Summary & Overview
CPT 81294: MLH1 Large Deletion/Duplication Analysis
CPT code 81294 represents molecular genetic testing for large deletions and duplications in the MLH1 gene, a key marker associated with Lynch syndrome and hereditary colorectal cancer risk. This CPT test identifies copy-number variants across long stretches of the MLH1 gene that may be missed by sequencing alone, informing genetic diagnosis, family risk assessment, and clinical management pathways. Nationally, such testing is important for precision oncology, hereditary cancer screening programs, and cascade testing in affected families.
Key payers in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. The publication outlines coverage and reimbursement context across major commercial plans and Medicare, highlights where molecular diagnostic testing for MLH1 fits in clinical workflows, and summarizes common billing considerations tied to the service line.
Readers will learn what CPT code 81294 covers clinically, where the test is typically performed, and what to expect in payer landscapes: coverage relevance for hereditary cancer evaluation, the role of copy-number analysis versus sequencing, and typical service line placement in clinical genetics and oncology pathways. Data not available in the input indicates that detailed payer-specific coverage policies, reimbursement rates, and associated ICD-10 pairings are not provided here but are referenced as areas for further review.
Billing Code Overview
CPT code 81294 describes a laboratory test that detects large deletions or duplications in long stretches of DNA within the MLH1 (mutL homolog 1) gene, a gene associated with hereditary nonpolyposis colorectal cancer (Lynch syndrome). The procedure is a molecular genetic diagnostic test performed by a laboratory analyst using techniques designed to identify copy number changes that affect gene function.
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Service type: Molecular genetic testing / DNA copy-number analysis
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Typical site of service: Clinical molecular diagnostic laboratory or reference genetic testing laboratory
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Clinical & Coding Specifications
Clinical Context
A typical patient is an adult referred for hereditary colorectal cancer evaluation after either a personal history of colorectal cancer at a young age (<50 years) or a strong family history suggestive of Lynch syndrome. The clinician orders molecular testing of the MLH1 gene to detect large deletions or duplications not found by single‑exon sequencing. The workflow begins with genetic counseling and informed consent, collection of a blood or saliva specimen, specimen accessioning and DNA extraction in the molecular laboratory, and performance of a targeted deletion/duplication assay (e.g., MLPA or NGS copy‑number analysis) by the lab analyst. Results are reviewed by a molecular pathologist or laboratory director for technical validation and clinical interpretation, then reported to the ordering provider. Typical sites of service include hospital outpatient laboratories, independent clinical molecular diagnostic laboratories, and specialized genetics clinics with laboratory services.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
26 | Professional component | Use when billing only the professional interpretation component separate from the technical lab work, if applicable. |
TC |