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    v1.0.30
    OpenPayerBilling CodesGenetic Analysis ProceduresCPT cpt-81229-chromosomal-microarray-cgh-cma-molecular-karyotype
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    CPT 81229: Chromosomal Microarray (CGH/CMA) for CNV Detection

    CPT code 81229 describes a laboratory technical service performing a genome-wide comparative genomic hybridization (CGH) microarray, also called chromosomal microarray (CMA) or molecular karyotype by microarray, to detect copy-number variants (CNVs) and evaluate single-nucleotide polymorphisms (SNPs) such as long runs of homozygosity; service type: high-resolution genomic microarray testing; typical site of service: clinical molecular genetics or reference diagnostic laboratory performing specialized cytogenomic testing.

    For related coverage guidance, see recent payer policy updates: Oral Cancer Screening and Testing, RTM Testing for Alpha-1 Antitrypsin Deficiency, Cytochrome P450 Genotype-Guided Treatment Strategy Corporate Medical Policy.

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    Clinical & Coding Specifications

    Clinical Context

    A child aged 18 months presents to a pediatric genetics clinic for evaluation of global developmental delay, hypotonia, and dysmorphic features. The pediatrician orders a high-resolution chromosomal microarray (comparative genomic hybridization / CMA) to detect copy-number variants (CNVs) or regions of homozygosity that could explain the phenotype. A genetics nurse obtains informed consent and collects a blood sample in an EDTA tube at an outpatient laboratory collection site. The sample is sent to the molecular diagnostics laboratory where a medical technologist extracts DNA and runs the CGH/SNP microarray platform. The lab analyst performs the technical test corresponding to 81229 and generates raw and analyzed data; a board-certified molecular geneticist reviews and signs the interpretive report. Results identifying a pathogenic CNV prompt genetic counseling and coordination of confirmatory testing or targeted family testing. Typical sites of service include outpatient hospital laboratories, independent reference laboratories, and hospital-based molecular diagnostics laboratories.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    88271Genome‑wide cytogenetic microarray analysis (interpretation and report)Often billed for interpretation components or historically used for some microarray services; complements 81229 when separate interpretation coding is required.
    81237Analysis of specific gene(s) by sequencing for constitutional single gene disorders (example)May be ordered after 81229 if CMA identifies a CNV suggesting a gene-level pathogenicity requiring sequencing confirmation.
    88381Surgical pathology or specimen handling (molecular specimens)May be used for specimen processing steps in certain laboratories that bill pathology services alongside molecular testing.
    81479Unlisted molecular pathology procedureUsed when a specific molecular test or custom analysis associated with microarray findings has no dedicated code.
    81229Comparative genomic hybridization (CMA) microarray — technical testThe primary technical laboratory procedure performed; included for workflow context.

    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…
    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…
    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…
    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…
    95Modifier 95 indicates that a service was provided via synchronous, real‑time audio‑video telehealth rather than in‑person. Per CMS, AAPC and professional associations, append modifier 95 to claim…- Use modifier 95 to indicate a service was furnished via synchronous, real‑time audiovisual telehealth (a live audio‑video conference between patient and provider) rather than in‑person. - Pair…

    Related Provider Taxonomies

    8 rows

    Taxonomy Code
    207Q00000X
    208000000X
    363L00000X
    261QR0400X
    364SX0106X
    1223X2210X
    175L00000X
    252Y00000X

    Related ICD-10-CM Codes

    24 rows

    ICD-10-CM CodeDescription
    F33.1Major depressive disorder, recurrent, moderate
    F70Mild intellectual disabilities
    F71Moderate intellectual disabilities
    F72Severe intellectual disabilities
    F79Unspecified intellectual disabilities
    F80.1Expressive language disorder
    F80.2Mixed receptive-expressive language disorder
    F80.9Developmental disorder of speech and language, unspecified
    F81.9Developmental disorder of scholastic skills, unspecified
    F82Specific developmental disorder of motor function

    Showing 1–10 of 24

    Related Payer Policy Updates

    Specialty: Genetic & Molecular Testing1 / 3

    10 rows

    PolicyPayerEffective Date
    Oral Cancer Screening and TestingOscar Health2027-01-01
    RTM Testing for Alpha-1 Antitrypsin DeficiencyOscar Health2027-01-01
    Cytochrome P450 Genotype-Guided Treatment Strategy Corporate Medical Policybcbsvermont2027-01-01
    Carrier Testing Panels for Genetic Diseases (for Kentucky Only)UnitedHealthcare2026-10-01
    Genetic Testing for Neurological Disorders (for Kansas Only)UnitedHealthcare2026-10-01
    Genetic and Molecular TestingProvidence Health Plan2026-10-01
    Cell-Free Fetal DNA Testing (for Idaho Only)UnitedHealthcare2026-10-01
    Next Generation Sequencing for Minimal Residual Disease DetectionProvidence Health Plan2026-10-01
    Pharmacogenetic Panel Testing (for Kansas Only)UnitedHealthcare2026-10-01
    Non-Covered Genetic Panel TestsProvidence Health Plan2026-10-01

    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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