A CALR mutation test looks for acquired changes in the calreticulin gene, usually small insertions or deletions in exon 9. These mutations are major drivers of essential thrombocythemia and primary myelofibrosis, two BCR::ABL1-negative myeloproliferative neoplasms. They activate the thrombopoietin receptor and JAK-STAT signaling, causing an abnormal blood stem-cell clone to expand.
Testing is most useful when platelet counts are persistently high or bone-marrow findings suggest myelofibrosis and the common JAK2 V617F mutation is absent. CALR, JAK2, and MPL results support clonality, but none replaces a blood-count history, marrow biopsy, exclusion of reactive causes, and assessment for other myeloid diseases. A positive CALR result is usually somatic rather than inherited. Type 1-like and type 2-like CALR variants can be associated with different clinical patterns, particularly in primary myelofibrosis. The allele fraction describes how much mutant DNA was detected; it is not a direct measure of symptom severity or clotting risk.
- A positive pathogenic CALR exon 9 mutation supports essential thrombocythemia or primary myelofibrosis when the clinical and marrow findings fit.
- CALR mutations are usually checked after or alongside JAK2 and MPL testing in suspected BCR::ABL1-negative MPNs.
- CALR-mutated essential thrombocythemia generally has lower thrombosis risk than JAK2-mutated disease, but risk is not zero.
- Type 1-like CALR mutations tend to have a more favorable survival association in primary myelofibrosis than type 2-like mutations.
- A negative CALR result does not rule out an MPN, because JAK2, MPL, rare drivers, or triple-negative disease remain possible.
Table of Contents
- What CALR Mutations Are
- When CALR Testing Is Ordered
- How the Test Is Performed
- How to Interpret CALR Results
- CALR in Essential Thrombocythemia
- CALR in Primary Myelofibrosis
- Treatment, Monitoring, and Prognosis
- Limitations and Next Steps
What CALR Mutations Are
CALR encodes calreticulin, a protein that normally helps other proteins fold inside the endoplasmic reticulum and participates in calcium balance. Myeloproliferative-neoplasm mutations alter the end of the protein. Nearly all are frameshift insertions or deletions in exon 9 that create a novel, positively charged tail and remove the normal retention signal.
Mutant calreticulin binds the thrombopoietin receptor, MPL, and brings it to the cell surface in an active form. This continuously stimulates JAK2 and downstream STAT signaling even without the normal hormone signal. Blood stem and progenitor cells then gain a growth advantage, especially in the megakaryocyte lineage that produces platelets and contributes to marrow fibrosis.
Two mutations are most common:
- Type 1, a 52-base-pair deletion, often written c.1092_1143del or p.Leu367Thrfs*46
- Type 2, a 5-base-pair insertion, often written c.1154_1155insTTGTC or p.Lys385Asnfs*47
Many rarer exon 9 changes are grouped as type 1-like or type 2-like according to the structure and charge of the altered protein. This grouping can be clinically relevant in primary myelofibrosis. The exact DNA and protein notation should appear in the report rather than only “CALR positive.”
CALR, JAK2, and MPL are called driver mutations because each can initiate the MPN phenotype. They are usually mutually exclusive, although rare patients have more than one driver, especially at low allele levels or in separate clones. A result showing two drivers should prompt technical confirmation and integrated review rather than being dismissed automatically.
The mutation is usually somatic, acquired in a blood-forming stem cell during life. It is not normally present in every body cell and does not follow a simple inherited pattern. Family members do not need targeted testing for the patient’s CALR mutation. Some families have an inherited tendency to develop MPNs, but affected relatives usually acquire different somatic drivers.
CALR is not a typical cause of reactive thrombocytosis. Infection, inflammation, iron deficiency, tissue injury, recent surgery, cancer, and loss of spleen function can raise platelets without a clonal mutation. The test is valuable because it helps separate clonal from reactive processes, but a negative result cannot complete that distinction alone. Persistent unexplained counts still require marrow, clinical, and laboratory correlation over time.
When CALR Testing Is Ordered
Testing is commonly ordered for persistent unexplained thrombocytosis, marrow fibrosis, or other findings that suggest a classic BCR::ABL1-negative MPN. Many laboratories follow a sequence: JAK2 V617F first, then CALR and MPL if JAK2 is negative. Broad next-generation sequencing may test all three at once.
Typical indications include:
- Platelet count repeatedly at or above 450 × 10^9/L after common reactive causes are assessed
- Bone-marrow megakaryocyte changes suspicious for essential thrombocythemia or prefibrotic primary myelofibrosis
- Marrow reticulin or collagen fibrosis with anemia, splenomegaly, or leukoerythroblastosis
- Suspected post-essential thrombocythemia myelofibrosis
- An MPN diagnosis that needs molecular confirmation or prognostic refinement
- A prior negative JAK2 V617F result in an appropriate clinical setting
- Unexplained splanchnic-vein thrombosis or another unusual clot with blood-count features suggesting MPN
The platelet threshold is not enough for diagnosis. Counts can remain high from iron deficiency or inflammation, and some MPN patients have counts near normal after bleeding, splenic sequestration, or treatment. Clinicians review several blood counts, ferritin and iron studies, inflammatory markers, medications, spleen status, and clinical history.
Bone-marrow morphology is essential for distinguishing essential thrombocythemia from prefibrotic primary myelofibrosis. Both can be CALR-positive and present with high platelets. In essential thrombocythemia, megakaryocytes are enlarged and mature with characteristic nuclear lobulation, without the granulocytic proliferation and atypia expected in prefibrotic myelofibrosis. This distinction affects prognosis and follow-up.
CALR testing is generally not the first test for erythrocytosis. Polycythemia vera is overwhelmingly associated with JAK2 mutation. It is also not the defining test for chronic myeloid leukemia, which requires BCR::ABL1. A complete myeloid workup uses the phenotype to choose the most relevant molecular targets.
A CALR result may also be obtained incidentally on a broad myeloid mutation panel. When found in a person without an established MPN, the allele fraction, blood counts, symptoms, and marrow findings determine whether it represents overt disease, an early clonal state, or a technical issue.
How the Test Is Performed
Peripheral blood is usually sufficient because the mutation is present in circulating myeloid cells. Bone marrow aspirate can also be tested, often as part of a diagnostic biopsy. No fasting is required. A standard blood draw is adequate unless the laboratory requests a specialized tube.
Fragment analysis and PCR
CALR exon 9 mutations change the length of the amplified DNA fragment. PCR followed by capillary electrophoresis can detect insertions and deletions quickly and sensitively. It shows that an abnormal fragment is present and often indicates its size, but sequencing may be needed to identify the exact variant.
Allele-specific PCR can target common type 1 and type 2 variants. It is highly sensitive but may miss rare exon 9 changes outside its design. A report should specify whether the method covers only common variants or the full clinically relevant region.
Sanger and next-generation sequencing
Sanger sequencing can identify the exact insertion or deletion when the mutant allele level is high enough. Next-generation sequencing detects CALR alongside JAK2, MPL, ASXL1, TET2, DNMT3A, SRSF2, U2AF1, EZH2, IDH1, IDH2, TP53, and other myeloid genes. This broader context can refine diagnosis and prognosis, especially in myelofibrosis.
CALR exon 9 can be technically challenging because repetitive sequence and mixed insertion/deletion reads may complicate alignment. A validated pipeline and manual review are important. Some general tumor panels are not optimized for these frameshifts, so a focused assay can be useful after a negative result that conflicts with the clinical picture.
Allele fraction
Next-generation sequencing may report variant allele frequency, or VAF. A VAF of 35% means about 35% of sequence reads at that location carried the mutation. It does not mean 35% of marrow cells are cancerous. Mature blood-cell composition, copy-number changes, homozygosity, sample purity, and treatment affect the value.
Serial VAF measurements are not a routine stand-alone response marker for most patients. Interferon can reduce driver-allele burden in some people, and transplantation can eliminate the clone, but clinical response is judged with blood counts, symptoms, spleen size, marrow, transfusion needs, and disease-specific criteria.
Turnaround ranges from a few days for focused PCR to two or three weeks for a comprehensive panel. A failed test may result from insufficient DNA, poor marrow aspirate, shipping problems, or technical interference and should not be interpreted as mutation-negative.
How to Interpret CALR Results
The report should identify the exact variant, pathogenicity, assay sensitivity, specimen, and allele fraction when available. CALR exon 9 frameshifts with the characteristic new tail are established MPN drivers. Other CALR changes outside this pattern may be uncertain and should not automatically be treated as diagnostic.
| Result | Usual meaning | Clinical caution |
|---|---|---|
| Pathogenic CALR exon 9 frameshift detected | Evidence of a clonal myeloid population and a major MPN driver. | Diagnosis still requires the blood and marrow phenotype. |
| CALR not detected | No covered mutation was found above the assay limit. | JAK2, MPL, rare drivers, or triple-negative MPN remain possible. |
| CALR variant of uncertain significance | The change is not established as an MPN driver. | Do not use it alone to diagnose or treat an MPN. |
| Low-level positive | A small CALR-mutant clone may be present. | Confirm the finding and correlate with persistent blood abnormalities. |
| Insufficient or failed | The assay could not produce a reliable result. | Repeat testing is usually needed if the result is clinically important. |
A positive result supports clonality but does not distinguish essential thrombocythemia from primary myelofibrosis by itself. It also cannot determine whether fibrosis is prefibrotic, overt, or secondary to prior essential thrombocythemia. The marrow pattern, blood counts, symptoms, spleen, and clinical history define the entity.
A negative result may be called “triple negative” only after adequately sensitive testing for JAK2, CALR, and MPL is negative. In apparent triple-negative essential thrombocythemia, careful marrow review and exclusion of reactive thrombocytosis are especially important. In triple-negative myelofibrosis, a broader panel may find other clonal mutations and can reveal adverse-risk biology.
A low VAF can reflect an early or small clone, dilution by normal cells, or assay artifact. Unlike DNMT3A or TET2, a canonical CALR exon 9 mutation is closely tied to MPN biology, but the person still needs phenotype-based assessment. Repeating the result on a new specimen can confirm persistence.
The result is not an inherited carrier test. If the laboratory analyzed only blood, the presence of CALR in blood is expected for a somatic MPN and should not be labeled germline based on VAF alone.
CALR in Essential Thrombocythemia
CALR mutations occur in roughly one quarter of essential thrombocythemia cases and in a large proportion of patients who lack JAK2. CALR-mutated patients are often younger, have higher platelet counts, and have lower hemoglobin and white-cell counts than those with JAK2-mutated disease. Type 2-like variants are relatively common in essential thrombocythemia.
The thrombosis pattern differs by driver. CALR-mutated essential thrombocythemia generally has a lower risk of arterial and venous thrombosis than JAK2-mutated disease. However, age, prior clot, cardiovascular risk factors, extreme blood counts, pregnancy, smoking, and additional mutations still matter. A CALR result does not make clot prevention unnecessary.
Very high platelet counts can cause acquired von Willebrand syndrome because large von Willebrand factor multimers are cleared from circulation. This can increase bleeding risk even though the platelet count is high. Before prescribing aspirin to a person with extreme thrombocytosis or bleeding symptoms, clinicians may check von Willebrand activity and consider the balance between clotting and bleeding.
Current ET risk models emphasize age, prior thrombosis, and JAK2 status. A young CALR-mutated patient without previous thrombosis may fall into a very-low-risk group and sometimes needs observation rather than cytoreduction. Aspirin decisions are individualized; microvascular symptoms, cardiovascular risks, platelet level, and bleeding risk influence use.
Cytoreductive treatment may be used for high-risk disease, troublesome symptoms, extreme thrombocytosis with complications, or pregnancy-related indications. Options include hydroxyurea, pegylated interferon, and selected alternatives. CALR status does not identify one universally preferred drug, although younger patients and those planning pregnancy may favor interferon for reasons beyond the mutation.
Essential thrombocythemia can evolve to myelofibrosis or acute myeloid leukemia, but most patients do not transform. CALR-mutated ET may have a higher long-term tendency toward fibrotic progression than JAK2-mutated ET in some studies. Regular review of anemia, rising white cells, falling platelets, spleen enlargement, constitutional symptoms, and leukoerythroblastosis can identify change.
CALR in Primary Myelofibrosis
CALR mutations occur in about one quarter to one third of primary myelofibrosis and are common among JAK2-negative cases. Patients may present with anemia, fatigue, night sweats, weight loss, enlarged spleen, bone pain, abnormal blood counts, tear-drop red cells, or immature blood cells in circulation.
The mutation subtype carries more prognostic information in myelofibrosis than in essential thrombocythemia. Type 1 and type 1-like CALR variants are generally associated with better survival than type 2/type 2-like variants and than some other driver contexts. The favorable association is not absolute and can be outweighed by age, anemia, blasts, severe symptoms, unfavorable chromosomes, or high-risk co-mutations.
Mutations in ASXL1, SRSF2, EZH2, IDH1, IDH2, U2AF1, TP53, and other genes can refine risk. Modern prognostic systems combine clinical variables, karyotype, driver mutation, and additional mutations. A CALR type should therefore appear in a broader risk assessment rather than being quoted alone.
CALR-mutated myelofibrosis can produce marked splenomegaly and symptoms through the same JAK-STAT pathway targeted by JAK inhibitors. Ruxolitinib, fedratinib, pacritinib, and momelotinib have setting-specific roles based on platelet count, anemia, prior therapy, and regulatory approval. These drugs improve symptoms and spleen size but do not require a JAK2 mutation; CALR-mutated disease can respond because signaling converges on JAK2.
Allogeneic stem-cell transplantation is the only established potentially curative therapy for myelofibrosis, but it carries substantial risk. The decision uses prognostic score, age, fitness, donor availability, symptoms, transfusion dependence, molecular risk, and patient preference. A favorable CALR type may support observation in a lower-risk patient but does not exclude transplantation when the overall disease is high risk.
After transplantation, sensitive CALR testing can serve as a measurable residual disease marker because the variant is clone-specific. This use differs from routine VAF tracking during noncurative therapy and should follow transplant-center protocols.
Treatment, Monitoring, and Prognosis
CALR is not yet a routine direct drug-selection biomarker in the way that BCR::ABL1 selects a tyrosine kinase inhibitor. It confirms a disease pathway and contributes to risk assessment. Treatment addresses the diagnosed MPN and the patient’s complications.
For essential thrombocythemia, the main aims are preventing thrombosis and bleeding while controlling troublesome symptoms. Management may include cardiovascular-risk reduction, aspirin when appropriate, and cytoreduction for higher-risk disease. Platelet normalization alone is not the only outcome; clot history, symptoms, drug toxicity, and bleeding are equally important.
For myelofibrosis, management may include observation, JAK inhibitors, anemia-directed therapies, transfusions, clinical trials, symptom control, and transplantation. CALR-mutant disease remains biologically heterogeneous. The same positive result can occur in an asymptomatic lower-risk patient and in advanced disease with adverse co-mutations.
Monitoring typically includes complete blood counts, symptom review, spleen examination or imaging when needed, chemistry tests, and periodic reassessment of disease risk. Repeat marrow is considered when counts change unexpectedly, blasts rise, transformation is suspected, or transplant planning requires it. Molecular retesting may be useful at progression because new mutations can emerge.
Investigational treatments target mutant calreticulin itself, including antibodies and immune approaches directed at the novel mutant tail. These strategies are promising because the abnormal tail is shared by many CALR frameshifts and is absent from normal cells. They remain clinical-trial approaches rather than standard care.
Pregnancy requires coordinated hematology and maternal-fetal medicine care. ET-related pregnancy risks include miscarriage, placental complications, thrombosis, and bleeding. CALR-mutated ET may have lower thrombosis risk than JAK2-mutated disease, but obstetric history and other risk factors guide aspirin, low-molecular-weight heparin, and interferon decisions.
Lifestyle cannot remove a CALR clone, but controlling smoking, blood pressure, cholesterol, diabetes, weight, and physical inactivity can lower competing vascular risk. New headaches, visual changes, chest pain, one-sided swelling, weakness, or unusual bleeding need prompt assessment.
Limitations and Next Steps
A molecular result can be technically correct yet clinically misapplied. CALR positivity does not eliminate the need for marrow morphology, and thrombocytosis does not automatically mean essential thrombocythemia. Prefibrotic myelofibrosis, chronic inflammation, iron deficiency, and another myeloid neoplasm can produce overlapping findings.
Questions to ask include:
- What exact CALR mutation and type were found?
- Was JAK2 V617F tested, and was MPL included?
- What was the allele fraction and assay sensitivity?
- Does the marrow meet criteria for ET, prefibrotic PMF, or overt PMF?
- Were reactive causes of high platelets excluded?
- Were BCR::ABL1 and other myeloid neoplasms considered?
- Are additional mutations or chromosome findings important for prognosis?
- Does the result change aspirin, cytoreduction, transplant, or trial decisions?
- Should molecular testing be repeated if the disease changes?
Seek urgent care for signs of a clot or major bleeding: sudden weakness, facial droop, speech difficulty, chest pain, shortness of breath, coughing blood, a painful swollen leg, black stools, vomiting blood, or severe uncontrolled bleeding. Contact the hematology team promptly for new fevers, rapid spleen enlargement, worsening night sweats, unexplained weight loss, or a sudden change in blood counts.
A well-written final diagnosis should connect genotype and phenotype, such as “CALR type 1-mutated primary myelofibrosis,” rather than “CALR positive” alone. That complete wording allows the mutation to support the right disease, risk model, and follow-up plan.
When the diagnosis remains uncertain
Some patients have persistent thrombocytosis, a low-level clonal mutation, and marrow findings that do not cleanly meet one category. In that setting, time can be diagnostically useful. The team may correct iron deficiency, repeat blood counts, review the marrow with an MPN specialist, and follow spleen size and symptoms before assigning a permanent label. Broad sequencing can document clonality, but mutations such as TET2 or DNMT3A can also occur in age-related clonal hematopoiesis. A canonical CALR exon 9 driver is more specific, yet the distinction between ET and prefibrotic PMF still rests on morphology and the total clinical pattern.
References
- International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data 2022 (Position Statement)
- Fifth edition WHO classification: myeloid neoplasms 2025 (Review)
- CALR—mutant myeloproliferative neoplasms 2025 (Review)
- A Review of the Pathological and Molecular Diagnosis of Myeloproliferative Neoplasms 2025 (Review)
- Impact of calreticulin mutations on treatment and survival outcomes in patients with primary myelofibrosis 2025
- Evolution of WHO diagnostic criteria in “Classical Myeloproliferative Neoplasms” compared with the International Consensus Classification 2025 (Review)
Disclaimer
This article is educational and does not replace diagnosis or treatment by a hematologist and hematopathologist. A CALR result must be interpreted with repeated blood counts, marrow morphology, JAK2/MPL and other molecular findings, clotting and bleeding history, symptoms, and current classification criteria. Seek emergency care for symptoms of stroke, pulmonary embolism, heart attack, or major bleeding.
