Summary & Overview
CPT 81300: MSH6 Large Deletion/Duplication Analysis
CPT code 81300 represents a molecular diagnostic laboratory test that detects large deletions and duplications in the MSH6 gene, a DNA mismatch repair gene with relevance to hereditary cancer syndromes. This test is clinically significant for identifying genetic alterations that can inform cancer risk assessment and management, and it is widely performed in specialized clinical molecular laboratories across the United States. Key national payers addressed include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will gain a concise briefing on what CPT code 81300 covers clinically and operationally, which payers commonly cover the service, and the typical settings where the technical laboratory component is performed. The publication outlines benchmarking and reimbursement context, relevant policy and coverage considerations, and clinical indications tied to large-sequence deletion/duplication testing of MSH6. It also highlights coding nuances and common modifier usage for billing workflows. Data not available in the input will be noted where applicable.
Billing Code Overview
CPT code 81300 describes a laboratory test performed by a lab analyst to detect genetic changes involving long sequences of deleted or duplicated DNA in the mutS homolog 6 gene, also known as the MSH6 gene. The procedure targets large-scale deletions and duplications within this specific gene.
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Service type: Clinical molecular diagnostic test for large-sequence deletion/duplication analysis of
MSH6 -
Typical site of service: Clinical laboratory or specialized molecular genetics laboratory performing technical laboratory testing
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Clinical & Coding Specifications
Clinical Context
A 42-year-old patient with a strong family history of colorectal and endometrial cancer is referred for hereditary cancer testing. The clinician orders targeted molecular testing to detect large deletions or duplications in the MSH6 gene after prior single-gene sequencing and immunohistochemistry (IHC) suggested mismatch repair deficiency. A peripheral blood specimen is collected and sent to a molecular diagnostics laboratory. The lab analyst performs the technical assay described by 81300 — a copy number or large rearrangement analysis of the MSH6 gene — using methods such as MLPA, quantitative PCR, or targeted NGS-based copy number analysis. The laboratory documents specimen receipt, DNA extraction, assay setup, data acquisition, and technical interpretation; the professional component (interpretation, report sign-out) may be billed separately by a molecular pathologist. Typical sites of service include outpatient phlebotomy clinics, physician offices for specimen collection, and specialized molecular diagnostic laboratories where the technical component is performed.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
26 | Professional component | Use when reporting the interpretation and report by a physician or qualified provider separate from the technical laboratory work. |