interfaces leading to respiratory distress (Ban et al. 2007. PubMed ID: 17267394).

Clinical Sensitivity - Sequencing with CNV PGxome

In a study of 21 individuals with a history of severe respiratory disease where both SFTPB and SFTPC surfactant deficiencies as well as other forms of lung disease were ruled out initially, pathogenic variants in the ABCA3 gene were identified in 16 of 21 patients. In two patients, only one pathogenic variant was identified in the ABCA3 gene (Shulenin et al. 2004. PubMed ID: 15044640). Analytical sensitivity is >95% for detection of causative variants in the ABCA3 gene by sequencing.

Clinical sensitivity for Copy Number Variants is less than 5% as gross deletions involving one or more exons have only been reported in a few cases (Garmany et al. 2008. PubMed ID: 18317237).

Testing Strategy

This test provides full coverage of all coding exons of the ABCA3 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Candidates for testing include individuals with histopathology, radiography and symptoms indicative of interstitial lung disease. Common symptoms in children with ABCA3-related surfactant deficiency include tachypnea, cough, hypoxemia, failure to thrive, crackles, clubbing, and pectus excavatum (Doan et al. 2008. PubMed ID: 18024538). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in ABCA3.


Official Gene Symbol OMIM ID
ABCA3 601615
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Surfactant Metabolism Dysfunction, Pulmonary, 3 AR 610921



Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

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2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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