CPT 81244 FMR1 Characterization Reimbursement | OpenPayer

Summary & Overview

CPT 81244: FMR1 Gene Characterization, Molecular Testing

CPT code 81244 is the Current Procedural Terminology (CPT) designation for the technical laboratory assay that characterizes changes in the FMR1 gene, typically to further define expanded alleles or determine methylation status following detection of an abnormality. This molecular diagnostic procedure informs clinical interpretation of fragile X-associated conditions and can affect genetic counseling and care planning at a national level.

Key payers covered in this overview include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise explanation of the clinical purpose and service setting for CPT code 81244, plus an outline of what to expect in payer coverage discussions, common billing modifiers, and where this code fits within molecular genetics service lines. The publication provides benchmarks for utilization and billing patterns, highlights relevant policy updates affecting molecular genetic testing reimbursement, and situates CPT 81244 within clinical workflows for laboratories and ordering clinicians. Practical context is provided for payers and providers considering claims submission, medical necessity review, and the sequencing of follow-up testing after initial FMR1 screening.

AetnaBlue Cross Blue ShieldCigna HealthUnitedHealthcareMedicareCPT 81244FMR1molecular genetic testingfragile Xlaboratory servicesgenetic diagnosticstechnical componentmethylation testingclinical laboratory

Billing Code Overview

CPT code 81244 describes a technical laboratory assay to characterize changes in the FMR1 (fragile X messenger ribonucleoprotein 1) gene, most commonly used to further define expanded alleles or assess methylation status after an initial abnormal result. The service involves laboratory analysis and reporting of molecular findings that clarify the nature of FMR1 expansions.

Service type: Molecular genetic testing (technical component) focused on FMR1 characterization
Typical site of service: Clinical laboratory or hospital laboratory performing specialized molecular diagnostics

Data not available in the input.

Clinical & Coding Specifications

Clinical Context

A pediatric or adult patient with a personal or family history suggestive of fragile X syndrome, intellectual developmental disorder, autism spectrum disorder, or unexplained developmental delay is referred for molecular characterization of the FMR1 gene. Initial screening (e.g., PCR or CGG repeat sizing) has identified an abnormality such as an expanded allele, mosaicism, or ambiguous repeat sizing. The laboratory performs 81244 to further characterize the FMR1 allele — typically to define the size of expanded alleles, determine methylation status, and resolve borderline or complex results. Specimens are most often peripheral whole blood collected in EDTA tubes and sent to a reference molecular genetics laboratory. Typical sites of service include outpatient genetics clinics, pediatric neurology practices, maternal-fetal medicine clinics, and specialized molecular diagnostic laboratories. The clinical workflow: clinician orders FMR1 reflex or follow-up testing after an initial abnormal screen; specimen is transported to the lab; a molecular technologist performs specialized testing (Southern blot, methylation-sensitive PCR, or other appropriate methods) to characterize expansions and methylation; the laboratory analyst documents technical results and the laboratory director signs out the report. Results guide genetic counseling, reproductive planning, and management of developmental or neurobehavioral conditions.

Coding Specifications

Modifier	Description	When to Use
`26`

Related Codes

CPT-81247-G6PD-GENE-VARIANT-ANALYSIS

CPT 81247: G6PD Gene Variant Analysis

CPT-81240-PROTHROMBIN-F2-GENE-VARIANT-TESTING

CPT 81240: Prothrombin (F2) Gene Variant Testing

CPT-81279-JAK2-GENE-SEQUENCING-EXONS-12-13

CPT 81279: JAK2 Gene Sequencing for Exons 12 and 13

CPT-81173-ANDROGEN-RECEPTOR-AR-GENE-SEQUENCING

CPT 81173: Androgen Receptor (AR) Gene Full-Gene Sequencing

CPT-81267-POST-TRANSPLANT-CHIMERISM-STR-ANALYSIS

CPT 81267: Post‑Transplant STR Chimerism (Engraftment) Analysis

CPT-81316-PML-RARA-FUSION-GENE-DETECTION

CPT 81316: PML/RARα (t(15;17)) Fusion Gene Detection

CPT-81286-FRATAXIN-FXN-GENE-SEQUENCING

CPT 81286: Full Sequencing of the Frataxin (FXN) Gene

CPT-81179-ATXN2-REPEAT-EXPANSION-TESTING

CPT 81179: ATXN2 (Ataxin 2) Repeat Expansion Testing

CPT-81252-GJB2-FULL-GENE-SEQUENCING

CPT 81252: Full Gene Sequencing of GJB2 (Connexin 26)

CPT-81352-TP53-TARGETED-SEQUENCING-LI-FRAUMENI

CPT 81352: Targeted TP53 Gene Sequencing for Li–Fraumeni Syndrome

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Taxonomy Code	Specialty	Notes
`207RG0100X`	Clinical Molecular Genetics Laboratory	Laboratory specialty performing FMR1 molecular testing.
`208000000X`	Clinical Laboratory	General clinical laboratory services performing technical testing.
`207LH0000X`	Cytogenetic and Molecular Genetics	Specialty for laboratories and clinicians providing genetic testing and interpretation.
`2084P0800X`	Pediatric Neurology	Ordering clinicians who commonly request FMR1 characterization.
`207K00000X`	Medical Genetics	Clinical geneticists providing interpretation and counseling related to FMR1 results.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`Q99.2`	Fragile X syndrome	Direct indication for FMR1 molecular characterization to confirm diagnosis and allele status.
`F84.0`	Autism spectrum disorder	FMR1 testing is indicated in some cases of autism to evaluate fragile X as an underlying cause.
`F79`	Intellectual developmental disorder, unspecified	Unexplained intellectual disability often prompts FMR1 testing to assess for fragile X.
`R62.0`	Delayed milestone in childhood	Developmental delays can trigger genetic testing including FMR1 characterization.
`Z13.79`	Encounter for screening for other genetic and chromosomal anomalies	Used when screening or cascade testing for family members is performed involving FMR1 testing.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81242`	Fragile X mental retardation 1 (FMR1) gene; detection of CGG repeat expansions, common allele sizing	Often performed as initial screening or repeat sizing before `81244` when an expanded allele is suspected.
`81243`	Fragile X mental retardation 1 (FMR1) gene; methylation analysis	Performed alongside or prior to `81244` to assess methylation status; `81244` further characterizes complex or expanded alleles.
`81479`	Unlisted molecular pathology procedure	Used when a specific molecular characterization falls outside established CPT codes; rarely used if `81244` does not fully capture the method.
`88271`	Preparatory procedures for molecular cytogenetic analysis (e.g., Southern blot preparation)	Lab technical steps such as DNA preparation or Southern blotting may be billed with preparatory specimen processing codes in complex workflows.
`0000U`	Proprietary or emerging genomic test (example code)	Some labs use proprietary test codes for specialized FMR1 assays; these may be ordered in conjunction with `81244` depending on methodology.