Summary & Overview
CPT 81402: Advanced Molecular Pathology Procedure for Genetic Variant Analysis
CPT code 81402 is a Level 3 molecular pathology procedure used for advanced genetic testing, including the analysis of multiple genetic variants and rearrangements. This code is significant nationally as it enables laboratories to provide critical diagnostic information for conditions such as chromosomal abnormalities, metabolic disorders, and certain cancers, including follicular lymphoma. The procedure is typically performed in specialized laboratories outside of hospital settings, reflecting the growing role of molecular diagnostics in modern healthcare.
Major payers covered in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, and UnitedHealthcare. Readers will gain insights into payer coverage policies, clinical benchmarks, and recent policy updates relevant to molecular pathology services. The publication also provides context on how CPT 81402 fits within the broader landscape of genetic testing codes, highlighting its clinical applications and importance for laboratory medicine.
This summary offers a comprehensive overview of the code’s clinical relevance, payer landscape, and key considerations for laboratories and healthcare organizations navigating molecular pathology billing and coverage.
CPT Code Overview
CPT 81402 represents a Level 3 molecular pathology procedure. This code is used for advanced genetic testing, including analysis of more than 10 single nucleotide polymorphisms (SNPs), 2-10 methylated variants, or 2-10 somatic variants, typically using non-sequencing target variant analysis. It also covers immunoglobulin and T-cell receptor gene rearrangements, as well as duplication or deletion variants involving a single exon. A common clinical example is the analysis of the IGH@/BCL2 translocation, which is relevant in conditions such as follicular lymphoma, focusing on both major breakpoint region (MBR) and minor cluster region (mcr) breakpoints.
The service type for CPT 81402 is Molecular Pathology, and the typical site of service is a laboratory other than a hospital (POS 81). This code is integral for laboratories performing complex genetic analyses that inform diagnosis and treatment decisions in a variety of clinical scenarios.
Clinical & Coding Specifications
Clinical Context
A patient presents to their healthcare provider with clinical suspicion of a genetic or chromosomal abnormality, metabolic disorder, or abnormal laboratory findings such as unusual results in urine or liver function studies. The provider orders a molecular pathology procedure to analyze specific genetic variants, such as immunoglobulin and T-cell receptor gene rearrangements or translocation analysis (e.g., IGH@/BCL2 (t(14;18)) for follicular lymphoma). The specimen is sent to a laboratory (other than a hospital, Place of Service 81) specializing in molecular genetic pathology. The laboratory performs a Level 3 molecular pathology procedure, which may involve qualitative or quantitative analysis of major and minor breakpoint regions. Results are reported back to the provider for clinical interpretation and management.
Coding Specifications
-
Modifier
26: Used to indicate the professional component of the molecular pathology procedure, typically when the physician interprets the results but does not perform the technical portion. -
Modifier
91: Used when the clinical diagnostic laboratory test is repeated on the same patient to obtain additional information.
| Modifier Code | Description |
|---|---|
26 | Professional Component |
91 | Repeat Clinical Diagnostic Laboratory Test |
- Associated Provider Taxonomies:
| Taxonomy Code | Specialty Description |
|---|---|
207ZP0007X | Molecular Genetic Pathology (Pathology) Physician |
- Specialty represented: Pathologists specializing in molecular genetic pathology.
Related Diagnoses
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Z13.79: Encounter for other screening for genetic and chromosomal anomalies- Used when the procedure is performed as part of a screening for genetic or chromosomal abnormalities.
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Q99.9: Chromosomal abnormality, unspecified- Relevant when the patient is suspected to have a chromosomal abnormality that has not been specifically identified.
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E88.9: Metabolic disorder, unspecified- Applied when the molecular pathology procedure is ordered to investigate a possible metabolic disorder.
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R82.90: Unspecified abnormal findings in urine- Used when abnormal urine findings prompt further molecular analysis.
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R94.5: Abnormal results of liver function studies- Relevant when abnormal liver function tests lead to molecular pathology testing to identify underlying genetic causes.
Related CPT Codes
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81403: Molecular pathology procedure, Level 4 (e.g., analysis of single exon by DNA sequence analysis, analysis of >10 amplicons using multiplex PCR in 2 or more independent reactions, mutation scanning or duplication/deletion variants of 2-5 exons) – includes JAK2 (Janus kinase 2) (e.g., myeloproliferative disorder), exon 12 sequence and exon 13 sequence, if performed. -
81401: Molecular pathology procedure, Level 2 (e.g., 2-10 variants in a single gene).
| CPT Code | Description |
|---|---|
81403 | Molecular pathology procedure, Level 4 – includes JAK2 analysis, mutation scanning, duplication/deletion variants |
81401 | Molecular pathology procedure, Level 2 – 2-10 variants in a single gene |
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81403may be used for more complex or extensive molecular analysis than81402, often as an alternative or when additional genetic information is required. -
81401is used for less extensive analysis and may be performed in conjunction with or as an alternative to81402depending on the clinical scenario.
National Reimbursement Benchmarks
For CPT code 81402, the national mean rate for BUCA (average commercial) payers is $122.73, which is higher than the Aetna mean rate of $103.79 and the UnitedHealth Group mean rate of $116.74. Blue Cross Blue Shield has the highest mean rate among the commercial payers at $138.64, while Cigna's mean rate stands at $129.92.
Rate dispersion, measured by the difference between the 75th and 25th percentiles, varies significantly across payers. Cigna exhibits the widest spread at $119.00, indicating substantial variability in rates. Blue Cross Blue Shield and UnitedHealth Group have moderate dispersions of $47.50 and $71.67, respectively. Aetna shows the tightest range at $54.33, suggesting more consistent rates nationally.
The table and chart below present a detailed breakdown of national mean rates and percentile values for each payer.
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