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Official Description

MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; promoter methylation analysis

© Copyright 2025 American Medical Association. All rights reserved.

Common Language Description

The CPT® Code 81288 refers to a specific laboratory test that analyzes the MLH1 gene, which is crucial in understanding certain types of colorectal cancer, particularly hereditary nonpolyposis colorectal cancer (HNPCC), also known as Lynch syndrome. This genetic condition is inherited in an autosomal dominant manner, meaning that a mutation in just one copy of the gene can increase an individual's risk of developing various cancers, especially in the colon and rectum, as well as benign polyps. The MLH1 gene, located on chromosome 3, plays a vital role in the DNA mismatch repair system. When mutations occur in this gene, the body's ability to correct errors that arise during DNA replication is compromised, leading to an increased likelihood of tumor formation. The test is specifically performed on tumor tissue when the detection of a BRAF codon 600 mutation is negative. This distinction is important as it helps differentiate between tumors associated with Lynch syndrome and those that are sporadic, which may also exhibit loss of the MLH1 gene. The process involves obtaining tumor tissue through a surgical or biopsy procedure, which must be reported separately. Once the sample is collected, it is fixed in paraffin and subjected to qualitative real-time polymerase chain reaction (PCR) for promoter methylation analysis. This method allows for the detection of methylation changes in the promoter region of the MLH1 gene, which can indicate whether the gene is silenced in the tumor, further aiding in the diagnosis and management of colorectal cancer associated with Lynch syndrome.

© Copyright 2025 Coding Ahead. All rights reserved.

1. Indications

The MLH1 gene analysis, as indicated by CPT® Code 81288, is performed under specific circumstances to aid in the diagnosis of hereditary nonpolyposis colorectal cancer (Lynch syndrome) versus sporadic tumors. The following conditions warrant this genetic testing:

  • Negative BRAF Codon 600 Mutation Detection - The test is indicated when previous testing for the BRAF codon 600 mutation has returned negative results, necessitating further analysis to distinguish the tumor's origin.
  • Suspicion of Lynch Syndrome - Patients with a family history of colorectal cancer or related cancers may be tested to determine if they have Lynch syndrome, which significantly increases their cancer risk.
  • Loss of MLH1 Gene Expression - The presence of tumors exhibiting loss of MLH1 gene expression may prompt this analysis to confirm whether the loss is due to hereditary factors or sporadic mutations.

2. Procedure

The procedure for conducting the MLH1 gene analysis involves several critical steps to ensure accurate results. The following outlines the detailed procedural steps:

  • Step 1: Tumor Tissue Collection - The first step involves obtaining tumor tissue from the patient. This is typically done through a surgical procedure or biopsy, which must be reported separately. The collected tissue is essential for the subsequent analysis.
  • Step 2: Tissue Fixation - Once the tumor tissue is collected, it is fixed in paraffin. This fixation process preserves the tissue and allows for the preparation of thin sections that can be analyzed in the laboratory.
  • Step 3: Qualitative Real-Time PCR - The fixed tissue is then subjected to qualitative real-time polymerase chain reaction (PCR). This technique amplifies specific DNA sequences, allowing for the detection of methylation patterns in the MLH1 gene's promoter region.
  • Step 4: Promoter Methylation Analysis - The final step involves analyzing the PCR results to determine the methylation status of the MLH1 gene promoter. This analysis helps in identifying whether the gene is silenced, which is a critical factor in diagnosing Lynch syndrome versus sporadic tumors.

3. Post-Procedure

After the MLH1 gene analysis is completed, the results are interpreted by a qualified healthcare professional. The findings can provide crucial information regarding the patient's risk for Lynch syndrome and guide further management and surveillance strategies. Patients may require genetic counseling to understand the implications of the test results, especially if a hereditary condition is identified. Additionally, ongoing monitoring for colorectal cancer and related malignancies may be recommended based on the results of the analysis. It is essential for healthcare providers to discuss the results with the patient and their family, considering the potential impact on family members who may also be at risk.

Short Descr MLH1 GENE
Medium Descr MLH1 GENE ANALYSIS PROMOTER METHYLATION ANALYSIS
Long Descr MLH1 (mutL homolog 1, colon cancer, nonpolyposis type 2) (eg, hereditary non-polyposis colorectal cancer, Lynch syndrome) gene analysis; promoter methylation analysis
Status Code Statutory Exclusion (from MPFS, may be paid under other methodologies)
Global Days XXX - Global Concept Does Not Apply
PC/TC Indicator (26, TC) 9 - Not Applicable
Multiple Procedures (51) 9 - Concept does not apply.
Bilateral Surgery (50) 9 - Concept does not apply.
Physician Supervisions 09 - Concept does not apply.
Assistant Surgeon (80, 82) 9 - Concept does not apply.
Co-Surgeons (62) 9 - Concept does not apply.
Team Surgery (66) 9 - Concept does not apply.
Diagnostic Imaging Family 99 - Concept Does Not Apply
CLIA Waived (QW) No
APC Status Indicator Service Paid under Fee Schedule or Payment System other than OPPS
Type of Service (TOS) 5 - Diagnostic Laboratory
Berenson-Eggers TOS (BETOS) T1H - Lab tests - other (non-Medicare fee schedule)
MUE 1
90 Reference (outside) laboratory: when laboratory procedures are performed by a party other than the treating or reporting physician or other qualified health care professional, the procedure may be identified by adding modifier 90 to the usual procedure number.
59 Distinct procedural service: under certain circumstances, it may be necessary to indicate that a procedure or service was distinct or independent from other non-e/m services performed on the same day. modifier 59 is used to identify procedures/services, other than e/m services, that are not normally reported together, but are appropriate under the circumstances. documentation must support a different session, different procedure or surgery, different site or organ system, separate incision/excision, separate lesion, or separate injury (or area of injury in extensive injuries) not ordinarily encountered or performed on the same day by the same individual. however, when another already established modifier is appropriate it should be used rather than modifier 59. only if no more descriptive modifier is available, and the use of modifier 59 best explains the circumstances, should modifier 59 be used. note: modifier 59 should not be appended to an e/m service. to report a separate and distinct e/m service with a non-e/m service performed on the same date, see modifier 25.
26 Professional component: certain procedures are a combination of a physician or other qualified health care professional component and a technical component. when the physician or other qualified health care professional component is reported separately, the service may be identified by adding modifier 26 to the usual procedure number.
91 Repeat clinical diagnostic laboratory test: in the course of treatment of the patient, it may be necessary to repeat the same laboratory test on the same day to obtain subsequent (multiple) test results. under these circumstances, the laboratory test performed can be identified by its usual procedure number and the addition of modifier 91. note: this modifier may not be used when tests are rerun to confirm initial results; due to testing problems with specimens or equipment; or for any other reason when a normal, one-time, reportable result is all that is required. this modifier may not be used when other code(s) describe a series of test results (eg, glucose tolerance tests, evocative/suppression testing). this modifier may only be used for laboratory test(s) performed more than once on the same day on the same patient.
GZ Item or service expected to be denied as not reasonable and necessary
XU Unusual non-overlapping service, the use of a service that is distinct because it does not overlap usual components of the main service
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2015-01-01 Added Added
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