CPT 81465: Mitochondrial Genome Deletion Analysis

Commercial payers pay $977 on average nationally for this procedure.

CPT code 81465 describes a genomic sequence analysis panel that evaluates the entire mitochondrial genome for large deletions associated with neuromuscular and mitochondrial disorders; the service is a mitochondrial genome deletion analysis (including heteroplasmy detection when performed) typically provided as a laboratory molecular diagnostic test in a clinical molecular genetics or specialized laboratory setting, often processed from blood or tissue specimens.

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National Reimbursement Benchmarks

BUCA’s national average commercial rate for CPT 81465 sits at $976.90, serving as a useful midpoint for comparing commercial payers. Blue Cross Blue Shield shows the highest overall spread with a P75–P25 range of $338.40 ($1,104.30 − $766.60), reflecting notable regional or contract variability. Cigna’s spread is $733.60 ($1,212.40 − $478.80), the widest among listed commercial payers, while UnitedHealth Group is comparatively tight with a spread of $542.90 ($936.00 − $393.10).

Aetna’s interquartile spread is $575.00 ($1,150.00 − $572.50), indicating moderate dispersion around BUCA’s average. Blue Cross Blue Shield and Cigna show the largest IQR-driven variability, suggesting greater upside and downside potential versus BUCA, while UnitedHealth Group and Aetna are comparatively more clustered around their medians and means.

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CPT 81465: Mitochondrial Genome Deletion Analysis

Commercial payers pay $977 on average nationally for this procedure.

Customize your policy alerts

Sign up for cpt 81465 policy alerts

Get alerted when payer policies referencing 81465 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 12-year-old child with progressive gait instability, muscle weakness, and episodic elevation of lactate is referred to a clinical genetics laboratory for molecular testing. The neurologist suspects a mitochondrial myopathy or mitochondrial DNA (mtDNA) deletion syndrome after prior metabolic testing showed lactic acidosis and electromyography suggested myopathic changes. The clinician orders a full mitochondrial genome deletion/duplication analysis to evaluate for large mtDNA deletions and to determine heteroplasmy levels.

Specimen collection and workflow: peripheral blood is collected in an EDTA tube and shipped to a reference molecular diagnostics laboratory. The laboratory performs DNA extraction, long-range PCR or next-generation sequencing of the entire mitochondrial genome, and analytic methods to detect large-scale deletions and estimate heteroplasmy fraction. Results are interpreted by a molecular genetics laboratory director and reported to the ordering provider, typically a neurologist or medical geneticist, with recommendations for correlation to clinical findings. Typical turnaround time ranges from several days to a few weeks depending on reflex testing (e.g., confirmation by alternate method). Typical site of service is an outpatient clinic or ambulatory phlebotomy collection with testing performed in a specialized clinical molecular genetics laboratory.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81479`	Unlisted molecular pathology procedure	Use when a specific molecular test is not otherwise represented; occasionally used for uncommon or custom mitochondrial assays.
`81229`	Cytogenomic constitutional (genome-wide) microarray analysis	Performed when broader copy-number evaluation is needed for chromosomal abnormalities that may present with developmental or syndromic features.
`81415`	Exome; sequence analysis	Used when a broader nuclear exome sequencing is indicated to evaluate suspected nuclear gene causes of neuromuscular or metabolic disease.
`81416`	Exome; sequence analysis, each comparator exome	Used when parental or familial comparator exomes are sequenced alongside the proband to assist variant interpretation.
`81417`	Exome; re-evaluation of previously obtained exome sequence	Used when reanalysis of prior exome data is performed to seek diagnoses missed on initial review.

Related Modifiers

8 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…
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…
62	Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…	- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…
78	CPT modifier -78 indicates an unplanned, related return to the operating or procedure room by the same provider during the global postoperative period. It is appended when treatment for a…	- Use modifier -78 when an unplanned, related complication during the original procedure’s global postoperative period requires the patient to return to a formal operating or procedure room and the…
80	CPT® Modifier 80 (Assistant Surgeon) is appended to a surgical CPT code when a physician (MD or DO) provides full, continuous assistance throughout the operative procedure. It is intended only for…	- Use CPT Modifier -80 when a physician (MD or DO) serves as an assistant surgeon and provides full, continuous assistance throughout the entire operative procedure; append -80 to the surgical CPT…
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…

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.
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
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…
207YX0905X	Otolaryngology/Facial Plastic Surgery Physician	An otolaryngologist who specializes in the diagnosis and surgical treatment of head and neck conditions.
363LP0808X	Psychiatric/Mental Health Nurse Practitioner	Physician Assistants & Advanced Practice Nursing Providers · Nurse Practitioner
152WL0500X	Low Vision Rehabilitation Optometrist	Optometrists who specialize in low-vision care having training to assess visual function, prescribe low-vision devices, develop treatment plans, and r…
225B00000X	Pulmonary Function Technologist	An individual who is trained and qualified to perform pulmonary diagnostic tests. In the course of conducting these tests, the Pulmonary Function Tec…

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.

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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
`81479`	Unlisted molecular pathology procedure	Use when a specific molecular test is not otherwise represented; occasionally used for uncommon or custom mitochondrial assays.
`81229`	Cytogenomic constitutional (genome-wide) microarray analysis	Performed when broader copy-number evaluation is needed for chromosomal abnormalities that may present with developmental or syndromic features.
`81415`	Exome; sequence analysis	Used when a broader nuclear exome sequencing is indicated to evaluate suspected nuclear gene causes of neuromuscular or metabolic disease.
`81416`	Exome; sequence analysis, each comparator exome	Used when parental or familial comparator exomes are sequenced alongside the proband to assist variant interpretation.
`81417`	Exome; re-evaluation of previously obtained exome sequence	Used when reanalysis of prior exome data is performed to seek diagnoses missed on initial review.

Related Modifiers

8 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…
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…
62	Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…	- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…
78	CPT modifier -78 indicates an unplanned, related return to the operating or procedure room by the same provider during the global postoperative period. It is appended when treatment for a…	- Use modifier -78 when an unplanned, related complication during the original procedure’s global postoperative period requires the patient to return to a formal operating or procedure room and the…
80	CPT® Modifier 80 (Assistant Surgeon) is appended to a surgical CPT code when a physician (MD or DO) provides full, continuous assistance throughout the operative procedure. It is intended only for…	- Use CPT Modifier -80 when a physician (MD or DO) serves as an assistant surgeon and provides full, continuous assistance throughout the entire operative procedure; append -80 to the surgical CPT…
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…

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.
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
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…
207YX0905X	Otolaryngology/Facial Plastic Surgery Physician	An otolaryngologist who specializes in the diagnosis and surgical treatment of head and neck conditions.
363LP0808X	Psychiatric/Mental Health Nurse Practitioner	Physician Assistants & Advanced Practice Nursing Providers · Nurse Practitioner
152WL0500X	Low Vision Rehabilitation Optometrist	Optometrists who specialize in low-vision care having training to assess visual function, prescribe low-vision devices, develop treatment plans, and r…
225B00000X	Pulmonary Function Technologist	An individual who is trained and qualified to perform pulmonary diagnostic tests. In the course of conducting these tests, the Pulmonary Function Tec…

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 81465: Mitochondrial Genome Deletion Analysis

Sign up for cpt 81465 policy alerts

National Reimbursement Benchmarks

CPT 81465: Mitochondrial Genome Deletion Analysis

Sign up for cpt 81465 policy alerts

National Reimbursement Benchmarks

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related Codes

What does CPT 81465 cover and where is the testing usually performed?

Which clinicians order and interpret this mitochondrial genome analysis?

Which billing modifiers are relevant for CPT 81465 and when might they be used?

What reimbursement benchmarks are reported for CPT 81465?

Are there related CPT codes I should consider when 81465 is not appropriate?

References

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related Codes

What does CPT 81465 cover and where is the testing usually performed?

Which clinicians order and interpret this mitochondrial genome analysis?

Which billing modifiers are relevant for CPT 81465 and when might they be used?

What reimbursement benchmarks are reported for CPT 81465?

Are there related CPT codes I should consider when 81465 is not appropriate?

References