CPT 81471: XLID Duplication and Deletion Gene Panel

Commercial payers pay $870 on average nationally for this procedure.

CPT code 81471 describes a laboratory genetic testing panel that evaluates a patient specimen for duplication and deletion mutations across at least 60 genes, including 15 genes associated with X-linked intellectual disability (XLID); this is a molecular diagnostic service typically performed by a clinical molecular genetics or cytogenetics laboratory and usually provided as a laboratory-based service in a clinical laboratory or reference lab setting.

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National Reimbursement Benchmarks

National commercial rates for CPT 81471 center around the BUCA average commercial rate of $870.40, with notable variation by insurer. Blue Cross Blue Shield presents a high mean and elevated 75th-percentile level suggesting upper-end pricing, while Cigna and UnitedHealth Group sit near the BUCA mean but with different skew: Cigna’s median and mean are closer together, whereas UnitedHealth Group’s median is lower than its mean. Aetna has a low mean and a very limited 90th-percentile presence relative to others, indicating less activity at higher price points.

Dispersion measured as P75–P25 highlights where rates are tight or wide: Blue Cross Blue Shield has a tight interquartile spread of $230.30 ($1,066.90–$834.60) versus Cigna’s wider spread of $738.90 ($1,207.90–$470.20). UnitedHealth Group shows moderate dispersion of $575.10 ($914.00–$383.90). BUCA’s interquartile spread is $323.80 ($912.80–$599.00). Aetna’s available percentiles are concentrated at lower values with P90 at $315.80, indicating limited upper-range variability.

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CPT 81471: XLID Duplication and Deletion Gene Panel

Commercial payers pay $870 on average nationally for this procedure.

Customize your policy alerts

Sign up for cpt 81471 policy alerts

Get alerted when payer policies referencing 81471 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 pediatric male or adult male with developmental delay, intellectual disability, or a family history suggesting X‑linked intellectual disability (XLID) is referred for comprehensive genetic testing. The ordering clinician (e.g., clinical geneticist, genetic counselor, or neurologist) collects a blood sample or saliva specimen and sends it to a molecular diagnostic laboratory. The lab performs a high‑resolution copy number and sequence‑level panel evaluating duplication and deletion mutations across at least 60 genes, including the 15 XLID genes specified in the test descriptor. Results are reported to the ordering provider, who reviews pathogenic or likely pathogenic copy number variants and deletions/duplications relevant to XLID; variants of uncertain significance are documented per laboratory policy. Results may guide cascade testing of family members, reproductive counseling, or targeted medical management. Typical sites of service include outpatient genetic clinics, hospital outpatient laboratories, and reference molecular diagnostic laboratories.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81436`	Targeted genomic sequence analysis panel covering at least five genes (e.g., MLH1, MSH2, EPCAM, SMAD4, STK11)	A smaller targeted panel CPT used for comparison in MolDX guidance; may be billed for narrower gene panels or when fewer genes are analyzed than for `81471`.

Related Modifiers

9 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…
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…
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…
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…

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.
207SC0300X	Clinical Cytogenetics Physician	A clinical cytogeneticist demonstrates competence in providing laboratory diagnostic and clinical interpretive services dealing with cellular componen…
207SG0202X	Clinical Biochemical Genetics Physician	A clinical biochemical geneticist demonstrates competence in performing and interpreting biochemical analyses relevant to the diagnosis and management…
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
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…
261QR0404X	Cardiac Rehabilitation Clinic/Center	Ambulatory Health Care Facilities · Clinic/Center
103G00000X	Clinical Neuropsychologist	A clinical psychologist who applies principles of assessment and intervention based upon the scientific study of human behavior as it relates to norma…
213EG0000X	Deactivated - Podiatrist

Related ICD-10-CM Codes

5 rows

ICD-10-CM Code	Description
Z15.01	Genetic susceptibility to malignant neoplasm of breast
Z13.79	Encounter for other screening for genetic and chromosomal anomalies
Z84.81	Family history of carrier of genetic disease
Z80.3	Family history of malignant neoplasm of breast
C50.919	Malignant neoplasm of unspecified site of unspecified female breast

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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Clinical & Coding Specifications

Clinical Context

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81436`	Targeted genomic sequence analysis panel covering at least five genes (e.g., MLH1, MSH2, EPCAM, SMAD4, STK11)	A smaller targeted panel CPT used for comparison in MolDX guidance; may be billed for narrower gene panels or when fewer genes are analyzed than for `81471`.

Related Modifiers

9 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…
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…
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…
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…

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.
207SC0300X	Clinical Cytogenetics Physician	A clinical cytogeneticist demonstrates competence in providing laboratory diagnostic and clinical interpretive services dealing with cellular componen…
207SG0202X	Clinical Biochemical Genetics Physician	A clinical biochemical geneticist demonstrates competence in performing and interpreting biochemical analyses relevant to the diagnosis and management…
207SG0203X	Clinical Molecular Genetics Physician	A clinical molecular geneticist demonstrates competence in performing and interpreting molecular analyses relevant to the diagnosis and management of …
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…
261QR0404X	Cardiac Rehabilitation Clinic/Center	Ambulatory Health Care Facilities · Clinic/Center
103G00000X	Clinical Neuropsychologist	A clinical psychologist who applies principles of assessment and intervention based upon the scientific study of human behavior as it relates to norma…
213EG0000X	Deactivated - Podiatrist

Related ICD-10-CM Codes

5 rows

ICD-10-CM Code	Description
Z15.01	Genetic susceptibility to malignant neoplasm of breast
Z13.79	Encounter for other screening for genetic and chromosomal anomalies
Z84.81	Family history of carrier of genetic disease
Z80.3	Family history of malignant neoplasm of breast
C50.919	Malignant neoplasm of unspecified site of unspecified female breast

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 81471: XLID Duplication and Deletion Gene Panel

Sign up for cpt 81471 policy alerts

National Reimbursement Benchmarks

CPT 81471: XLID Duplication and Deletion Gene Panel

Sign up for cpt 81471 policy alerts

National Reimbursement Benchmarks

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Codes

What clinical service does CPT 81471 represent and where is it typically performed?

Which billing modifiers are commonly used with CPT 81471 and when are they applied?

How do reimbursement rates for CPT 81471 vary across major payers?

Which patients and clinicians are typical candidates for this XLID duplication/deletion panel?

Are there related CPT or diagnosis codes to consider when billing or documenting 81471?

References

Clinical & Coding Specifications

Clinical Context

Related CPT Codes

Related Modifiers

Related Provider Taxonomies

Related ICD-10-CM Codes

Related Codes

What clinical service does CPT 81471 represent and where is it typically performed?

Which billing modifiers are commonly used with CPT 81471 and when are they applied?

How do reimbursement rates for CPT 81471 vary across major payers?

Which patients and clinicians are typical candidates for this XLID duplication/deletion panel?

Are there related CPT or diagnosis codes to consider when billing or documenting 81471?

References