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.

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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.

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CPT 81336: SMN1 Full-Gene Sequencing

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Billing Code Overview

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.

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.

Related Modifiers

7 rows

Modifier	Description	When to Use
26	Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…	- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
90	Modifier ‑90 (Reference/Outside Laboratory) indicates that a laboratory test was performed by an entity other than the treating or reporting provider. The American Medical Association defines…	- Use CPT modifier -90 when a laboratory test is performed by an outside/reference laboratory (an entity other than the treating or reporting physician or qualified professional) and the claim needs…
91	Modifier 91 — “Repeat Clinical Diagnostic Laboratory Test” — is appended when the exact same CPT laboratory test is performed more than once for the same patient on the same day because serial,…	- Use modifier 91 when the exact same CPT laboratory test is performed more than once on the same patient on the same date because serial or repeated testing is medically necessary to monitor…
59	Modifier 59 indicates a distinct procedural service when two procedures that are not normally billed together are clinically and procedurally separate. The CPT definition (as reiterated by CMS)…	- Use modifier -59 to report a distinct procedural service when documentation supports that the procedure reported is not normally billed together with another service on the same day because of a…
22	Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…	- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
52	Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…	- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
53	Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…	- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…

Related Provider Taxonomies

8 rows

Taxonomy Code	Specialty	Notes
207RG0100X	Gastroenterology Physician	An internist who specializes in diagnosis and treatment of diseases of the digestive organs including the stomach, bowels, liver and gallbladder. This…
2084P0800X	Psychiatry Physician	A Psychiatrist specializes in the prevention, diagnosis, and treatment of mental disorders, emotional disorders, psychotic disorders, mood disorders, …
207L00000X	Anesthesiology Physician	An anesthesiologist is trained to provide pain relief and maintenance, or restoration, of a stable condition during and immediately following an opera…
208000000X	Pediatrics Physician	A pediatrician is concerned with the physical, emotional and social health of children from birth to young adulthood. Care encompasses a broad spectru…
133VN1005X	Renal Nutrition Registered Dietitian	An individual who is a Board Certified Specialist in Renal Nutrition and works directly with adult and/or pediatric patients with acute kidney injury,…
385HR2055X	Child Mental Illness Respite Care	A facility or distinct part of a facility that provides short term, residential care to children, diagnosed with mental illness, as respite for the re…
2279G0305X	Geriatric Care Registered Respiratory Therapist	Care of older patients who have age and/or disease related decremental pulmonary changes. Diagnosis and treatment is very important for this group si…
207LP3000X	Pediatric Anesthesiology Physician	An anesthesiologist who has had additional skill and experience in and is primarily concerned with the anesthesia, sedation, and pain management needs…

CPT 81105: HPA-1 (CD61/ITGB3) Platelet Antigen Genotyping

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

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

CPT-81107-HPA-3-GENETIC-ANALYSIS-TECHNICAL-COMPONENT

CPT 81107: HPA‑3 (I843S) Platelet Antigen Genotyping

CPT-81108-HPA-4-R143Q-GENOTYPING

CPT 81108: HPA-4 (R143Q) Genotyping, Technical Component

CPT-81109-HPA-5-K505E-GENETIC-ANALYSIS

CPT 81109: HPA-5 (K505E) Genetic Analysis

CPT-81110-HPA-6-R489Q-GENOTYPING

CPT 81110: HPA-6 (R489Q) Genotyping, Technical Component

CPT-81111-HPA-9-V837M-ALLELE-ANALYSIS

CPT 81111: HPA-9 (V837M) Allele Analysis, Laboratory Technical Component

CPT-81112-HPA-15-GENETIC-ANALYSIS-S682Y

CPT 81112: HPA-15 (S682Y) Genetic Analysis

CPT-81120-IDH1-MOLECULAR-DIAGNOSTIC-TEST

CPT 81120: IDH1 Molecular Diagnostic Test

CPT-81121-IDH2-MOLECULAR-DIAGNOSTIC-TEST

CPT 81121: IDH2 (NADP+) Molecular Diagnostic Test

Showing 1–10 of 199

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

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Clinical & Coding Specifications

Clinical Context

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.

Related Modifiers

7 rows

Modifier	Description	When to Use
26	Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…	- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
90	Modifier ‑90 (Reference/Outside Laboratory) indicates that a laboratory test was performed by an entity other than the treating or reporting provider. The American Medical Association defines…	- Use CPT modifier -90 when a laboratory test is performed by an outside/reference laboratory (an entity other than the treating or reporting physician or qualified professional) and the claim needs…
91	Modifier 91 — “Repeat Clinical Diagnostic Laboratory Test” — is appended when the exact same CPT laboratory test is performed more than once for the same patient on the same day because serial,…	- Use modifier 91 when the exact same CPT laboratory test is performed more than once on the same patient on the same date because serial or repeated testing is medically necessary to monitor…
59	Modifier 59 indicates a distinct procedural service when two procedures that are not normally billed together are clinically and procedurally separate. The CPT definition (as reiterated by CMS)…	- Use modifier -59 to report a distinct procedural service when documentation supports that the procedure reported is not normally billed together with another service on the same day because of a…
22	Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…	- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
52	Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…	- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
53	Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…	- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…

Related Provider Taxonomies

8 rows

Taxonomy Code	Specialty	Notes
207RG0100X	Gastroenterology Physician	An internist who specializes in diagnosis and treatment of diseases of the digestive organs including the stomach, bowels, liver and gallbladder. This…
2084P0800X	Psychiatry Physician	A Psychiatrist specializes in the prevention, diagnosis, and treatment of mental disorders, emotional disorders, psychotic disorders, mood disorders, …
207L00000X	Anesthesiology Physician	An anesthesiologist is trained to provide pain relief and maintenance, or restoration, of a stable condition during and immediately following an opera…
208000000X	Pediatrics Physician	A pediatrician is concerned with the physical, emotional and social health of children from birth to young adulthood. Care encompasses a broad spectru…
133VN1005X	Renal Nutrition Registered Dietitian	An individual who is a Board Certified Specialist in Renal Nutrition and works directly with adult and/or pediatric patients with acute kidney injury,…
385HR2055X	Child Mental Illness Respite Care	A facility or distinct part of a facility that provides short term, residential care to children, diagnosed with mental illness, as respite for the re…
2279G0305X	Geriatric Care Registered Respiratory Therapist	Care of older patients who have age and/or disease related decremental pulmonary changes. Diagnosis and treatment is very important for this group si…
207LP3000X	Pediatric Anesthesiology Physician	An anesthesiologist who has had additional skill and experience in and is primarily concerned with the anesthesia, sedation, and pain management needs…

CPT 81105: HPA-1 (CD61/ITGB3) Platelet Antigen Genotyping

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

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

CPT-81107-HPA-3-GENETIC-ANALYSIS-TECHNICAL-COMPONENT

CPT 81107: HPA‑3 (I843S) Platelet Antigen Genotyping

CPT-81108-HPA-4-R143Q-GENOTYPING

CPT 81108: HPA-4 (R143Q) Genotyping, Technical Component

CPT-81109-HPA-5-K505E-GENETIC-ANALYSIS

CPT 81109: HPA-5 (K505E) Genetic Analysis

CPT-81110-HPA-6-R489Q-GENOTYPING

CPT 81110: HPA-6 (R489Q) Genotyping, Technical Component

CPT-81111-HPA-9-V837M-ALLELE-ANALYSIS

CPT 81111: HPA-9 (V837M) Allele Analysis, Laboratory Technical Component

CPT-81112-HPA-15-GENETIC-ANALYSIS-S682Y

CPT 81112: HPA-15 (S682Y) Genetic Analysis

CPT-81120-IDH1-MOLECULAR-DIAGNOSTIC-TEST

CPT 81120: IDH1 Molecular Diagnostic Test

CPT-81121-IDH2-MOLECULAR-DIAGNOSTIC-TEST

CPT 81121: IDH2 (NADP+) Molecular Diagnostic Test

Showing 1–10 of 199

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

Published by

Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

OpenPayer

CPT 81336: SMN1 Full-Gene Sequencing

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Billing Code Overview

OpenPayer

CPT 81336: SMN1 Full-Gene Sequencing

Sign up for cpt 81336 policy alerts

Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Related Diagnoses

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related Codes

References

Clinical & Coding Specifications

Clinical Context

Related Diagnoses

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related Codes

References