CPT 81336 SMN1 Sequencing Reimbursement | OpenPayer

Summary & Overview

CPT 81336: SMN1 Full-Gene Sequencing

CPT code 81336 covers technical laboratory sequencing that analyzes the entire telomeric sequence of the SMN1 gene. This full-gene sequencing test is clinically important for identifying pathogenic variants linked to spinal muscular atrophy and related neuromuscular conditions. Nationally, such molecular diagnostic codes inform coverage policies, laboratory billing practices, and utilization monitoring for rare genetic disorders.

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, payer coverage considerations, and the clinical context for ordering full-gene SMN1 sequencing. The publication summarizes common billing modifiers and service-line implications, explains typical sites of service, and outlines where data was provided or is not available. It also highlights benchmarks and policy updates relevant to molecular diagnostic sequencing codes and operational impacts for laboratories and billing teams.

This summary is intended for a national audience of laboratory administrators, billing professionals, and policy analysts seeking a concise briefing on CPT code 81336 and its role in molecular genetic testing workflows.

AetnaBlue Cross Blue ShieldCigna HealthUnitedHealthcareMedicareCPT 81336SMN1 sequencingmolecular diagnosticsgenetic testinglaboratory billingtechnical componentfull gene sequencingspinal muscular atrophy

Billing Code Overview

CPT code 81336 describes a laboratory test in which a lab analyst performs the technical procedures to analyze the entire gene sequence for the survival of motor neuron 1 (SMN1, telomeric). This is a molecular genetic sequencing service focused on detecting variants in the SMN1 gene sequence.

Service type: Technical laboratory sequencing service for full-gene analysis
Typical site of service: Clinical laboratory or molecular diagnostics laboratory (hospital-based or independent reference lab)

Data not available in the input for associated taxonomies, ICD-10 diagnoses, and related codes.

Clinical & Coding Specifications

Clinical Context

A typical patient is an infant or young child with suspected spinal muscular atrophy (SMA) based on hypotonia, progressive muscle weakness, delayed motor milestones, or family history of SMA. The specimen (usually blood or buccal swab) is collected in an outpatient clinic, pediatric neurology office, or genetic counseling visit. The sample is sent to a molecular genetics laboratory where a laboratory analyst performs full gene sequencing of the telomeric survival motor neuron 1 gene using next-generation sequencing or Sanger confirmatory testing to detect point mutations, small insertions/deletions, and sequence-level variants. Results are reported to the ordering clinician and genetic counselor; positive or uncertain findings prompt confirmatory testing, cascade testing of family members, or discussion of treatment options and enrollment in disease-specific registries. Typical site of service: outpatient clinic, specialty clinic (pediatric neurology or genetics), or reference molecular diagnostic laboratory.

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	Use when reporting only the professional interpretation component separate from the technical laboratory processing if billing split components.
`TC`

CPT 81120: IDH1 Molecular Diagnostic Test

CPT-81190-TARGETED-CSTB-FAMILY-SPECIFIC-GENETIC-TEST-TECHNICAL

CPT 81190: Targeted CSTB Genetic Test, Family-Specific (Technical Component)

CPT-81267-POST-TRANSPLANT-CHIMERISM-STR-ANALYSIS

CPT 81267: Post‑Transplant STR Chimerism (Engraftment) Analysis

CPT-81204-ANDROGEN-RECEPTOR-GENE-CHARACTERIZATION

CPT 81204: Androgen Receptor Gene Characterization

CPT-81200-ASPA-GENE-VARIANT-DETECTION-LAB-TEST

CPT 81200: ASPA Gene Variant Detection, Technical Laboratory Test

CPT-81253-GJB2-TARGETED-FAMILIAL-MUTATION-TESTING

CPT 81253: Targeted Familial Mutation Test for GJB2

CPT-81181-ATAXIN-7-ATXN7-EXPANSION-DETECTION

CPT 81181: ATXN7 (ataxin 7) Repeat Expansion Detection

CPT-81238-FACTOR-IX-F9-GENE-FULL-SEQUENCE

CPT 81238: Full-Gene Sequencing of Coagulation Factor IX (F9)

CPT-81171-AFF2-FMR2-EXPANDED-SEQUENCE-DETECTION

CPT 81171: AFF2 (FMR2) Expanded-Sequence Detection

CPT-81333-TGFBI-GENE-DETECTION-MOLECULAR-TEST

CPT 81333: TGFBI Gene Detection, Technical Laboratory Test

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Taxonomy Code	Specialty	Notes
207RG0100X	Medical Genetics	Clinical and laboratory geneticists oversee test selection and interpretation.
2084P0800X	Pediatric Neurology	Pediatric neurologists order testing for infants/children with neuromuscular concerns.
261QM0800X	Clinical Laboratory Geneticist	Laboratory directors and molecular pathologists manage sequencing and reporting.
207L00000X	Pathology	Molecular pathology specialists interpret sequence variants.
208000000X	Pediatrics	General pediatricians may order initial testing based on clinical screening.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`G12.0`	Infantile spinal muscular atrophy, type I	Primary diagnosis prompting `SMN1` sequencing to confirm SMA due to pathogenic variants or deletions.
`G12.1`	Other inherited spinal muscular atrophy	Used for other hereditary SMA forms where SMN1 testing helps define genotype.
`G12.8`	Other spinal muscular atrophies and related syndromes	Captures less common presentations where sequencing may identify causative variants.
`R29.898`	Other symptoms and signs involving the nervous and musculoskeletal systems	Used for nonspecific neuromuscular signs prompting genetic evaluation, including SMN1 testing.
`Z13.79`	Encounter for other screening for genetic and chromosomal anomalies	Used for family history or carrier screening where SMN1 sequencing or targeted testing is indicated.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81220`	SMN1 and SMN2 gene analysis, quantification of gene copy number (e.g., deletion/duplication analysis)	Performed alongside sequencing to detect exon deletions or copy number variants not detected by sequencing; complementary for SMA diagnosis.
`81479`	Unlisted molecular pathology procedure	Used when a specific sequence analysis does not have a precise CPT correlate; rarely used if novel methods are applied.
`81162`	APC gene full sequence analysis (example sequencing code)	Example of full gene sequencing CPTs; demonstrates similar billing and laboratory workflow as sequencing of `SMN1`.
`88360`	Immunohistochemistry (IHC), per single antibody stain	Not typically used for SMN1 sequencing but may be performed in related neuromuscular tissue assessments.
`G0452`	Laboratory test management fee (Medicare)	May be used in specific Medicare billing scenarios for molecular test ordering and coordination.

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