CPT 81272 KIT Partial Gene Sequence — Reimbursement | OpenPayer

Summary & Overview

CPT 81272: KIT Gene Partial Sequence Analysis, Technical Component

CPT code 81272 represents a targeted molecular diagnostic test: the technical component of a partial sequence analysis for the KIT gene, frequently focused on hotspot exons (for example, exons 8, 11, 13, 17, 18). This code captures laboratory work that identifies clinically relevant variants in the KIT gene without performing full-gene sequencing. The code matters nationally because KIT variants inform diagnosis, prognosis, and targeted therapy decisions across oncology and precision medicine programs, and molecular testing volume and coverage policies affect access and laboratory workflows.

Key payers in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise overview of the clinical purpose and typical laboratory setting for CPT code 81272, common payer coverage patterns and policy considerations, benchmark metrics for utilization and reimbursement where available, and operational implications for laboratories performing targeted KIT testing. The publication also outlines coding context and where CPT code 81272 fits in molecular diagnostic service lines. Data not available in the input is identified explicitly in sections that require payer-specific policies, associated taxonomies, ICD-10 pairings, and related codes.

AetnaBlue Cross Blue ShieldCigna HealthUnitedHealthcareMedicareCPT 81272molecular diagnosticsKIT genetargeted sequencingmolecular pathologylaboratory technical componentoncology testinggenetic testing

Billing Code Overview

CPT code 81272 describes a technical laboratory test for partial gene sequence analysis of the v-kit Hardy–Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) gene. The service analyzes selected segments of the KIT gene rather than sequencing the entire gene; commonly tested regions may include exons 8, 11, 13, 17, and 18. The procedure is a molecular diagnostic test performed by a clinical laboratory's technical staff.

Service type: Molecular pathology / targeted gene sequencing (technical component)

Typical site of service: Clinical or hospital-based molecular diagnostics laboratory

Clinical & Coding Specifications

Clinical Context

A typical patient is an adult or pediatric oncology patient with a suspected or confirmed mast cell tumor or gastrointestinal stromal tumor where targeted molecular information about the v-kit Hardy–Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) gene will inform prognosis or eligibility for targeted therapy. A surgical or interventional oncology team or outpatient clinic identifies a tissue specimen (formalin-fixed paraffin-embedded tumor block or fresh/frozen tissue) or a peripheral blood sample requiring molecular testing. The specimen is accessioned into the molecular pathology laboratory where a pathology requisition documents clinical history, relevant diagnoses, specimen type, and physician ordering information. A molecular technologist performs DNA extraction and a targeted partial gene sequence analysis of KIT, typically covering hotspot exons such as exon 8, 11, 13, 17, and 18. Results are analyzed by a molecular pathologist, who issues a report interpreting detected pathogenic or likely pathogenic variants, variants of uncertain significance, or no actionable variants. The report is routed back to the ordering oncologist or surgeon to guide treatment decisions (for example, tyrosine kinase inhibitor selection), clinical trial eligibility, or prognostic counseling. Typical sites of service include hospital-based molecular pathology laboratories, reference diagnostic laboratories, and outpatient specialty clinics that collect and submit specimens.

Coding Specifications

Modifier	Description

CPT 81288: MLH1 Promoter Methylation Analysis

CPT-81251-GBA-GENE-VARIANT-DETECTION-MOLECULAR-GENETIC-TEST

CPT 81251: GBA Gene Variant Detection, Molecular Genetic Test

CPT-81174-ANDROGEN-RECEPTOR-TARGETED-GENETIC-TEST

CPT 81174: Targeted Androgen Receptor (AR) Gene Variant Analysis

CPT-81106-HPA-2-T145M-GENETIC-ALLELE-ANALYSIS

CPT 81106: HPA-2 (T145M) Genetic Allele Analysis

CPT-81320-PLCG2-MOLECULAR-GENETIC-TESTING

CPT 81320: PLCG2 Gene Variant Detection, Molecular Diagnostic Test

CPT-81303-TARGETED-MECP2-FAMILIAL-MUTATION-TESTING

CPT 81303: Targeted MECP2 Familial Mutation Testing

CPT-81328-SLCO1B1-GENETIC-VARIANT-TESTING

CPT 81328: SLCO1B1 Genetic Variant Testing

CPT-81232-DPYD-VARIANT-ANALYSIS

CPT 81232: DPYD Variant Analysis, Targeted Molecular Test

CPT-81363-HBB-GENE-DUPLICATION-DELETION-ANALYSIS

CPT 81363: HBB Gene Duplication and Deletion Analysis

CPT-81185-CACNA1A-FULL-GENE-SEQUENCING

CPT 81185: CACNA1A Full Gene Sequencing

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Taxonomy Code	Specialty	Notes
207K00000X	Internal Medicine	Oncologists and internists order molecular testing for targeted therapy selection.
207P00000X	Hematology and Oncology	Medical oncologists or hematologist-oncologists commonly order KIT testing for tumor profiling.
207L00000X	Surgical Oncology	Surgical oncologists submit tumor specimens for molecular pathology.
207Y00000X	Pathology	Molecular pathologists interpret and sign out assay results.
2080S0120X	Clinical Laboratory Director	Laboratory medicine specialists oversee test performance and compliance.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`C96.2`	Mast cell sarcoma	KIT mutations are commonly assessed in mast cell neoplasms for prognostic and therapeutic implications.
`C49.6`	Malignant neoplasm of peripheral nerves and autonomic nervous system, pelvis and lower limb	Tumor profiling including KIT may be considered in select soft tissue tumors.
`C22.9`	Malignant neoplasm of liver, unspecified	KIT testing may be part of broader molecular panels when liver lesions represent metastatic disease.
`D47.9`	Neoplasm of uncertain behavior of lymphoid, hematopoietic and related tissue, unspecified	KIT testing can be relevant when mast cell disorders or related hematologic neoplasms are suspected.
`Z85.3`	Personal history of malignant neoplasm of breast	Included as a history code when prior malignancy prompts broader tumor profiling including KIT.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81275`	KIT gene full sequence analysis	Performed when comprehensive sequencing of the entire KIT coding region is required rather than a targeted partial analysis.
`81479`	Unlisted molecular pathology procedure	Used when an atypical or novel molecular assay related to KIT testing does not map to a specific CPT code.
`88305`	Level IV surgical pathology, gross and microscopic examination	Often billed by pathology when evaluating the tumor specimen and preparing tissue for molecular testing.
`84155`	Amylase; alternate method (example of enzymatic assay)	Data not applicable; included as an unrelated lab example — not typically related to KIT testing.
`81161`	KRAS gene partial sequence analysis	Other oncogene sequencing tests frequently ordered alongside KIT testing for comprehensive tumor profiling.

`26`	Professional component	Use when billing only the professional interpretation component separate from the technical lab work.
`TC`	Technical component	Use when billing only the technical component (laboratory testing) without the professional interpretation.
`59`	Distinct procedural service	Use when this molecular test is distinct from other services performed on the same date and documentation supports separate reporting.
`90`	Reference (outside) laboratory	Use when the service was performed by an outside reference laboratory.
`QK`	Medical direction of two or more qualified individuals (anesthesia)	Not typically used for this procedure; included only if anesthesia services are billed and meet criteria.
`QX`	Qualified nonphysician anesthetist with medical direction by physician	Not typically applicable; included only if anesthesia circumstances meet CMS definitions.
`AS`	Physician assistant, nurse practitioner, or clinical nurse specialist services	Use when a PA/NP/CNS furnishes professional services eligible under payer rules.
`52`	Reduced services	Use when the laboratory performed a reduced or partially reduced test relative to the full service.
`53`	Discontinued procedure	Use if testing was started but discontinued and documentation supports why the full test was not completed.
`59`	Distinct procedural service	Use when anatomic source or test performed is distinct from other billed services on the same day.
`90`	Reference (outside) laboratory	Use when the test was performed by an external lab and only the ordering facility is billing.

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