PTPN22 is a gene that helps regulate your immune system. It provides instructions for making a protein called lymphoid tyrosine phosphatase (Lyp).

Lyp acts as a brake on immune cells called T cells and B cells. These cells protect your body from infections, but if they become too active, they can mistakenly attack healthy tissues.

Changes in PTPN22 can reduce this braking ability. This may increase your risk for developing autoimmune diseases, where the immune system turns against your body.

• Also Known As: LYP, Lyp, lymphoid tyrosine phosphatase

  Location: Chromosome 1p13.2

  Type: Protein-coding gene

  Primary Role: Helps regulate immune cell activation and signaling

  Mechanism and Impact:
  PTPN22 makes Lyp, which reduces signals that activate T cells and B cells. When functioning properly, this keeps the immune system balanced. Changes in this gene can weaken these brakes, causing the immune system to become overactive.

  Key Stats:

  Prevalence: Certain PTPN22 variants are present in 5–15 percent of people in European populations. Less common in Asian and African populations.

  Demographic Trends: Variants linked to autoimmunity are more frequent in people of Northern European descent.

  Known Associations: Strong links to several autoimmune diseases, including type 1 diabetes, rheumatoid arthritis, lupus, and others.

  
  

One well-studied PTPN22 variant is known as R620W (arginine to tryptophan change at position 620).

This change weakens Lyp’s ability to regulate T and B cell signals. The result is a higher chance that immune cells may target your body’s own tissues.

Other rare variants and deletions are being explored, but R620W remains the most studied in relation to autoimmune risk.

• SNP ID: rs2476601

• Gene: PTPN22

• Risk allele: T (encodes the W620 variant)

• Effect: Reduces T and B cell regulation, increasing immune activity

Rheumatoid Arthritis
Role: May allow overactivation of T cells, promoting joint inflammation.

Type 1 Diabetes
Role: May contribute to immune attacks on insulin-producing beta cells.

Systemic Lupus Erythematosus
Role: May impair immune tolerance and promote autoantibody formation.

Graves’ Disease
Role: May promote overactive immune responses against the thyroid.

Hashimoto’s Thyroiditis
Role: May weaken immune control, leading to thyroid tissue damage.

Others: Associated with vitiligo, autoimmune hepatitis, and multiple sclerosis in some studies.

Gene/Protein: Lyp (product of PTPN22)

Type: Phosphatase (enzyme that removes phosphate groups from proteins)

Biological Role: Helps turn off immune signaling pathways in T and B cells

Interaction Network: Works with TCR complex, CD28, CTLA-4, PD-1, CSK, and downstream kinases involved in T cell activation

Relevance: Changes may disrupt immune tolerance and contribute to chronic inflammation

Additional Info: May influence balance between immune activation and regulation across many tissues

PTPN22 helps keep your immune system balanced.

When this gene is altered, it may reduce immune system control. This can raise your risk for developing autoimmune diseases.

The R620W variant is the most well-studied change in PTPN22. It affects how your immune cells communicate and may contribute to diseases like type 1 diabetes, lupus, and rheumatoid arthritis.

Learning about your PTPN22 profile may help you better understand your immune system and support your health journey.

What is PTPN22?
PTPN22 is a gene that helps regulate your immune system.

How does it affect the immune system?
It helps prevent T cells and B cells from becoming too active and attacking your body.

Is it linked to autoimmune diseases?
Yes. Variants in PTPN22 are linked to several autoimmune diseases.

How do genetic variations in PTPN22 affect health?
They may reduce immune control, increasing the risk of inflammation and tissue damage.

What SNPs in PTPN22 are linked to autoimmune conditions?
The rs2476601 (R620W) variant is strongly linked to multiple autoimmune diseases.

How is this gene different from a SNP?
PTPN22 is a gene. SNPs are tiny changes within that gene.

Should I talk to my doctor if I have changes in this gene?
Yes. Always discuss genetic findings with your doctor.

How does Silver Gene’s test help me understand PTPN22?
Our test helps uncover genetic patterns linked to your immune function, including PTPN22.

Can lifestyle changes support healthy gene function?
Your doctor can guide you on healthy lifestyle choices that may support immune balance.

Where can I learn more about PTPN22 and immunity?
Visit trusted sources such as PubMed or the National Institutes of Health, and consult your healthcare team.

This report is for informational purposes only. It is not intended to diagnose, treat, cure, or prevent any disease, nor should it be used as a substitute for professional medical advice, diagnosis, or treatment. Always consult with your doctor or a qualified healthcare provider before making any decisions about your health based on genetic information. Silver Gene, LLC is not responsible for any actions taken or not taken based on the content of this report. The information presented is accurate to the best of our research and knowledge as of June 10, 2025, and may evolve as new scientific data emerges.