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    v1.0.28
    OpenPayerBilling CodesGenetic Analysis ProceduresCPT cpt-81329-smn1-deletion-analysis-genetic-testing
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    CPT 81329: SMN1 Deletion Analysis, May Include SMN2

    CPT code 81329 describes a laboratory genetic test where the technical component detects deletions in the survival of motor neuron 1 (SMN1), telomeric, gene and may include analysis of the survival of motor neuron 2 (SMN2), centromeric, gene; service type: molecular diagnostic / genetic deletion analysis; typical site of service: clinical diagnostic laboratory or reference molecular laboratory performing DNA deletion testing.

    For related coverage guidance, see recent payer policy updates: RTM Testing of Homocysteine Metabolism-Related Conditions, Multimarker Serum Testing Related to Ovarian Cancer, Genomic Profiling for Selecting Targeted Cancer Therapies.

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    Clinical & Coding Specifications

    Clinical Context

    A neonate or infant with hypotonia, poor feeding, progressive muscle weakness, or a family history of spinal muscular atrophy (SMA) is referred for genetic testing. A pediatric neurologist or geneticist orders molecular diagnostic testing to detect deletions in the survival motor neuron 1 gene (SMN1) with potential analysis of copy number for SMN2. A blood sample (EDTA) is collected in an outpatient clinic, hospital inpatient ward, or neonatal intensive care unit (NICU) and sent to a clinical molecular diagnostics laboratory. The laboratory analyst performs the technical assay — commonly PCR-based copy number analysis, multiplex ligation-dependent probe amplification (MLPA), or quantitative PCR — to detect homozygous deletions or exon-specific deletions in SMN1, and may report SMN2 copy number which informs prognosis and therapeutic considerations. Results are transmitted to the ordering clinician and incorporated into the patient record; the ordering provider interprets results for diagnosis, family counseling, and potential referral for disease-modifying therapies or genetic counseling. Typical sites of service include outpatient specialty clinics, hospital laboratories, and reference molecular diagnostic laboratories supporting NICU and pediatric services.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    81220SMN1 (survival motor neuron 1) gene analysis; common exon 7 and 8 deletion analysisAlternative or component testing that overlaps with 81329 when focused specifically on exon deletions; may be reported when only standard exon 7/8 deletion testing is performed.
    81479Unlisted molecular pathology procedureUsed when a specific molecular test does not have a direct CPT code; rarely used if test methodology for SMN1 deletion detection is unique and not covered by existing codes.
    81221SMN1 (survival motor neuron 1) gene analysis; duplication/deletion analysis by quantitative methodsRelated quantitative methods for copy-number assessment that can complement 81329 reporting, especially for SMN2 copy number evaluation.
    81162Methylation analysis for disease-specific loci (example for complex molecular testing workflow)Occasionally performed in broader genetic testing panels or differential diagnostic workflows alongside SMA testing when complex genetic etiologies are considered.
    0000FData not available in the input.Data not available in the input.

    Related Modifiers

    7 rows

    ModifierDescriptionWhen to Use
    26Modifier 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…
    91Modifier 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…
    59Modifier 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…
    90Modifier ‑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…
    22Modifier –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…
    52Modifier ‑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…
    53Modifier 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 CodeSpecialtyNotes
    207RH0000XHematology (Internal Medicine) PhysicianAn internist with additional training who specializes in diseases of the blood, spleen and lymph. This specialist treats conditions such as anemia, cl…
    207K00000XAllergy & Immunology PhysicianAn allergist-immunologist is trained in evaluation, physical and laboratory diagnosis, and management of disorders involving the immune system. Select…
    207L00000XAnesthesiology PhysicianAn anesthesiologist is trained to provide pain relief and maintenance, or restoration, of a stable condition during and immediately following an opera…
    2080P0207XPediatric Hematology & Oncology PhysicianA pediatrician trained in the combination of pediatrics, hematology and oncology to recognize and manage pediatric blood disorders and cancerous disea…
    208D00000XGeneral Practice PhysicianA physician who specializes in the general practice of diagnosing, treating, and managing patients with a variety of illnesses and conditions.
    207QP0002XPhysician Nutrition Specialist (Family Medicine)A physician who specializes in the diagnosis and treatment of primary nutritional diseases (e.g., undernutrition, overnutrition, and genetic or acquir…
    207RI0001XClinical & Laboratory Immunology (Internal Medicine) PhysicianAn internal medicine physician who specializes in clinical and laboratory immunology disease management.
    146D00000XPersonal Emergency Response AttendantIndividuals that are specially trained to assist patients living at home with urgent/emergent situations. These individuals must be able to perform C…

    Related Payer Policy Updates

    Specialty: Genetic & Molecular Testing1 / 3

    10 rows

    PolicyPayerEffective Date
    RTM Testing of Homocysteine Metabolism-Related ConditionsOscar Health2026-10-01
    Multimarker Serum Testing Related to Ovarian CancerBlue Cross Blue Shield - Rhode Island2026-09-01
    Genomic Profiling for Selecting Targeted Cancer TherapiesBlue Cross Blue Shield - Rhode Island2026-09-01
    Whole Exome and Whole Genome Sequencing for Diagnosis of Genetic DisordersBlue Cross Blue Shield - Rhode Island2026-09-01
    Biomarker and Genetic/Molecular Testing Coverage and Prior AuthorizationBlue Cross Blue Shield - Rhode Island2026-09-01
    Non-Invasive Prenatal Testing (NIPT)univerahealthcare2026-08-17
    Lumizyme (alglucosidase alfa) — Pompe Disease (acid alpha‑glucosidase deficiency)Cigna2026-08-15
    Molecular Oncology Testing for Solid Tumor Cancer Diagnosis, Prognosis, and Treatment DecisionsColorado Rocky Mountain Health Plans2026-08-01
    Carrier Testing Panels for Genetic DiseasesColorado Rocky Mountain Health Plans2026-08-01
    Molecular Oncology Testing for Hematologic Cancer Diagnosis, Prognosis, and Treatment DecisionsColorado Rocky Mountain Health Plans2026-08-01

    Related Codes

    CPT-81105-HPA-1-PLATELET-ANTIGEN-1-GENOTYPING-ITGB3-CD61

    CPT 81105: HPA-1 (ITGB3/CD61) Genotyping, Technical Component

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

    CPT 81106: HPA-2 (T145M) Platelet Antigen Genotyping

    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

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

    CPT 81109: HPA-5 (K505E) Genotyping Test

    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) Genotyping, Technical Test

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

    CPT 81112: HPA-15 (S682Y) Platelet Antigen Genotyping

    CPT-81120-IDH1-MOLECULAR-DIAGNOSTIC-TEST

    CPT 81120: IDH1 Mutation Detection, Technical Component

    CPT-81121-IDH2-MOLECULAR-DIAGNOSTIC-TEST

    CPT 81121: IDH2 Mutation Detection, Technical Component

    Showing 1–10 of 199

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    Frequently Asked Questions

    References

    1. 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. 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. 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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