Summary & Overview
CPT 81471: Genomic Sequencing for X-Linked Intellectual Disability
CPT code 81471 represents a comprehensive genomic sequencing procedure for X-linked intellectual disability (XLID), encompassing both syndromic and non-syndromic presentations. This test involves duplication and deletion analysis across a panel of at least 60 genes, including key genes such as ARX, ATRX, CDKL5, FGD1, FMR1, and others. The procedure is classified under Genomic Sequencing Procedures and Other Molecular Multianalyte Assays and is most commonly performed in an office setting.
Major national payers, including Aetna, Blue Cross Blue Shield, Cigna Health, and UnitedHealthcare, are covered in this analysis. Readers will gain insight into payer coverage policies, relevant clinical indications, and billing considerations for CPT 81471. The publication also provides context on associated ICD-10 diagnoses, common modifiers used in Medicare billing, and related CPT codes for comparison. Benchmarks and policy updates are included to inform stakeholders about current trends in coverage and utilization.
This summary offers a clear overview of the clinical and billing landscape for CPT 81471, highlighting its importance in the diagnosis and management of XLID. The information is designed to support healthcare professionals, billing specialists, and policy analysts in understanding the scope and implications of this genomic testing procedure.
CPT Code Overview
CPT 81471 is used for genomic sequencing procedures targeting X-linked intellectual disability (XLID), including both syndromic and non-syndromic forms. This code covers duplication and deletion gene analysis and requires the examination of at least 60 genes, such as ARX, ATRX, CDKL5, FGD1, FMR1, HUWE1, IL1RAPL, KDM5C, L1CAM, MECP2, MED12, MID1, OCRL, RPS6KA3, and SLC16A2. The service type is Genomic Sequencing Procedures and Other Molecular Multianalyte Assays, typically performed in an office setting (POS 11).
Clinical & Coding Specifications
Clinical Context
A male pediatric patient presents to a genetics clinic with developmental delays, intellectual disability, and a family history suggestive of X-linked inheritance. The clinical workflow involves a medical geneticist evaluating the patient, obtaining a detailed family history, and recommending genomic sequencing to identify potential duplications or deletions in genes associated with X-linked intellectual disability. The procedure is performed in an office setting (Place of Service 11), and the results are used to guide further management, genetic counseling, and risk assessment for family members.
Coding Specifications
-
Modifiers:
GX: Used when a provider attests that a service is statutorily excluded or does not meet the definition of any Medicare benefit.GY: Used when a service is statutorily excluded from Medicare coverage or is not a Medicare benefit.
-
Provider Taxonomies:
| Taxonomy Code | Specialty Name |
|---|---|
207SG0201X | Medical Genetics, Ph.D. Medical Genetics |
207SC0300X | Medical Genetics, Clinical Genetics (M.D.) |
207SG0202X | Medical Genetics, Clinical Biochemical Genetics |
207SG0203X | Medical Genetics, Clinical Cytogenetics |
207SG0205X | Medical Genetics, Clinical Molecular Genetics |
These taxonomies represent providers specializing in medical genetics, including clinical, biochemical, cytogenetic, and molecular genetics.
Related Diagnoses
-
Z15.01: Genetic susceptibility to malignant neoplasm of breast- Relevant for patients with a family history or genetic risk factors for breast cancer, which may be considered in broader genetic testing scenarios.
-
C50.919: Malignant neoplasm of unspecified site of unspecified female breast- Used when a patient has a diagnosis of breast cancer, potentially relevant if genetic testing is performed for risk assessment.
-
Z80.3: Family history of malignant neoplasm of breast- Indicates a family history of breast cancer, supporting the need for genetic evaluation.
-
Z84.81: Family history of carrier of genetic disease- Supports genetic testing when there is a known family history of genetic disease, relevant for X-linked intellectual disability.
-
Z13.79: Encounter for other screening for genetic and chromosomal anomalies- Used for patients undergoing screening for genetic or chromosomal anomalies, directly relevant to the use of
81471for X-linked intellectual disability.
- Used for patients undergoing screening for genetic or chromosomal anomalies, directly relevant to the use of
Related CPT Codes
81436: Targeted genomic sequence analysis panel covering at least five genes (e.g., MLH1, MSH2, EPCAM, SMAD4, STK11) used for comparison in MolDX guidance.
81436 is related to 81471 as both are genomic sequencing procedures. 81436 is typically used for targeted panels involving fewer genes, while 81471 is used for broader panels specifically for X-linked intellectual disability, requiring analysis of at least 60 genes. These codes may be used as alternatives depending on the clinical indication and payer guidance. They are not commonly billed together but may be referenced in MolDX policy comparisons.
National Reimbursement Benchmarks
National mean rates for CPT code 81471 show that BUCA (average commercial) payers reimburse at $679.11, which is substantially higher than Aetna's mean rate of $208.92. Blue Cross Blue Shield, Cigna, and UnitedHealth Group all have mean rates above $650, with Blue Cross Blue Shield leading at $835.93.
Rate dispersion varies significantly across payers. Blue Cross Blue Shield has a relatively tight range between the 25th and 75th percentiles ($274.00), while Cigna exhibits the widest spread ($752.00), indicating greater variability in contracted rates. Aetna's percentiles are all at $0.00, suggesting limited or no contracted rates for this code nationally.
The table and chart below present a detailed breakdown of national mean rates and percentile values for each payer.
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.