CPT code 81240: F2 gene analysis, coverage and billing guide

CPT code 81240 bills F2 gene analysis for the 20210G>A variant, the inherited change behind prothrombin-linked clotting risk. Under MolDX LCD L36089, Medicare treats the test as non-covered for almost every patient it sees. One narrow pregnancy indication survives, and it pays a flat national rate of $65.69.

So the payer question gets settled before the specimen leaves the room. An order placed on clinical logic alone comes back denied, whatever the chart note says.

The sections below cover the descriptor, that one covered indication, the diagnosis codes clinicians attach, the flat fee schedule, and the denials worth heading off.

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Key takeaways

CPT code 81240 covers F2 gene analysis for one variant, 20210G>A, and no CPT code exists for a multi-gene thrombophilia panel

MolDX LCD L36089 is a non-coverage policy, so Medicare pays 81240 only for pregnant patients who meet one narrow exception

The Clinical Laboratory Fee Schedule sets a flat national rate of $65.69, with no locality adjustment and no facility differential

Missing MolDX lab registration, an excluded indication, and an unsigned ABN are the denials that show up most often

Practice management software like Pabau keeps the code, its diagnoses, the ABN and the authorization on one record, so claims leave complete

CPT code 81240 covers a single variant in the F2 gene

The American Medical Association defines the code as: F2 (prothrombin, coagulation factor II) (eg, hereditary hypercoagulability) gene analysis, 20210G>A variant. The test looks for the prothrombin G20210A mutation in the F2 gene. Carriers produce elevated prothrombin levels, which raises the risk of deep vein thrombosis and pulmonary embolism.

The code sits in the Tier 1 molecular pathology section of the CPT code set, and it describes one variant in one gene. There is no CPT code for a multi-gene hereditary thrombophilia panel. When a lab runs several thrombophilia markers together, each marker is reported on its own code.

Medicare covers CPT code 81240 for one patient group only

Medicare does not cover CPT code 81240 for most patients. MolDX Local Coverage Determination L36089 and its companion billing article A56899 set out a non-coverage policy. Palmetto GBA, Noridian and the other MolDX contractors administer it.

The LCD says so in its own words: This is a non-coverage policy. It then rules out testing for all risk factors, signs, symptoms, diseases, or conditions, including cardiovascular risk assessment, except for pregnant patients.

That exception is narrow. Testing is indicated for a pregnant patient with a personal history of VTE tied to a non-recurrent, transient risk factor. She must also not already be receiving anticoagulant prophylaxis. The decision below is the whole policy in one view, and a claim is sorted by it before medical necessity is ever read.

The pregnancy exception still denies on first submission

Even a claim that meets the exception denies initially. The LCD says these claims will deny per the policy, and that they should then be appealed with medical records supporting the necessity for testing. The appeal has to show how the result changed anticoagulant prophylaxis management for that patient.

Here is how that runs in practice. A pregnant patient has a prior DVT that followed surgery, and she is not on prophylaxis. Her hematologist orders the test, and a MolDX-registered lab submits the claim with Z86.718. The remittance returns CARC 96, non-covered charge, exactly as the policy predicts.

The appeal then goes out with three documents:

• The hematologist’s note stating the indication
• The surgical history that establishes the transient trigger
• The plan showing prophylaxis was started on the result

A practice that expects the first denial has those three ready on day one, instead of losing a cycle assembling them.

What the LCD rules out by name

Four scenarios are excluded outright, and each one is a common reason practices order this test:

• Asymptomatic screening: There is no Medicare benefit for assessing thrombosis risk in patients without signs or symptoms of disease
• Family-history screening: Testing asymptomatic people whose relatives have documented inherited thrombophilia is excluded in the same note
• Recurrent pregnancy loss: ACOG advises against thrombophilia testing after recurrent fetal loss or placental abruption, and the LCD follows that position
• MTHFR testing: CPT 81291 has no clinical utility in any clinical scenario according to the LCD. It is investigational and is not a Medicare benefit

The LCD also limits who can order. Only providers with board eligibility or certification in hematology/oncology, hematopathology, or coagulation disorders satisfy the reasonable and necessary criteria. An order from a general practitioner fails that test before the diagnosis code is even read.

MolDX registration comes before the first claim

Labs performing tests billed under MolDX LCDs must register those tests with the MolDX program before Medicare will reimburse them.

Registration is a one-time compliance step per lab, per test. An unregistered lab billing CPT code 81240 in a MolDX jurisdiction receives a systematic denial, so confirm the status with Palmetto GBA or Noridian first.

Registration on its own creates no coverage. A registered lab still receives a non-coverage denial outside the pregnancy exception.

No ICD-10 code makes CPT 81240 payable under Medicare

Every claim still needs at least one ICD-10-CM diagnosis code, yet none of them buys coverage here. Billing article A56899 publishes its ICD-10-CM medical necessity section as N/A, so no Medicare-approved diagnosis list exists for this code at all.

The codes below are the ones clinicians commonly attach to a thrombophilia order. They still carry weight on commercial claims and in the appeal record, and full definitions for each sit in our ICD-10-CM code library.

MolDX revises its policies, so check the current version of article A56899 before billing. For a Medicare patient, though, the more useful question is whether the pregnancy exception applies at all.

CPT code 81240 pays one flat rate in every locality

Medicare prices CPT code 81240 on the Clinical Laboratory Fee Schedule (CLFS), not the Physician Fee Schedule. Clinical diagnostic laboratory tests sit on the CLFS, and 81240 is one of them. The CY2026 Q3 CLFS public use file lists a single national rate of $65.69.

That rate does not move by locality. CLFS payment amounts are exempt from geographic adjustment under 42 U.S.C. 1395m-1(b)(4)(B), so no GPCI multiplier applies.

No facility versus non-facility split applies either, because CLFS pricing carries no practice expense RVUs. In the CMS relative value file, 81240 carries status indicator X, a statutory exclusion from the Physician Fee Schedule.

Treat the published amount as a ceiling rather than a quote. Medicare pays the lower of the billed charge or the fee schedule amount, so a charge set below the schedule is paid at the charge. Check the current quarterly file on the CMS Clinical Laboratory Fee Schedule files page before you set yours.

Practices running practice management software like Pabau submit 81240 through Claim.MD, our US clearinghouse partner. It reaches thousands of US payers and returns an electronic remittance advice automatically.

Compare that remittance against the published CLFS amount after adjudication. Because the rate is flat nationally, a difference points to a coverage or coding problem rather than a locality adjustment.

Which codes travel with 81240 on a thrombophilia workup

Thrombophilia workups rarely test one variant in isolation. Clinicians commonly order Factor II analysis alongside Factor V Leiden and MTHFR testing in the same encounter. Each of those has its own code, and knowing how they interact with CPT code 81240 heads off duplicate-billing denials.

CPT 81240 and CPT 81241 are commonly ordered together as a two-marker screen. Current Correct Coding Initiative (CCI) guidance does not bundle them against each other. Report both on the same date of service, with medical necessity documented for each. For Medicare, both sit under the same non-coverage rule.

Adding CPT 81291 is a separate problem. The LCD states that MTHFR genotyping has no clinical utility in any clinical scenario. That line will not be paid, and it invites a closer look at the rest of the claim.

What the chart note needs before you bill CPT code 81240

Documentation is the one variable a practice fully controls here. A claim denied for missing documentation cannot be argued on clinical grounds afterwards, because the record either supports medical necessity or it does not.

Run this list before the order is placed, not after the denial lands:

• Clinical indication: Document the reason for the order, the date of any prior thrombotic event, and whether a transient risk factor was involved
• Ordering provider note: The note must reference the indication, not just the test name. “Thrombophilia panel ordered” is insufficient
• Ordering provider qualification: LCD L36089 limits reasonable and necessary testing to hematology/oncology, hematopathology, or coagulation disorders specialists
• Patient history: Include relevant personal and family history, prior diagnostic results, and any earlier thrombotic events with dates
• ICD-10 linkage: Each diagnosis code on the claim must be explicitly supported by the clinical note, not inferred
• MolDX registration: Labs in MolDX-contracted jurisdictions confirm the test is registered before the claim is submitted
• ABN on file: A Medicare patient outside the pregnancy exception signs an advance beneficiary notice before the specimen is collected
• Superbill accuracy: Check that the CPT-to-ICD-10 pairing on the superbill matches the documented indication

Commercial requirements overlap with Medicare’s and then add plan-specific items. Many insurers require prior authorization for molecular genetic tests ordered in an outpatient setting. Confirm eligibility and authorization status before the specimen is collected, because the lab cannot unrun a test that the payer later refuses.

Where CPT code 81240 claims go wrong most often

This code denies more often than most molecular pathology codes, because Medicare starts from non-coverage instead of from medical necessity. Billing teams that recognize the patterns stop most of them at submission.

The triggers below come from applying denial management practice to molecular code billing:

• Non-covered indication: Test ordered for screening, family history, recurrent pregnancy loss, or cardiovascular risk assessment. LCD L36089 rules each one out by name
• Missing ICD-10 linkage: Claim submitted without a diagnosis code that matches the documented indication. No MolDX covered-code list exists for 81240, so the linkage has to hold up on review
• No ABN on file: A Medicare patient billed for a service the policy already treats as non-covered, with nothing signed to support patient responsibility
• Unregistered lab: A lab submitting under MolDX jurisdiction has not registered CPT code 81240, which produces a systematic denial at the MAC level
• Unqualified ordering provider: Order placed by a clinician outside the specialties the LCD names, which fails the reasonable and necessary test
• Wrong panel code: Billing 81443 as though it were a thrombophilia panel. It describes an unrelated group of severe inherited conditions
• Missing prior authorization: Commercial payers requiring PA for outpatient molecular tests, with no valid authorization number on the claim

The remittance names the category for you. Expect CARC 96, non-covered charge, on this code. CARC 50 marks a service the payer does not deem medically necessary, and CARC 29 means the filing deadline passed. Each one leads to a different appeal, and only one of them is worth appealing quickly.

Claims tracking software earns its place by routing each denial to the right correction workflow. Teams that track denial categories by CPT code spot a systemic problem faster than teams working denials one at a time.

Commercial plans are where CPT code 81240 gets paid

Most of the revenue on this test comes from commercial plans. Many major insurers cover it once their own clinical criteria are met, and those criteria run broader than Medicare’s. Thresholds, required documentation and authorization steps then differ from one plan to the next.

Blue Cross Blue Shield of Mississippi, for example, covers genetic testing for inherited thrombophilia, including the prothrombin G20210A mutation. Its criteria include a personal or family history of thromboembolism. Other BCBS affiliates operate independently and may apply different criteria.

Each commercial plan publishes its own medical policy, and those policies are not synchronized across parent brands. A claim approved by BCBS Illinois may be denied by BCBS Texas on the same code and indication. So verify coverage at plan level, never at carrier brand level. Four checks before ordering:

• Confirm the specific plan’s medical policy for thrombophilia genetic testing, not just the parent brand’s general policy
• Check whether prior authorization is required, and obtain it before specimen collection
• Confirm that the ordered indication matches that plan’s covered criteria
• Record the prior authorization number on the claim form

How Pabau supports billing for genetic tests like CPT code 81240

A test that Medicare denies by default puts the weight on the front end of the billing process. Handled manually, that means checking the payer policy, chasing the prior authorization, collecting an ABN signature, then rekeying the same details into a claim form.

Practice management software like Pabau keeps that work on one record. The CPT code, its paired ICD-10 diagnoses, the ABN and the authorization reference sit on the same patient file the clinician documented in. That data then carries through to the claim without a second entry.

Denials come back categorized, so a billing team can see when L36089 non-coverage is driving a run of rejections on one code. That pattern is the cue to move those orders onto an ABN or a commercial authorization before the next specimen is collected. Staff then spend their time on the claims that can still be rescued.

Streamline genetic test billing from order to payment

Pabau’s claims management module supports CPT code entry, payer rule configuration, and claim status tracking. Your billing team spends less time chasing denials and more time on patient care.

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Conclusion

CPT code 81240 is a simple code with a hard rule behind it, and the rule is settled before the claim is built. Decide the payer path at the point of order. A Medicare patient outside the pregnancy exception needs a signed ABN, and a commercial patient needs an authorization number on file.

Get those two steps right and the flat $65.69 rate stops mattering much. The claim either pays, or it converts cleanly to patient or plan responsibility. Skip them and the test still runs, with no one left to bill. That is the trade worth remembering on every genetic order.

Pabau keeps the ABN, the authorization and the coded order on one patient record. The decision you made at the point of order is still attached when the claim goes out. Book a demo to see how your team would bill a non-covered genetic test in Pabau.

Continue your research

Need the full picture of how a claim moves? Medical billing fundamentals walks the lifecycle from code entry through remittance reconciliation.

Working a run of rejections on one code? Denial management in healthcare covers how to categorize, appeal and prevent the denial types molecular codes attract.

Billing a genetic test with no specific CPT code? 81479 explains how unlisted molecular pathology claims are priced and documented.

Confusing the gene test with the clotting test? 85610 covers prothrombin time billing, which is a different service on a different fee schedule line.

Chasing authorizations before collection? Insurance eligibility verification sets out the checks that keep a molecular test from being run against a plan that will not pay.

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