CPT code 81299: MSH6 testing, known familial variants2026 Medicare lab fee · Clinical Laboratory Fee Schedule
Targeted MSH6 testing checks for a previously identified familial variant, often to assess inherited Lynch syndrome risk in relatives.
Medicare pays $308.00 for 81299 under the 2026 Clinical Laboratory Fee Schedule: one national amount, the same in every state and setting.
Medicare lab fee · CLFS 2026 Q4
National CLFS amount
$308.00
In effect since Jan 1, 2026. The same amount in every state, payment locality and setting.
- Geographic adjustment
- None
- Office vs facility
- Same
- Since 2020
- Unchanged
- CMS updates
- Quarterly
Medicare pays the lesser of the lab’s charge and this amount. Patients usually owe no Part B deductible or coinsurance for covered clinical lab tests.
On this page 8 sections
What 81299 covers
This molecular genetic test examines MSH6 for a variant already identified in the family. MSH6 is one of the mismatch repair genes associated with Lynch syndrome, an inherited cancer predisposition. Clinicians may order targeted testing for relatives when a familial MSH6 variant is documented; the laboratory evaluates the patient’s DNA for that known variant rather than performing full-gene sequencing. Clinical molecular laboratories perform and report the analysis for ordering clinicians, including genetics and oncology providers.
Report 81299 for known familial MSH6 variant analysis, not for full MSH6 sequencing. The code is paid only through the CLFS, with one national amount across localities and no geographic or office/facility adjustment. The 2026 national CLFS amount is $308.00, unchanged since 2020. The physician fee schedule excludes this test by statute, so it is paid only from the CLFS.
This summary was written with AI assistance from CMS Clinical Laboratory Fee Schedule data. Amounts on this page come directly from CMS files.
How Medicare pays 81299
Clinical lab tests aren’t priced like physician services. They’re paid from their own fee schedule, with its own rules. See the whole lab fee schedule.
One national amount
CMS sets a single Clinical Laboratory Fee Schedule amount for 81299. There’s no geographic (GPCI) adjustment, so it pays the same in every state and payment locality.
No office or facility rate
Lab tests aren’t built from relative value units, so there’s no office and facility split: the place of service doesn’t change the CLFS amount.
Updated every quarter
CMS republishes the CLFS each quarter. New tests, often proprietary laboratory analyses (PLA codes), join during the year; existing amounts are updated each January.
Excluded from the physician fee schedule
The physician fee schedule lists 81299 with status X (excluded by statute), so the test itself is paid only from the CLFS.
81299 on the lab fee schedule since 2020
81299 · CLFS 2026 Q4 (current)
$308.00
Unchanged since Jan 1, 2020
27 quarterly CLFS releases on file, first CLFS 2020 Q1. A code missing from a quarter wasn’t on that release.
81299 compared with similar tests
- 81298MSH6 testingFull sequence analysis$641.85
- Choose 81299 for targeted testing of a previously identified familial MSH6 variant. Choose 81298 when the service is full MSH6 gene sequencing.
- 81296MSH2 testingKnown familial variants$337.73
- 81296 targets known familial MSH2 variants; 81299 targets known familial MSH6 variants. Select the code for the gene tested.
- 81297MSH2 analysisDuplication and deletion variants$213.30
- 81297 is MSH2 deletion/duplication analysis. It differs from 81299, which targets known familial variants in MSH6.
81299 billing questions
When should 81299 be chosen instead of 81298?
Use 81299 when testing for a known familial MSH6 variant. Code 81298 represents full MSH6 gene sequencing.
Does 81299 test all MSH6 variants?
No. It targets known familial variant(s); it is not the code for full-gene sequencing.
What should the documentation support?
The record should identify the familial MSH6 variant being tested and the clinical reason for targeted testing, such as evaluation of an at-risk relative.
How does Medicare price 81299?
CMS sets one national CLFS amount for the code. The payment is the same across states and localities, without geographic or office/facility adjustment.
Where this amount comes from
FeeBase reads lab amounts directly from the CMS Clinical Laboratory Fee Schedule file for the quarter: one row per code, with its payment indicator and national amount. Contractor-priced tests are labeled, never given a made-up amount. Amounts are Medicare payment limits, not a patient’s bill or a commercial rate.
CMS CLFS 2026 Q4 · effective Oct 1, 2026 through the day before Jan 1, 2027
Show the CMS file line behind this amount
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