CPT 0162U: CustomNext® + RNA Lynch mRNA Sequence Analysis

CPT code 0162U designates a Proprietary Laboratory Analyses (PLA) test: the CustomNext® + RNA: Lynch (MLH1, MSH2, MSH6, PMS2) mRNA sequencing assay from Ambry Genetics®. This code is used in conjunction with the primary full-sequence analysis code to report mRNA sequence analysis specific to the four Lynch syndrome genes. Nationally, PLA codes like 0162U matter because they identify manufacturer-specific molecular assays that can affect coding consistency, claims adjudication, and lab reporting.

Key payers in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find an overview of what the code represents, typical clinical and laboratory contexts for use, and the payer landscape relevant to coverage and billing practices. The publication summarizes benchmarking points, common billing modifiers, and clinical context for Lynch syndrome mRNA testing, and highlights areas where policy updates or payer guidance commonly appear. Data not available in the input will be noted where applicable.

Billing Code Overview

CPT code 0162U is a Proprietary Laboratory Analyses (PLA) code for the CustomNext® + RNA: Lynch (MLH1, MSH2, MSH6, PMS2) test from Ambry Genetics®. The code applies to the mRNA sequence analysis of the four listed Lynch syndrome–associated genes when reported in conjunction with the primary code for full sequence analysis. This PLA designation indicates the code is specific to a single manufacturer or laboratory test.

Service type: Molecular diagnostic laboratory testing for mRNA sequence analysis of Lynch syndrome genes
Typical site of service: Clinical laboratory or outpatient laboratory setting

Data not available in the input.

Clinical Context

A patient with a personal or family history suggestive of Lynch syndrome—such as early-onset colorectal or endometrial cancer, multiple Lynch-associated tumors, or a first-degree relative with confirmed pathogenic variants—undergoes comprehensive germline testing. The ordering clinician (typically a geneticist, oncologist, or colorectal surgeon) requests full sequence analysis of the four Lynch genes (MLH1, MSH2, MSH6, PMS2) and the laboratory performs mRNA (RNA) sequence analysis as an adjunct to DNA testing to detect splicing abnormalities or expression-level consequences of suspected variants. The workflow: the clinician obtains informed consent, collects a blood sample (or other validated specimen) and sends it to the lab with clinical indication and prior test results. The lab performs DNA full sequence analysis (primary test) and, when indicated by variant interpretation needs, runs the Ambry Genetics CustomNext® + RNA: Lynch test reported under 0162U for mRNA sequence analysis of MLH1, MSH2, MSH6, and PMS2. Results are reported back to the ordering provider for integration into genetic counseling, risk assessment, and management planning.

Coding Specifications

Modifier	Description	When to Use

Taxonomy Code	Specialty	Notes
`207V00000X`	Clinical Molecular Genetics Laboratory	Laboratories performing specialized molecular diagnostic testing including PLA tests.
`207L00000X`	Laboratory Director	Laboratory directors overseeing high-complexity molecular testing workflows.
`207K00000X`	Medical Genetics & Genomics	Clinical geneticists ordering and interpreting hereditary cancer testing.
`207P00000X`	Pathology	Molecular pathology specialists involved in test interpretation and variant classification.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`Z15.09`	Genetic susceptibility to other malignant neoplasm	Used when testing is ordered for known family history or genetic susceptibility to cancers associated with Lynch syndrome.
`Z80.0`	Family history of malignant neoplasm of digestive organs	Captures family history prompting hereditary colorectal cancer testing.
`Z80.49`	Family history of malignant neoplasm of other female genital organs	Used when family history of endometrial or ovarian cancer prompts Lynch testing.
`C18.9`	Malignant neoplasm of colon, unspecified	Represents patients with colorectal cancer undergoing germline evaluation for Lynch syndrome.
`C54.9`	Malignant neoplasm of corpus uteri, unspecified	Represents patients with endometrial cancer in whom Lynch-associated testing is indicated.
`R19.5`	Other fecal abnormalities	May be present in symptomatic patients with colorectal disease leading to diagnosis and subsequent genetic testing.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81443`	Molecular pathology procedure; full gene sequence analysis, one gene (e.g., full sequence analysis of a single gene)	Often billed for full sequence analysis of individual Lynch genes as the primary DNA-based test; `0162U` is reported in conjunction with the primary full sequence analysis when RNA analysis is performed.
`81479`	Unlisted molecular pathology procedure	May be used when a laboratory-specific RNA analysis or combined proprietary algorithm lacks a precise category; PLA `0162U` supplants use of unlisted codes when applicable.
`G0452`	Pharmacogenomics testing (note: use varies by payer)	Not directly related but sometimes ordered in the same oncology/genetics workup for therapy guidance; included here as a commonly paired molecular code.
`0000U`	Data not available in the input.	Data not available in the input.
`0143U`	Data not available in the input.	Data not available in the input.

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Summary & Overview