CPT 81304: MECP2 Large Deletion/Duplication Analysis

CPT code 81304 describes the laboratory technical procedure to detect large deletions or duplications in the MECP2 gene (methyl CpG binding protein 2), used for molecular genetic testing to identify copy number variants in this gene; service type: molecular genetic pathology / targeted deletion/duplication analysis; typical site of service: clinical molecular laboratory or reference diagnostic laboratory.

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CPT 81304: MECP2 Large Deletion/Duplication Analysis

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Get alerted when payer policies referencing 81304 are released or updated.

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Clinical & Coding Specifications

Clinical Context

A female pediatric patient, age 2–5 years, presents to a genetics clinic with developmental delay, intellectual disability, delayed speech, loss of acquired language, hand-wringing stereotypies, and hypotonia. The pediatric neurologist orders targeted genetic testing for abnormalities in the MECP2 gene to evaluate for Rett syndrome and related neurodevelopmental disorders. A specimen (peripheral blood) is collected in the outpatient clinic, accompanied by the clinician’s requisition specifying clinical indications and prior testing. The laboratory receives the specimen and performs a technical genetic assay to detect long-sequence deletions or duplications in the MECP2 gene (81304). The testing workflow includes accessioning, DNA extraction, assay setup (e.g., MLPA or comparable copy-number analysis), instrument run, data analysis by laboratory personnel, and generation of a technical report. Results are routed to the ordering clinician, who integrates findings with clinical assessment and counseling. Typical site of service is an outpatient hospital-based genetics clinic or independent clinical molecular diagnostic laboratory with capabilities for molecular cytogenetics and copy-number analysis.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81225`	Sequencing of the MECP2 gene (e.g., full gene sequencing)	Performed when single-nucleotide variants or small indels are suspected; sequencing often precedes or follows copy-number testing to provide comprehensive MECP2 analysis.
`81226`	Deletion/duplication analysis, MECP2 (alternative assay codes may apply)	Alternative or confirmatory copy-number assay for MECP2 large deletions/duplications; can be used in combination with `81304` depending on methodology.
`88271`	Molecular cytogenetics (e.g., FISH) — targeted probe	Used when a targeted FISH assay is indicated to confirm a specific large deletion detected by copy-number testing.
`88368`	Morphometric analysis and report (if applicable)	Used in some specialized labs for supplemental analysis and reporting of complex results.
`86580`	Specimen handling/collection code (example)	Billed by the collecting facility for specimen procurement and handling prior to molecular testing.

Related Modifiers

5 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…
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…
2080P0208X	Pediatric Infectious Diseases Physician	A pediatrician trained to care for children in the diagnosis, treatment and prevention of infectious diseases. This specialist can apply specific know…
2084P0800X	Psychiatry Physician	A Psychiatrist specializes in the prevention, diagnosis, and treatment of mental disorders, emotional disorders, psychotic disorders, mood disorders, …
1835S0206X	Solid Organ Transplant Pharmacist	A licensed pharmacist who has demonstrated specialized knowledge and skill delivering direct patient care and the safe and effective use of medication…
305R00000X	Preferred Provider Organization	A group of physicians and/or hospitals who contract with an employer to provide services to their employees. In a PPO, the patient may got to the phys…
344600000X	Taxi	A land commercial vehicle used for the transporting of persons in non-emergency situations. The vehicle meets local, county or state regulations set f…
2251H1200X	Hand Physical Therapist	Respiratory, Developmental, Rehabilitative and Restorative Service Providers · Physical Therapist
332BX2000X	Oxygen Equipment & Supplies (DME)	Suppliers · Durable Medical Equipment & Medical Supplies

Related ICD-10-CM Codes

24 rows

ICD-10-CM Code	Description
F70	Mild intellectual disabilities
F71	Moderate intellectual disabilities
F72	Severe intellectual disabilities
F73	Profound intellectual disabilities
F79	Unspecified intellectual disabilities
F80.1	Expressive language disorder
F80.2	Mixed receptive-expressive language disorder
F80.9	Developmental disorder of speech and language, unspecified
F82	Specific developmental disorder of motor function
F84.0	Autistic disorder

Showing 1–10 of 24

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

Frequently Asked Questions

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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Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.

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Clinical & Coding Specifications

Clinical Context

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81225`	Sequencing of the MECP2 gene (e.g., full gene sequencing)	Performed when single-nucleotide variants or small indels are suspected; sequencing often precedes or follows copy-number testing to provide comprehensive MECP2 analysis.
`81226`	Deletion/duplication analysis, MECP2 (alternative assay codes may apply)	Alternative or confirmatory copy-number assay for MECP2 large deletions/duplications; can be used in combination with `81304` depending on methodology.
`88271`	Molecular cytogenetics (e.g., FISH) — targeted probe	Used when a targeted FISH assay is indicated to confirm a specific large deletion detected by copy-number testing.
`88368`	Morphometric analysis and report (if applicable)	Used in some specialized labs for supplemental analysis and reporting of complex results.
`86580`	Specimen handling/collection code (example)	Billed by the collecting facility for specimen procurement and handling prior to molecular testing.

Related Modifiers

5 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…
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…
2080P0208X	Pediatric Infectious Diseases Physician	A pediatrician trained to care for children in the diagnosis, treatment and prevention of infectious diseases. This specialist can apply specific know…
2084P0800X	Psychiatry Physician	A Psychiatrist specializes in the prevention, diagnosis, and treatment of mental disorders, emotional disorders, psychotic disorders, mood disorders, …
1835S0206X	Solid Organ Transplant Pharmacist	A licensed pharmacist who has demonstrated specialized knowledge and skill delivering direct patient care and the safe and effective use of medication…
305R00000X	Preferred Provider Organization	A group of physicians and/or hospitals who contract with an employer to provide services to their employees. In a PPO, the patient may got to the phys…
344600000X	Taxi	A land commercial vehicle used for the transporting of persons in non-emergency situations. The vehicle meets local, county or state regulations set f…
2251H1200X	Hand Physical Therapist	Respiratory, Developmental, Rehabilitative and Restorative Service Providers · Physical Therapist
332BX2000X	Oxygen Equipment & Supplies (DME)	Suppliers · Durable Medical Equipment & Medical Supplies

Related ICD-10-CM Codes

24 rows

ICD-10-CM Code	Description
F70	Mild intellectual disabilities
F71	Moderate intellectual disabilities
F72	Severe intellectual disabilities
F73	Profound intellectual disabilities
F79	Unspecified intellectual disabilities
F80.1	Expressive language disorder
F80.2	Mixed receptive-expressive language disorder
F80.9	Developmental disorder of speech and language, unspecified
F82	Specific developmental disorder of motor function
F84.0	Autistic disorder

Showing 1–10 of 24

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

Frequently Asked Questions

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 81304: MECP2 Large Deletion/Duplication Analysis

Sign up for cpt 81304 policy alerts

OpenPayer

CPT 81304: MECP2 Large Deletion/Duplication Analysis

Sign up for cpt 81304 policy alerts

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Codes

References

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Codes

References

CPT 81304: MECP2 Large Deletion/Duplication Analysis

Sign up for cpt 81304 policy alerts

CPT 81304: MECP2 Large Deletion/Duplication Analysis

Sign up for cpt 81304 policy alerts

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Codes

What does CPT code 81304 represent?

Which modifiers are commonly used with 81304 and when should they be applied?

What other CPT codes are commonly billed alongside or instead of 81304?

What clinical scenarios or diagnoses commonly prompt ordering of 81304?

Where is CPT 81304 typically performed and which payers are referenced in the analysis?

References

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Codes

What does CPT code 81304 represent?

Which modifiers are commonly used with 81304 and when should they be applied?

What other CPT codes are commonly billed alongside or instead of 81304?

What clinical scenarios or diagnoses commonly prompt ordering of 81304?

Where is CPT 81304 typically performed and which payers are referenced in the analysis?

References