Genetic Testing Colon Cancer Inherited Risk
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Defines medical necessity, coverage criteria, prior authorization, and limitations for genetic testing to evaluate inherited colorectal cancer syndromes for Aloha Care members (QUEST Integration Medicaid & Medicare).
No material clinical or coverage changes in this revision.
Coverage Criteria for Genetic Testing
Lynch syndrome
Genetic testing for Lynch Syndrome (MLH1, MSH2, MSH6, PMS2, EPCAM) is covered when ANY of the following family or personal history criteria are met:
APC (FAP/AFAP)
Genetic testing for APC (FAP/AFAP) is covered when ANY of the following are met:
MUTYH (MAP)
Genetic testing for MUTYH (MUTYH-associated polyposis, MAP) is covered when ANY of the following are met:
Not Medically Necessary
Not medically necessary when any of the following apply:
Prior authorization is required for genetic testing for inherited colorectal cancer risk. Testing is covered only when results are expected to change clinical management and improve health outcomes. Coverage for Lynch syndrome testing includes targeted analysis of MLH1, MSH2, MSH6, PMS2, and EPCAM when the enumerated personal or family history criteria or a model-predicted risk threshold are met. Testing must be performed in laboratories with CLIA and CAP certification.
Genetic testing for APC (FAP/AFAP) is covered when any of the policy-specified criteria are met, including a personal history of ≥10 adenomas, a history of associated extracolonic findings (for example desmoid tumor or hepatoblastoma), or a close relative with a confirmed diagnosis of FAP/AFAP. MUTYH testing is covered for indicated scenarios such as ≥10 adenomas with normal APC testing or when a known deleterious MUTYH variant exists in a close relative. Repeat testing is limited to once in a lifetime unless clear documentation justifies a repeat (e.g., disease recurrence or change in disease behavior).
The policy lists specific items considered not medically necessary. These include: genetic screening of the general population; APC testing solely to confirm classical FAP; testing other genes for hereditary colorectal cancer outside the named indications; testing unaffected relatives when affected-family-member testing fails to identify a pathogenic variant; MMR tumor sequencing when MSI and/or IHC are normal; additional redundant MMR testing; testing individuals under age 18 without documented adolescent-onset risk; multigene panels unless every included gene has demonstrated clinical utility for the individual; carrier-status testing without documented pretest genetic counseling; genetic testing in patients with FCCXS; and any other indication not otherwise specified.
Not Medically Necessary conditions are explicitly enumerated in the policy under the Limitations section. Refer to that list when assessing coverage for indications outside the policy’s covered criteria.
Specific Covered Indications
Evaluation for Lynch syndrome, FAP/AFAP (APC), and MUTYH-associated polyposis when specified personal or family history criteria or model-predicted risk thresholds are met.
Evaluation for Lynch syndrome, FAP/AFAP (APC), and MUTYH-associated polyposis is covered when specified personal or family history criteria or validated model-predicted risk thresholds are met:
Refer to earlier sections (not present in this window) for covered clinical indications; this window contains the policy's limitations and not-medically-necessary list only.
Refer to earlier sections of the policy for the full list of covered clinical indications; the current window contains the policy's limitations and not-medically-necessary list.
Eligibility Requirements
No additional eligibility top-level requirements are specified in this section.
No additional eligibility top-level requirements are specified in this section.
No additional eligibility top-level requirements are specified in this section.
No additional eligibility top-level requirements are specified in this section.
Provider Actions and Documentation Requirements
Prior authorization required
Prior authorization is required for genetic testing; testing is covered only when results will change clinical management. Medicare referrals should follow the referenced Local Coverage Determination (LCD L36370).
- Testing must be clinically indicated — results must be expected to change management
Relevant CPT / panel codes
Use the CPT/Panel codes listed in the policy when requesting authorization or submitting claims; examples include single-gene and panel codes such as 81201, 81202, 81294–81301, 81317–81319, 81401, 81406, 81435, and 81436. Prior authorization may be required per payer practice for these tests.
Genetic counseling visits covered for specified histories
One pre-test genetic counseling visit and one post-test genetic counseling visit are covered for members with family history of FAP, known APC mutation, Lynch syndrome–associated cancer, or a personal history of features of FAP or Lynch syndromes; document these visits when submitting for coverage.
- Cover one pre-test and one post-test genetic counseling visit for the listed family/personal history indications
Order testing per clinical guidelines
Policy references clinical practice guidelines (e.g., NCCN, ASCO) for appropriate ordering of genetic testing; follow guideline-based indications when requesting authorization.
- Order tests consistent with cited guidelines to support medical necessity
Document need for repeat testing
Requests for repeat genetic testing must include documentation demonstrating medical need (examples: recurrence of disease or a change in disease behavior); testing for colon cancer risk is considered a once‑in‑a‑lifetime test unless justified.
- Repeat testing requires clear documentation of need (e.g., disease recurrence or change in behavior)
- Policy states testing is once in a lifetime unless justified
Justify repeat test requests
Include a clear clinical justification when requesting repeat testing — for example, documented recurrence of disease or a change in disease behavior that would alter management.
- Justification must be specific and linked to management change to be considered medically necessary
Require pretest genetic counseling documentation for carrier testing
For carrier-status testing, include documentation of pretest genetic counseling; absence of pretest counseling documentation is listed as not medically necessary.
- Pretest genetic counseling documentation must be present when submitting carrier status testing requests
Prior authorization and medical necessity — denial risk
Prior authorization is required and testing is covered only when results will change clinical management; tests that do not meet covered indications or are listed as not medically necessary may be denied.
- Ensure indication meets the policy’s covered criteria to avoid denial
Denial risk for undocumented repeat testing
Requests for repeat testing that lack clear documentation of clinical need (e.g., recurrence or change in disease behavior) may be denied.
- Provide explicit clinical documentation to support repeat testing requests
Laboratory certification required (CLIA & CAP)
Testing must be performed in laboratories with CLIA and CAP certifications; tests performed in laboratories lacking these certifications risk denial.
- Verify the performing laboratory has CLIA and CAP certification before submitting claims or authorization requests
Document genetic counseling visits for covered indications
Document pre-test and post-test genetic counseling visits when applicable; one pre-test and one post-test counseling visit are covered for family history of FAP, APC mutation, Lynch syndrome–associated cancer, or personal history of syndrome features.
- Document counseling encounters in the medical record and include them in the authorization/claim documentation
Pretest counseling required for carrier testing (duplicate)
Pretest genetic counseling documentation is required for carrier-status testing; absence of documentation is listed as not medically necessary and may result in denial.
- Include evidence of counseling in requests for carrier testing
Pretest counseling required (duplicate)
Pretest genetic counseling documentation is required for carrier-status testing; ensure counseling is documented before requesting coverage.
- Failure to document pretest counseling is a listed not‑medically‑necessary condition
Prior authorization and expected genetic counseling
Prior authorization is required; genetic counseling (pre- and post-test) is expected for covered indications and should be documented when submitting authorization requests.
- Include counseling documentation with prior authorization submissions
Repeat testing: documentation requirement and denial risk
Requests for repeat testing must include clear documentation of the need (e.g., recurrence of disease or change in disease behavior); without such documentation requests may be denied.
- Testing is generally once in a lifetime; show why repeat testing is medically necessary
Coding and Billing
| 81201 | APC (adenomatous polyposis coli) (eg, familial adenomatosis polyposis [FAP], attenuated FAP) gene analysis; full gene sequence. |
| 81202 | APC (adenomatous polyposis coli) (eg, familial adenomatosis polyposis [FAP], attenuated FAP) gene analysis; known familial variants. |
| 81294 | MLH1 (mutL homolog 1) gene analysis; promoter methylation analysis / duplication/deletion variants. |
| 81295 | MSH2 (mutS homolog 2) gene analysis; full sequence analysis. |
| 81296 | MSH2 (mutS homolog 2) gene analysis; known familial variants. |
| 81297 | MSH2 (mutS homolog 2) gene analysis; duplication/deletion variants. |
| 81298 | MSH6 (mutS homolog 6) gene analysis; full sequence analysis. |
| 81299 | MSH6 (mutS homolog 6) gene analysis; known familial variants. |
| 81300 | MSH6 (mutS homolog 6) gene analysis; duplication/deletion variants. |
| 81301 | Microsatellite instability analysis (eg., markers for mismatch repair deficiency; includes comparison of neoplastic and normal tissue, if performed). |
Not Covered / Not Medically Necessary
Multigene panels are considered not covered unless every gene in the panel has demonstrated clinical utility for the individual being tested. Genetic testing in patients with FCCXS, population screening of unaffected individuals, and other listed redundant or confirmatory tests are also not covered per the policy’s Limitations section.
See the policy’s Not Medically Necessary list for specific non-covered indications, including population screening, APC testing solely to confirm classical FAP, and multigene panels when per-gene clinical utility is not established.
Definitions and Guideline Criteria
Background
Colorectal cancer (CRC) is a common malignancy; the majority of cases are sporadic, with an estimated 5-6% of CRC attributable to hereditary syndromes. Lynch syndrome is the most common hereditary form, accounting for approximately 2-3% of CRC, and is caused by pathogenic variants in mismatch repair genes (MLH1, MSH2, MSH6, PMS2) or EPCAM leading to microsatellite instability. Other inherited syndromes include FAP/AFAP (APC) and MUTYH-associated polyposis (MAP).
Revision History
Policy MP-09 (Genetic Testing Colon Cancer Inherited Risk) became effective.
Policy MP-09 was last revised/reviewed on this date (document header lists Last revised 2020-12-01).
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