MLH1: Definition

by Jason Wasserman MD PhD FRCPC
March 24, 2026

MLH1 is a gene that produces a protein involved in repairing mistakes in a cell’s DNA. It is one of four key mismatch repair (MMR) proteins — along with PMS2, MSH2, and MSH6 — that work together to find and fix small errors that occur when DNA is copied during cell division. MLH1 and PMS2 work as a pair: when MLH1 is lost, PMS2 is almost always lost at the same time.

If your pathology report mentions MLH1, it is likely because your tumour was tested to see whether this protein is present or absent. The result has important implications for understanding your diagnosis and, in some cases, whether you or your family members may be at increased risk for certain cancers.

What does it mean if MLH1 is “lost” in my tumour?

When a pathology report states that MLH1 expression is lost or absent, it means the tumour cells are not producing the MLH1 protein. Without this protein, the cell’s DNA repair system cannot function properly. This is called mismatch repair deficiency (dMMR). Errors in the DNA that would normally be caught and corrected are instead allowed to accumulate, which can contribute to cancer development and affect how the cancer behaves.

Loss of MLH1 is one of the most common causes of mismatch repair deficiency, particularly in colorectal and endometrial cancers.

What does it mean if MLH1 is “retained” in my tumour?

When a pathology report states that MLH1 expression is retained or intact, it means the tumour cells are producing a normal amount of MLH1 protein. This is a normal result for this test. It means that loss of MLH1 is not contributing to the tumour’s development and that the tumour is likely MMR-proficient (pMMR) — though this should be confirmed by reviewing the results for all four MMR proteins together.

Why do pathologists test for MLH1?

MLH1 testing is performed for two main reasons:

• To guide treatment. Tumours that have lost MLH1 (and are therefore mismatch repair deficient) often respond well to a type of treatment called immunotherapy, specifically immune checkpoint inhibitors. Knowing the MLH1 status helps your oncologist determine whether this type of treatment may be appropriate for you.
• To assess the risk of Lynch syndrome. Loss of MLH1 can sometimes be caused by an inherited condition called Lynch syndrome. Identifying whether the loss is inherited or acquired helps determine whether you and your family members need further genetic testing.

How is MLH1 tested?

Pathologists test for MLH1 using a laboratory technique called immunohistochemistry (IHC). In this test, a special antibody that binds to the MLH1 protein is applied to a thin slice of your tumour tissue on a glass slide. If the MLH1 protein is present, the cells change colour and are visible under the microscope. If the protein is absent, those cells remain unstained.

Importantly, the pathologist looks for MLH1 staining in the tumour cells, and always compares this to the surrounding normal cells (such as blood vessels and immune cells), which should stain normally and serve as an internal control. A result is only considered a true loss if the tumour cells are unstained while the surrounding normal cells show normal staining.

MLH1 is always tested together with the other three MMR proteins — PMS2, MSH2, and MSH6 — as a panel, since the proteins work in pairs and the combination of proteins lost helps guide the next steps.

What causes loss of MLH1 in a tumour?

There are two main reasons MLH1 can be lost in a tumour:

• Acquired (somatic) loss — the most common cause. The most common cause of MLH1 loss is non-inherited chemical modification of the MLH1 promoter, called MLH1 promoter methylation. This change silences the MLH1 gene only in the tumour cells. It is not inherited and does not affect other cells in the body. Because this is a sporadic (non-inherited) event, it does not increase cancer risk in family members.
• Inherited (germline) mutation — Lynch syndrome. Less commonly, MLH1 loss is caused by an inherited mutation in the MLH1 gene that is present in every cell of the body from birth. This is Lynch syndrome. People with Lynch syndrome have a significantly increased lifetime risk of developing colorectal, endometrial, and other cancers. Because the mutation is inherited, it can be passed on to children and may also be present in other biological relatives.

How do doctors determine whether MLH1 loss is inherited or acquired?

When MLH1 loss is identified on IHC testing, an additional test, MLH1 promoter methylation testing, is usually performed on the tumour tissue. This test looks for the chemical change that silences the MLH1 gene in a sporadic, non-inherited way.

• If methylation is found, the MLH1 loss is most likely due to a sporadic (acquired) change in the tumour. Lynch syndrome is unlikely, though not entirely excluded in all cases.
• If methylation is absent, the MLH1 loss is more likely due to an inherited mutation, and germline genetic testing — a blood or saliva test — is usually recommended to check for Lynch syndrome.

What will my pathology report say?

MLH1 is always included in a four-protein MMR panel alongside PMS2, MSH2, and MSH6. The result for each protein will be described using one of the following terms:

• Retained (or intact) — the protein is present in the tumour cells. This is a normal result for this test.
• Lost (or absent, or loss of expression) — the protein is missing from the tumour cells. This is an abnormal result.

The overall MMR result will then be summarized as one of the following:

• MMR-proficient (pMMR) — all four proteins are retained. The DNA repair system is intact.
• MMR-deficient (dMMR) — one or more proteins are lost. The report will specify which proteins are absent — for example, “loss of MLH1 and PMS2.”

Because MLH1 and PMS2 work as a pair, loss of MLH1 is almost always accompanied by loss of PMS2. This combined pattern is the most common finding in dMMR colorectal and endometrial cancers. If MLH1 promoter methylation testing was also performed, the report will additionally state whether methylation was detected or not detected — a key result that helps distinguish a sporadic cause from Lynch syndrome.

Questions to ask your doctor

• My report shows loss of MLH1 — what does this mean for my diagnosis and treatment?
• Was MLH1 promoter methylation testing performed, and what did it show?
• Based on these results, should I be referred for genetic testing for Lynch syndrome?
• Does this result affect whether I am eligible for immunotherapy?
• Should my family members be informed or offered genetic testing?