Summary & Overview
CPT 81400: Molecular Pathology Procedure, Level I
CPT code 81400 is a foundational billing code for molecular pathology procedures, specifically Level I tests that identify single germline variants such as SNPs. This code is widely used in clinical laboratories and hospital outpatient settings to support genetic screening and diagnostic services. The procedure is integral to modern precision medicine, enabling clinicians to detect genetic anomalies that may influence patient management and treatment decisions.
Major national payers including Aetna, Blue Cross Blue Shield, Cigna Health, and UnitedHealthcare provide coverage for services billed under CPT code 81400. Understanding payer policies and coverage criteria is crucial for laboratories and providers to ensure appropriate billing and reimbursement. This publication offers a comprehensive overview of payer coverage, clinical indications, and relevant benchmarks for CPT code 81400.
Readers will gain insights into the clinical context of molecular pathology Level I procedures, recent policy updates, and the role of this code in genetic testing workflows. The summary also highlights associated ICD-10 diagnoses, common modifiers, and related CPT codes, equipping stakeholders with the information needed to navigate the evolving landscape of molecular diagnostics billing and compliance.
CPT Code Overview
CPT code 81400 represents a Level I molecular pathology procedure. This code is used for the identification of a single germline variant, such as a single nucleotide polymorphism (SNP), utilizing techniques like restriction enzyme digestion or melt curve analysis. The service type is molecular pathology and is typically performed in a laboratory setting (POS 81) or in a hospital outpatient department (POS 22). These procedures are essential for genetic screening and diagnostic purposes, providing critical information for patient care.
Clinical & Coding Specifications
Clinical Context
A patient presents for genetic screening or evaluation due to a family history of chromosomal abnormalities, unexplained metabolic disorders, or abnormal laboratory findings. The ordering provider, such as a family medicine physician, internist, or obstetrician/gynecologist, requests a molecular pathology test to identify a single germline variant (such as a single nucleotide polymorphism [SNP]). The laboratory performs the procedure using techniques like restriction enzyme digestion or melt curve analysis. Results are interpreted by a pathologist and reported back to the ordering provider for further clinical management. This workflow typically occurs in a laboratory setting (POS 81) or hospital outpatient department (POS 22).
Coding Specifications
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Modifier
26: Used to indicate the professional component of the service, typically when the provider is responsible for interpreting the results but not performing the technical aspects of the test. -
Modifier
TC: Used to indicate the technical component, which covers the performance of the test in the laboratory, including equipment and staff.
| Provider Taxonomy Code | Specialty Name |
|---|---|
207ZP0102X | Pathology |
207Q00000X | Family Medicine |
207R00000X | Internal Medicine |
207V00000X | Obstetrics & Gynecology |
207L00000X | Anatomic Pathology & Clinical Pathology |
Related Diagnoses
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Z13.79: Encounter for other screening for genetic and chromosomal anomalies- Relevant for patients undergoing genetic screening, which is a common indication for molecular pathology procedures like
81400.
- Relevant for patients undergoing genetic screening, which is a common indication for molecular pathology procedures like
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Q99.9: Chromosomal abnormality, unspecified- Used when a patient is suspected to have a chromosomal abnormality but the specific type is not yet identified, warranting molecular testing.
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E88.9: Metabolic disorder, unspecified- Applied when there is suspicion of a metabolic disorder that may have a genetic basis, justifying molecular analysis.
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R82.90: Unspecified abnormal findings in urine- Indicates abnormal urine findings that may prompt further genetic investigation, including molecular pathology testing.
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R79.9: Abnormal finding of blood chemistry, unspecified- Used when abnormal blood chemistry results suggest a possible underlying genetic or metabolic disorder, leading to molecular testing.
Related CPT Codes
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81401: Molecular pathology procedure, Level 2 (e.g., 2‑10 SNPs, 1 methylated variant, or 1 somatic variant [typically using nonsequencing target variant analysis], or detection of a dynamic mutation disorder/triplet repeat)- Used when more extensive variant analysis is required, such as multiple SNPs or detection of triplet repeat disorders. May be ordered if initial single variant testing (
81400) is inconclusive or further analysis is needed.
- Used when more extensive variant analysis is required, such as multiple SNPs or detection of triplet repeat disorders. May be ordered if initial single variant testing (
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81402: Molecular pathology procedure, Level 3 (e.g., >10 SNPs, 2‑10 methylated variants, or 2‑10 somatic variants [typically using non‑sequencing target variant analysis], immunoglobulin and T‑cell receptor gene rearrangements, duplication/deletion variants 1 exon)- Applied for broader genetic analysis, including multiple variants or gene rearrangements. Used as an alternative or follow-up to
81400when more complex testing is indicated.
- Applied for broader genetic analysis, including multiple variants or gene rearrangements. Used as an alternative or follow-up to
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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)- Utilized for detailed exon analysis or multiplex PCR testing. May be used in cases where single variant testing (
81400) is insufficient.
- Utilized for detailed exon analysis or multiplex PCR testing. May be used in cases where single variant testing (
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81404: Molecular pathology procedure, Level 5 (e.g., analysis of 2‑5 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of 6‑10 exons, or characterization of a dynamic mutation disorder/triplet repeat by Southern blot analysis)- Reserved for highly complex molecular testing, such as multi-exon analysis or Southern blot characterization. Typically not used together with
81400, but may be ordered sequentially as clinical needs evolve.
- Reserved for highly complex molecular testing, such as multi-exon analysis or Southern blot characterization. Typically not used together with
National Reimbursement Benchmarks
National mean rates for CPT code 81400 among commercial payers show Blue Cross Blue Shield and Cigna at the higher end, with mean rates of $54.05 and $54.92, respectively. UnitedHealth Group and Aetna are lower, at $50.41 and $50.81. The BUCA average stands at $52.63. Medicare rates are not available in the input for comparison.
Rate dispersion, measured by the difference between the 75th and 25th percentiles, varies significantly across payers. Cigna exhibits the widest spread ($48.67), indicating greater variability in reimbursement, while Aetna ($19.87) and Blue Cross Blue Shield ($24.50) are tighter. UnitedHealth Group also shows a relatively narrow range ($31.00). The table and chart below present the full breakdown of national benchmarks for each payer.
Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.