CPT 81460: Mitochondrial Genome Sequencing Panel

Commercial payers pay $1323 on average nationally for this procedure.

CPT code 81460 describes a genomic sequencing panel that analyzes the entire mitochondrial genome from a patient specimen to detect pathogenic variants and assess heteroplasmy levels related to neuromuscular or mitochondrial disorders; service type is molecular genetic diagnostic testing (mitochondrial genome sequence analysis) typically performed in an clinical molecular genetics laboratory or reference diagnostic laboratory with testing carried out on blood, tissue, or other appropriate clinical specimens.

Customize your policy alerts

Sign up for cpt 81460 policy alerts

Get alerted when payer policies referencing 81460 are released or updated.

Monitor payer policy activity

Receive email alerts as soon as relevant payer policies are published or updated.

National Reimbursement Benchmarks

National commercial rates for CPT 81460 cluster around the BUCA average commercial rate of $1,323.40, with individual payers showing meaningful variation. Blue Cross Blue Shield has the highest spread in central tendency (P75–P25 = $489.30), suggesting wider negotiated outcomes, while Cigna and UnitedHealth Group show intermediate dispersion at $1,042.00 and $731.50 respectively. Aetna’s distribution is relatively tight with a P75–P25 of $713.00.

Overall dispersion highlights that Blue Cross Blue Shield delivers the widest interquartile range, signaling more heterogeneity in contracted rates, whereas Aetna is among the tighter payers. UnitedHealth Group’s lower median relative to its mean indicates skew toward higher outliers, and Cigna’s larger P75–P25 reflects broader variability around its median of $1,153.20.

Explore openpayer tools

View all tools

CPT 81460: Mitochondrial Genome Sequencing Panel

Commercial payers pay $1323 on average nationally for this procedure.

Customize your policy alerts

Sign up for cpt 81460 policy alerts

Get alerted when payer policies referencing 81460 are released or updated.

Monitor payer policy activity

Receive email alerts as soon as relevant payer policies are published or updated.

National Reimbursement Benchmarks

National Payer Mean Reimbursement Rates

Clinical & Coding Specifications

Clinical Context

A 28-year-old patient with progressive external ophthalmoplegia, exercise intolerance, and proximal muscle weakness is referred by a neurologist for comprehensive mitochondrial genome sequencing. Prior workup included elevated lactate and an uninformative chromosomal microarray. The clinician orders the mitochondrial full genome panel to detect pathogenic variants and quantify heteroplasmy that may explain the neuromuscular presentation. The specimen (peripheral blood; sometimes skeletal muscle biopsy if blood testing is nondiagnostic) is collected in an appropriate tube, labeled, and couriered to a molecular genetics laboratory specializing in mitochondrial testing. The lab performs DNA extraction, library preparation, next-generation sequencing of the entire mitochondrial genome, bioinformatic alignment, variant calling with heteroplasmy quantification, and interpretation by a board-certified molecular geneticist. Results are reported to the ordering clinician with variant classification and heteroplasmy levels; genetic counseling is offered for family implications and reproductive risk discussion.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81479`	Unlisted molecular pathology procedure	Used when a specific molecular test does not have a dedicated CPT code; rarely used for novel or highly customized mitochondrial assays.
`81228`	Cytogenomic constitutional (genome-wide) microarray analysis	Alternative or complementary test when chromosomal copy-number variants are suspected alongside mitochondrial disease; often performed earlier in the diagnostic cascade.
`81229`	Cytogenomic constitutional (genome-wide) microarray analysis; each additional microarray	Billed when multiple distinct microarray analyses are performed in the same episode of care.
`81425`	Genome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis	Used for broad genomic sequencing (exome/genome) when a mitochondrial genome panel is nondiagnostic and broader nuclear gene analysis is required.
`81426`	Genome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis, each additional genome	Used when additional genome sequencing is performed beyond the primary genome analysis in complex cases.

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…
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…
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…
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
207SG0201X	Clinical Genetics (M.D.) Physician	A clinical geneticist demonstrates competence in providing comprehensive diagnostic, management and counseling services for genetic disorders.
207SG0202X	Clinical Biochemical Genetics Physician	A clinical biochemical geneticist demonstrates competence in performing and interpreting biochemical analyses relevant to the diagnosis and management…
207SG0205X	Ph.D. Medical Genetics Physician	A medical geneticist works in association with a medical specialist, is affiliated with a clinical genetics program and serves as a consultant to medi…
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
1223P0700X	Prosthodontics	That branch of dentistry pertaining to the restoration and maintenance of oral functions, comfort, appearance and health of the patient by the restora…
247100000X	Radiologic Technologist	A medical imaging or radiation therapy professional who is appropriately educated and trained to perform medical imaging procedures using ionizing and…
174200000X	Meals Provider	A public or privately owned facility providing meals to individuals traveling long distances or receiving prolonged outpatient medical services away f…
2084P0301X	Brain Injury Medicine (Psychiatry & Neurology) Physician	A Brain Injury Medicine physician specializes in disorders of brain function due to injury and disease. These disorders encompass a range of medical,…

Related Codes

CPT-81410-GENOMIC-PANEL-AORTIC-DISEASE

CPT 81410: Heritable Thoracic Aortic Disease Targeted Gene Panel

CPT-81411-GENETIC-DUPLICATION-DELETION-PANEL-AORTIC-DISEASE

CPT 81411: Genetic Panel for Aortic Dysfunction Copy Number Analysis

CPT-81412-ASHKENAZI-JEWISH-GENOMIC-SEQUENCE-PANEL

CPT 81412: Ashkenazi Jewish–Associated Genetic Sequence Panel

CPT-81413-GENOMIC-PANEL-CARDIAC-ION-CHANNELOPATHIES

CPT 81413: Cardiac Ion Channelopathy Targeted Gene Panel

CPT-81414-CARDIAC-ION-CHANNELOPATHY-CNV-PANEL

CPT 81414: Cardiac Ion Channelopathy Copy Number Variant Panel

CPT-81415-EXOME-SEQUENCE-ANALYSIS-UNEXPLAINED-DISORDER

CPT 81415: Exome Sequence Analysis for Unexplained Disorder

CPT-81416-FAMILIAL-EXOME-SEQUENCE-ANALYSIS

CPT 81416: Relative Exome Sequence Analysis for Reference Exome

CPT-81417-EXOME-SEQUENCE-REEVALUATION

CPT 81417: Exome Reanalysis for New Clinical Information

CPT-81418-PHARMACOGENOMIC-MULTIGENE-DRUG-METABOLISM-PANEL

CPT 81418: Pharmacogenetic Multigene Panel Including CYP2C19 and CYP2D6

CPT-81419-GENOMIC-SEQUENCE-PANEL-EPILEPSY

CPT 81419: Genomic Sequence Analysis Panel for Epilepsy

Showing 1–10 of 43

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.

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.

Explore openpayer tools

View all tools

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81479`	Unlisted molecular pathology procedure	Used when a specific molecular test does not have a dedicated CPT code; rarely used for novel or highly customized mitochondrial assays.
`81228`	Cytogenomic constitutional (genome-wide) microarray analysis	Alternative or complementary test when chromosomal copy-number variants are suspected alongside mitochondrial disease; often performed earlier in the diagnostic cascade.
`81229`	Cytogenomic constitutional (genome-wide) microarray analysis; each additional microarray	Billed when multiple distinct microarray analyses are performed in the same episode of care.
`81425`	Genome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis	Used for broad genomic sequencing (exome/genome) when a mitochondrial genome panel is nondiagnostic and broader nuclear gene analysis is required.
`81426`	Genome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis, each additional genome	Used when additional genome sequencing is performed beyond the primary genome analysis in complex cases.

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…
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…
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…
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
207SG0201X	Clinical Genetics (M.D.) Physician	A clinical geneticist demonstrates competence in providing comprehensive diagnostic, management and counseling services for genetic disorders.
207SG0202X	Clinical Biochemical Genetics Physician	A clinical biochemical geneticist demonstrates competence in performing and interpreting biochemical analyses relevant to the diagnosis and management…
207SG0205X	Ph.D. Medical Genetics Physician	A medical geneticist works in association with a medical specialist, is affiliated with a clinical genetics program and serves as a consultant to medi…
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
1223P0700X	Prosthodontics	That branch of dentistry pertaining to the restoration and maintenance of oral functions, comfort, appearance and health of the patient by the restora…
247100000X	Radiologic Technologist	A medical imaging or radiation therapy professional who is appropriately educated and trained to perform medical imaging procedures using ionizing and…
174200000X	Meals Provider	A public or privately owned facility providing meals to individuals traveling long distances or receiving prolonged outpatient medical services away f…
2084P0301X	Brain Injury Medicine (Psychiatry & Neurology) Physician	A Brain Injury Medicine physician specializes in disorders of brain function due to injury and disease. These disorders encompass a range of medical,…

Related Codes

CPT-81410-GENOMIC-PANEL-AORTIC-DISEASE

CPT 81410: Heritable Thoracic Aortic Disease Targeted Gene Panel

CPT-81411-GENETIC-DUPLICATION-DELETION-PANEL-AORTIC-DISEASE

CPT 81411: Genetic Panel for Aortic Dysfunction Copy Number Analysis

CPT-81412-ASHKENAZI-JEWISH-GENOMIC-SEQUENCE-PANEL

CPT 81412: Ashkenazi Jewish–Associated Genetic Sequence Panel

CPT-81413-GENOMIC-PANEL-CARDIAC-ION-CHANNELOPATHIES

CPT 81413: Cardiac Ion Channelopathy Targeted Gene Panel

CPT-81414-CARDIAC-ION-CHANNELOPATHY-CNV-PANEL

CPT 81414: Cardiac Ion Channelopathy Copy Number Variant Panel

CPT-81415-EXOME-SEQUENCE-ANALYSIS-UNEXPLAINED-DISORDER

CPT 81415: Exome Sequence Analysis for Unexplained Disorder

CPT-81416-FAMILIAL-EXOME-SEQUENCE-ANALYSIS

CPT 81416: Relative Exome Sequence Analysis for Reference Exome

CPT-81417-EXOME-SEQUENCE-REEVALUATION

CPT 81417: Exome Reanalysis for New Clinical Information

CPT-81418-PHARMACOGENOMIC-MULTIGENE-DRUG-METABOLISM-PANEL

CPT 81418: Pharmacogenetic Multigene Panel Including CYP2C19 and CYP2D6

CPT-81419-GENOMIC-SEQUENCE-PANEL-EPILEPSY

CPT 81419: Genomic Sequence Analysis Panel for Epilepsy

Showing 1–10 of 43

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.

CPT 81460: Mitochondrial Genome Sequencing Panel

Sign up for cpt 81460 policy alerts

National Reimbursement Benchmarks

CPT 81460: Mitochondrial Genome Sequencing Panel

Sign up for cpt 81460 policy alerts

National Reimbursement Benchmarks

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related Codes

What clinical indications support ordering CPT 81460?

What specimen types are mentioned for testing under CPT 81460?

How is heteroplasmy handled in the testing process described for CPT 81460?

When might other CPT codes be billed instead of or alongside 81460?

Which payers are listed as covered in the summary metadata for this code?

References

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related Codes

What clinical indications support ordering CPT 81460?

What specimen types are mentioned for testing under CPT 81460?

How is heteroplasmy handled in the testing process described for CPT 81460?

When might other CPT codes be billed instead of or alongside 81460?

Which payers are listed as covered in the summary metadata for this code?

References