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EPCAM deletions that switch off MSH2 | CION Cancer Clinics
An EPCAM deletion is a missing piece of DNA in the gene next door to MSH2. It leaves MSH2 intact but switches it off, mainly in the bowel. The result counts as Lynch syndrome, with a bowel risk close to that of an MSH2 fault and usually a lower womb risk. This page explains how it works, why older tests could miss it, and what it means for your family. At CION Cancer Clinics, our oncologists explain what a gene result means for you and your family, and plan the checks that follow.
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Medically reviewed by Dr. Naresh GunduConsultant Medical Oncologist · MBBS, DNB (Internal Medicine), DM (Medical Oncology, AIIMS) · last reviewed September 2026, next review due September 2027
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On this page
- How can a fault in EPCAM switch off MSH2?
- What does an EPCAM deletion mean for my risk?
- Why did my MSH2 test look normal at first?
- What do the words on an EPCAM report mean?
- How does an EPCAM deletion compare with an MSH2 fault?
- What this page cannot tell you
- Four things families say about EPCAM, and what is true
- Common questions about EPCAM deletions
The short answer
How can a fault in EPCAM switch off MSH2?
EPCAM is a gene that sits right next to MSH2 in your DNA. It is not a repair gene. But certain deletions at the tail end of EPCAM remove its stop signal. The cell then keeps reading past EPCAM and into the start of MSH2, and that runaway reading coats the MSH2 on-switch with chemical tags that shut it down. MSH2 itself is perfectly intact. It simply stops being used.
Why it only happens in some tissues
EPCAM is active mainly in the linings of the body, especially the bowel. Only where EPCAM is being read does the silencing spread into MSH2. That is why an EPCAM deletion raises bowel cancer risk much like an MSH2 fault, while its effect on other organs is usually smaller.
Why it counts as Lynch syndrome
The end result in the bowel is the same as an MSH2 fault. The cell loses its DNA proofreader, errors build up, and cancer can form faster than usual. So people with an EPCAM deletion are treated as having Lynch syndrome, and their relatives are offered testing in the same way.
EPCAM deletions are a small share of Lynch families, and they are easy to miss on older tests.Organ by organ
What does an EPCAM deletion mean for my risk?
The pattern differs from a classic MSH2 fault. How far the deletion stretches matters.
Bowel
The bowel risk is broadly similar to that of an MSH2 carrier. Most guidelines therefore recommend the same frequent colonoscopy plan, starting in early adulthood.
Womb
In most studies the womb cancer risk is lower than with an MSH2 fault. It rises when the deletion reaches close to MSH2 or into it.
The exact end points of your deletion shape this advice.Other organs
Evidence for the stomach, urinary tract and other Lynch sites is thin, because EPCAM families are few. Your counsellor will usually lean on your own family history here.
The rest of the family
The deletion is inherited exactly like any other Lynch fault.
What that means
- Each child has a one in two chance
- Sons and daughters equally
- Relatives can be tested for the same deletion
Not sure whether this applies to you?
Ask an oncologistHow it is usually found
Why did my MSH2 test look normal at first?
The tumour points to MSH2
A bowel tumour is stained and the MSH2 and MSH6 proteins are missing. That pattern sends the team looking for an inherited MSH2 problem.
Reading MSH2 letter by letter finds nothing
Standard sequencing reads the spelling of MSH2. An EPCAM deletion leaves that spelling untouched, so this step comes back clear.
A deletion check looks for missing pieces
A separate method checks whether whole blocks of DNA are missing or doubled. Most modern Lynch panels include EPCAM in this check. Some older tests did not.
The report names EPCAM
The deletion is found, and the report should say where it starts and ends. That detail guides the womb advice and lets relatives be tested for the exact same change.
On your report
What do the words on an EPCAM report mean?
- EPCAM
- The neighbouring gene. Its own job has nothing to do with DNA repair.
- Deletion
- A stretch of DNA that is missing altogether, rather than a single misspelt letter.
- Methylation
- Chemical tags that sit on a gene's on-switch and keep it turned off. Here they are what silences MSH2.
- Epigenetic silencing
- A gene switched off without its spelling being changed. It is the mechanism behind EPCAM-linked Lynch syndrome.
- Deletion and duplication analysis
- The test that looks for missing or extra blocks of DNA. It is needed to find an EPCAM deletion.
- Breakpoints
- The exact points where the deletion starts and ends. They show how close it comes to MSH2.
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Side by side
How does an EPCAM deletion compare with an MSH2 fault?
EPCAM deletion
MSH2 fault
MSH2 is intact but switched off
MSH2 itself is broken
Silencing mainly in bowel lining
Every tissue affected
Bowel risk broadly similar
Bowel risk high
Womb risk usually lower
Womb risk high
Needs a deletion check to find
Often found by standard sequencing
Being straight with you
What this page cannot tell you
It cannot tell you whether your deletion reaches MSH2. That depends on the breakpoints listed on your report, and on how the laboratory measured them. What your specific result means is a question for the counsellor who ordered the test.
It cannot tell you whether an old test missed something
If you or a relative had Lynch testing many years ago and it came back clear despite a tumour that lost MSH2, the test may not have checked for deletions. Ask your counsellor whether a repeat test is worth doing. Do not assume the old answer is final.
Who this does not apply to
EPCAM also appears on some tumour and blood reports as a protein marker used to count cancer cells. That use of the name has nothing to do with inheritance. Tumour-only testing like this belongs with targeted therapy, not here. And most people with bowel cancer have no EPCAM deletion at all.
Commonly believed
Four things families say about EPCAM, and what is true
"EPCAM is not a repair gene, so it does not matter."
It matters because of what it does to MSH2. In the bowel, the result is the same loss of proofreading, and the same need for frequent colonoscopy.
"My MSH2 test was normal, so I do not have Lynch."
A normal spelling check does not rule out a deletion. If a tumour in the family lost MSH2, ask whether deletions, including EPCAM, were checked.
"The chemical tags can be removed with diet or supplements."
There is no evidence for this. The silencing comes from a missing piece of DNA, and that deletion cannot be corrected or reversed. Surveillance is what protects you.
"EPCAM carries exactly the same risks as MSH2."
For the bowel, broadly yes. For the womb, usually not, unless the deletion reaches into MSH2. That is why the exact result matters to women in the family.
Questions we are asked
Common questions about EPCAM deletions
Is an EPCAM deletion the same as Lynch syndrome?
Yes. It is one of the recognised causes of Lynch syndrome. The deletion switches off MSH2 in the bowel lining, so the bowel risk and the colonoscopy plan are much the same as for an MSH2 carrier. Other parts of the plan may differ, and your counsellor will set them out.
Do women with an EPCAM deletion need womb checks?
It depends on where the deletion ends. If it stays well away from MSH2, the womb risk is usually lower than in MSH2 carriers. If it reaches close to or into MSH2, the advice moves closer to the MSH2 plan. Your counsellor will read the breakpoints with you.
How do I know if my old test checked for EPCAM?
Look at the methods section of the report for deletion and duplication analysis and a list of genes. If EPCAM is not named, or the report is only a spelling check, show it to a genetic counsellor. They can tell you whether retesting makes sense.
Can my children inherit an EPCAM deletion?
Yes. Each child of a carrier has a one in two chance of inheriting it, sons and daughters alike. Testing is usually offered in adulthood, before bowel checks would begin. A child who does not inherit it cannot pass it on to their own children.
Will my relatives need the same kind of test?
They need a test that can find the same deletion. A spelling-only test would miss it and could give false reassurance. Share a copy of your report so their laboratory knows exactly what to look for. That targeted test is usually simpler and cheaper than a full panel.
Does an EPCAM deletion affect cancer treatment?
A bowel tumour in an EPCAM carrier usually has the same failed mismatch repair as other Lynch tumours. That can open up immunotherapy and may shape surgical decisions. Your oncologist will say whether this applies to your cancer.
Is an EPCAM deletion common in India?
Reliable Indian figures are not yet available. Worldwide, EPCAM deletions make up a small share of Lynch families. Specific deletions can cluster in families from one community, which is one more reason to test relatives for the exact change once it is found.
Who should I see about an EPCAM result?
A genetic counsellor or clinical geneticist, together with a gastroenterologist for the colonoscopy plan. Women should also see a gynaecologist familiar with Lynch syndrome. Call the CION helpline if you are not sure where to begin.
Your Specialists
Meet CION's oncologists. Bring your family history or genetic report to them.
Our medical oncologists see people with a strong family history of cancer, arrange genetic counselling and testing where it fits, and plan the checks that follow.
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Dr. C. Raghavendra Reddy
MBBS(Gold Medal), DNB(General Medicine), DM(Medical Oncology)(Gold Medal)
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Dr. Bharati Devi Gorantla
MBBS, MD(General Medicine), DM(Medical Oncology)(Adyar,Chennai), ECMO, MRCP SCE(UK)
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Dr. Owais Mohammed
MBBS, MD (General Medicine), DrNB (Medical Oncology), ECMO, MRCP SCE (Medical Oncology) (UK)
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Sources
- MedlinePlus Genetics — EPCAM gene
- GeneReviews (NCBI) — Lynch Syndrome
- National Cancer Institute — Genetics of Colorectal Cancer (PDQ)
- MedlinePlus Genetics — Lynch syndrome
This page is general information, not a prescription. Do not change or stop any treatment based on what you read here. If anything is worrying you, contact your own treating team — or call our helpline and we will help you reach the right specialist.
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Was your EPCAM result explained to you properly?
Bring the full report, including the breakpoints, and we will help you arrange time with a genetic counsellor to go through it. One helpline serves every CION centre.