Factor V Leiden (rs6025) in your raw data

Genetic marker guide · Updated June 2026

23andMe & raw DNA

A quick primer on how blood clots form

To understand what Factor V Leiden changes, it helps to know what a normal clot is. Clotting — properly, coagulation — is one of the body's most tightly balanced systems. When a blood vessel is injured, a chain reaction of proteins called clotting factors activates one after another, each switching on the next, until the system produces a mesh of fibrin that seals the wound. This is often described as the clotting cascade, and Factor V is one of the proteins in the middle of it. Its job, once activated, is to dramatically speed up the step that generates thrombin, the enzyme at the heart of clot formation.

The important word above is balanced. A clot has to form fast enough to stop bleeding, but it also has to be switched off before it grows out of control or spreads where it isn't needed. So alongside the "on" signals, the body runs a set of natural brakes. One of the most important brakes is a protein called protein C. When clotting has done its job, protein C is activated (becoming activated protein C, or APC), and APC's role is to inactivate Factor V and its partner Factor VIII — effectively taking a foot off the accelerator so the clot stops growing.

In a person without the variant, this cycle runs smoothly: clot when injured, then damp it down. Factor V Leiden interferes with the "damp it down" half of that cycle.

What the Factor V Leiden variant changes

The Factor V Leiden variant is a single-letter change in the F5 gene — the gene that codes for Factor V. It is catalogued as rs6025, and you may also see it written as R506Q or Arg506Gln. That notation describes exactly what happens at the protein level: at position 506 in the Factor V protein, the amino acid arginine (R) is swapped for glutamine (Q).

Position 506 matters because it is one of the very spots where activated protein C normally cuts Factor V to switch it off. Change the amino acid there, and APC can no longer cut cleanly. The result is a condition often called activated protein C resistance: Factor V stays active longer than it should because the brake can't grip it properly. Clotting is therefore harder to switch off, and the balance tips — modestly — toward forming clots.

The clots this predisposes to are on the venous side of the circulation, grouped under the term venous thromboembolism (VTE). The two most common forms are deep vein thrombosis (DVT) — a clot, usually in a leg — and pulmonary embolism (PE), where a clot travels to the lungs. Factor V Leiden is the most common inherited cause of this kind of clotting tendency in people of European descent, which is a large part of why it shows up so often in raw data.

One copy versus two: heterozygous and homozygous

You inherit two copies of the F5 gene, one from each parent, and the variant can affect one copy or both.

• Heterozygous means you carry one Leiden allele and one common allele. This is by far the more frequent situation. It is associated with a modest increase in the risk of venous clots. Crucially, in absolute terms most heterozygous carriers go their whole lives without ever having a clot.
• Homozygous means you carry two Leiden alleles. This is much less common and carries a larger increase in risk than a single copy.

It's worth sitting with the phrase modest absolute increase, because it's easy to read a genotype and hear "danger." A raised relative risk still starts from a low baseline for most people. The variant is best thought of as a standing risk factor you carry in the background — something that matters most in specific situations, rather than a switch that has been flipped to "will clot."

Why the variant matters more in combination

Factor V Leiden rarely acts alone. What makes it clinically relevant is how it stacks with other things that also nudge the body toward clotting. When several risk factors line up at once, the combined effect is what a clinician pays attention to. Common multipliers include:

• Estrogen exposure — combined (estrogen-containing) contraceptive pills and some forms of hormone replacement therapy raise baseline clotting risk on their own, and that effect is layered on top of the variant.
• Pregnancy and the postpartum period — pregnancy shifts the body toward clotting naturally, and the weeks after birth carry the highest risk.
• Surgery, especially major or orthopedic surgery, and the immobility that follows it.
• Prolonged immobility — long-haul flights, long car journeys, extended bed rest, a cast on a limb.
• Smoking, which independently increases clotting risk.
• Increasing age and obesity, both of which raise baseline risk.
• A personal or family history of clots, which suggests other factors may be in play too.

None of these guarantees a clot, and none of them is unique to carriers. The point is simply that Factor V Leiden turns some ordinary situations — a big operation, a first pregnancy, starting the pill — into moments worth an informed conversation.

Situations that genuinely warrant a clinician's input

Knowing you carry rs6025 is useful precisely because it lets you and a healthcare professional plan ahead. These are the moments where the information earns its keep:

• Planning a pregnancy or already pregnant. Clotting risk changes across pregnancy and postpartum, and management is individual.
• Choosing contraception. If you're deciding between methods, your F5 status is relevant context — but the choice belongs with a clinician, not a self-assessment.
• Before a major surgery or a long stretch of immobility. Surgical teams routinely take steps to reduce clot risk; telling them you carry the variant lets them factor it in.
• After an unexplained blood clot. If you've already had a DVT or PE without an obvious cause, testing for thrombophilias including Factor V Leiden is a standard part of the workup.
• A strong family history of clots. If close relatives have had DVT or PE, that pattern is worth discussing regardless of what your raw file shows.

In each case the theme is the same: your genotype is one input a clinician weighs alongside your full history — not an instruction you act on alone.

Why raw data isn't a diagnosis

Consumer DNA services generate your raw file with a genotyping array — a chip that reads hundreds of thousands of pre-selected positions across the genome. It's a remarkable tool for exploration, but it is not a clinical-grade diagnostic test, and there are two specific reasons that matter for a variant as consequential as this one:

1. Arrays can misread a single position. Genotyping is highly reliable across the whole file, but any individual marker can occasionally be miscalled. For a variant where the readout carries medical weight, a single uncorroborated call isn't enough to act on.
2. Strand orientation varies between files. DNA is double-stranded, and different files report different strands, so the exact letters shown for rs6025 can differ from one service to another even when they describe the same genotype. This is a frequent source of confusion when people compare results.

For both reasons, a positive raw-data result for Factor V Leiden should be treated as a prompt to seek confirmatory clinical testing, not as a conclusion. A clinical lab test — typically a genetic test or an activated protein C resistance assay — is what confirms the picture and puts it in the context of your health.

How to find rs6025 in your raw data

1. Download your raw data (or from AncestryDNA / MyHeritage).
2. Search it for rs6025 and read your genotype. The Leiden (risk) allele is the less common one.
3. Or use our free DNA explorer — it reads your file in your browser, nothing uploaded.

Two important caveats for this marker specifically: strand orientation varies between files (so the exact letters differ), and consumer genotyping arrays can occasionally miscall a single position. For a variant with real medical weight, never treat the raw-data readout as final.

What a carrier can reasonably do

If rs6025 flags as a carrier result — or if you have a personal or family history of clots regardless of what your file says — the useful next steps are calm and concrete:

• Confirm it clinically rather than treating the raw call as final.
• Tell your doctor, and mention it proactively before surgery, pregnancy planning, or a contraception decision so it can be part of the conversation.
• Know the warning signs of a clot — such as swelling, pain, warmth or redness in one leg (possible DVT), or sudden shortness of breath, chest pain, or coughing (possible PE) — and treat a suspected clot as an emergency.
• Be sensible about the everyday multipliers you can influence: move and hydrate on long flights or drives, don't smoke, and stay active.
• Keep it in proportion. Being a carrier is common, and most carriers never have a clot. This is background information to manage thoughtfully, not a diagnosis to fear.

For a companion variant that also affects the clotting system and often turns up in the same files, see our guide to the prothrombin G20210A variant. For the rest of what your file contains, see our complete guide to analyzing 23andMe raw data, or browse the rest of the Quanome blog.

Frequently asked questions

What is Factor V Leiden?

Factor V Leiden is a common inherited variant (rs6025, also called R506Q) in the F5 clotting gene. It makes Factor V resistant to being switched off by activated protein C, which tips the balance toward clotting and raises the risk of deep vein thrombosis and pulmonary embolism.

How do I find Factor V Leiden in my 23andMe raw data?

Search your raw DNA file for rs6025 and read the genotype. The Leiden (risk) allele is the less common one. Because strand orientation varies between files, and because consumer arrays can misread single markers, any result should be confirmed with clinical testing before you act on it.

Does Factor V Leiden mean I will get a blood clot?

No. It's a standing risk factor, not a diagnosis or a certainty. Most carriers never have a clot. The variant raises risk, especially when it stacks with other triggers such as surgery, immobility, pregnancy, or estrogen-containing medications — but on its own it is only one factor among many.

What's the difference between heterozygous and homozygous Factor V Leiden?

Heterozygous means you carry one copy of the Leiden allele; homozygous means two. One copy confers a modest increase in venous clot risk, and most single-copy carriers never have a clot. Two copies carry a larger increase. Either way, the clinically important question is how it interacts with your other risk factors, which is a conversation for a doctor.

Is a raw-data result a diagnosis?

No. Consumer raw data is not a clinical test. A single-marker readout can be wrong, and clotting risk is a medical matter. If rs6025 flags in your file, or you have a personal or family history of clots, see a clinician for confirmatory testing and advice.

When should I talk to a clinician about Factor V Leiden?

Good moments include: planning a pregnancy, choosing contraception, before a major surgery or a long period of immobility, after an unexplained blood clot, or if close relatives have had clots. In those situations your F5 status is genuinely useful context to share with a healthcare professional.

Should I stop taking the pill or start a blood thinner if I'm a carrier?

Not on your own. Do not start, stop, or change any medication — including contraceptives or anticoagulants — based on a raw-data result. Those decisions belong to a clinician who can weigh your full history and, if needed, order confirmatory testing.

Is Factor V Leiden related to the prothrombin clotting variant?

They're separate variants in different genes, but both affect the clotting system and both turn up in raw data. Some people carry both. See our guide to the prothrombin G20210A variant for the companion marker.