CPT code 81460: Mitochondrial genome, complete genome with heteroplasmy2026 Medicare lab fee · Clinical Laboratory Fee Schedule
Whole mitochondrial genome sequencing with heteroplasmy detection is reported when clinicians evaluate suspected mitochondrial disorders such as MELAS or Leigh syndrome.
Medicare pays $1,287.00 for 81460 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
$1,287.00
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 81460 covers
81460 is used for analysis of the entire mitochondrial genome, including detection of heteroplasmy. Clinicians may order the test when evaluating suspected mitochondrial disorders such as Leigh syndrome, MELAS, MERRF, NARP, or LHON. A molecular laboratory performs and reports the sequencing; the code represents whole-genome analysis rather than testing only selected mitochondrial genes. The analysis can identify mitochondrial genomic variants associated with these disorders.
Report 81460 for entire-genome sequence analysis with heteroplasmy detection. Medicare pays it through the CLFS at one national amount: $1,287.00 in 2026, unchanged since 2020. The same amount applies in every locality, with no geographic or office-versus-facility adjustment. The physician fee schedule excludes the test by statute; Medicare payment is through 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 81460
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 81460. 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 81460 with status X (excluded by statute), so the test itself is paid only from the CLFS.
81460 on the lab fee schedule since 2020
81460 · CLFS 2026 Q4 (current)
$1,287.00
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.
81460 compared with similar tests
- 81440Mitochondrial gene panelAt least 100 nuclear genes$3,324.00
- 81440 is identified as mitochondrial gene testing. 81460 represents sequencing the entire mitochondrial genome with heteroplasmy detection.
- 81465Mitochondrial genomeLarge deletion analysis$936.00
- 81465 is also labeled for whole mitochondrial genome testing. 81460 specifically represents entire-genome sequence analysis with heteroplasmy detection; select the code that matches the performed assay.
- 81479Molecular pathologyUnlisted procedureNo national amount
- 81479 is an unlisted molecular pathology code. Use 81460 when the assay performed matches its specific whole-genome sequencing service.
81460 billing questions
When should 81460 be selected instead of 81440?
81460 represents sequencing of the entire mitochondrial genome with heteroplasmy detection. 81440 is identified as mitochondrial gene testing.
What should the laboratory report support?
The report should support analysis of the entire mitochondrial genome with heteroplasmy detection. Testing only selected mitochondrial genes is a different scope of service.
Is modifier 26 appropriate for 81460?
81460 is paid only through the CLFS; the physician fee schedule lists the test as excluded by statute.
How does Medicare pay for 81460?
Medicare pays 81460 through the CLFS at one national amount, with the same payment across localities and no office-versus-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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