A CALR mutation test looks for acquired mutations in the calreticulin gene that are strongly associated with certain myeloproliferative neoplasms, especially essential thrombocythemia (ET) and primary myelofibrosis (PMF). CALR is one of the three major myeloproliferative driver genes, together with JAK2 and MPL. Most clinically important CALR mutations occur in exon 9 and create a frameshift that produces an abnormal protein capable of activating the MPL–JAK2–STAT signaling pathway. A positive result can provide strong evidence that persistently high platelets or marrow fibrosis are clonal rather than reactive, but it does not by itself distinguish ET from prefibrotic or overt myelofibrosis. Bone marrow morphology, blood counts, symptoms, spleen findings, and exclusion of other myeloid diseases remain essential. CALR-mutated ET generally has a lower thrombosis risk than JAK2-mutated ET, while specific CALR mutation types can also carry prognostic information in myelofibrosis. The test should therefore be interpreted as part of an integrated diagnosis rather than as a stand-alone cancer result.
- A positive CALR mutation supports a clonal myeloproliferative neoplasm, most commonly ET or primary myelofibrosis, when the blood and marrow findings fit.
- CALR mutations are usually found in exon 9 and commonly include type 1–like and type 2–like frameshift variants.
- JAK2, CALR, and MPL driver mutations are usually mutually exclusive, so testing often follows a stepwise or panel-based MPN approach.
- CALR positivity does not explain the platelet count by itself or determine whether the diagnosis is ET versus myelofibrosis; bone marrow morphology is crucial.
- There is no numeric “normal CALR level.” Results are usually reported as detected/not detected, with the exact variant and sometimes a variant allele frequency.
Table of Contents
- What CALR is and why mutations matter
- When a CALR mutation test is ordered
- CALR mutations in essential thrombocythemia
- CALR mutations in primary myelofibrosis
- How CALR testing is performed and reported
- What positive, negative, and VAF results mean
- How CALR results fit into diagnosis and risk
What CALR is and why mutations matter
CALR encodes calreticulin, a protein normally found in the endoplasmic reticulum, where it helps with protein folding and calcium balance. In myeloproliferative neoplasms, the clinically important mutations are not ordinary single-letter substitutions spread randomly across the gene. Most are insertions or deletions in exon 9 that shift the reading frame and create a novel, positively charged C-terminal portion of the protein.
That abnormal calreticulin interacts with the thrombopoietin receptor MPL and drives persistent JAK2–STAT signaling. The result is growth and survival signaling in hematopoietic stem and progenitor cells even without normal physiologic control. This mechanism explains why CALR mutations are especially linked to disorders with megakaryocyte and platelet abnormalities.
Two broad mutation patterns are often described. Type 1 is a 52-base-pair deletion, while type 2 is a 5-base-pair insertion. Other exon 9 variants can be grouped as type 1–like or type 2–like based on their predicted structural effect. The distinction can matter most in primary myelofibrosis, where type 1 or type 1–like CALR mutations have generally been associated with more favorable survival than some other driver categories.
CALR is one of the three classic MPN driver genes. In ET and PMF, JAK2, CALR, and MPL mutations account for most cases, and they are usually mutually exclusive. A practical myeloproliferative neoplasm molecular panel therefore evaluates these drivers together or in sequence.
CALR mutations are not the usual driver of polycythemia vera. PV is overwhelmingly associated with JAK2 mutations. Finding CALR in a patient with erythrocytosis should therefore prompt careful review of the overall diagnosis rather than automatic labeling as PV.
When a CALR mutation test is ordered
CALR testing is commonly ordered during evaluation of persistent thrombocytosis or suspected myelofibrosis. In ET, the platelet count is at least 450 × 10^9/L, but many noncancerous conditions can also cause thrombocytosis. Iron deficiency, inflammation, infection, recent surgery, tissue injury, malignancy, and recovery after blood loss can all raise platelets reactively. Molecular testing helps determine whether a clonal MPN is more likely.
A common testing sequence begins with JAK2 V617F because it is the most frequent driver in ET and PMF and is also the dominant mutation in PV. If JAK2 is negative, CALR and MPL are assessed, either sequentially or on a single next-generation sequencing panel. Many laboratories now use combined panels because they can also detect additional myeloid genes relevant to prognosis.
CALR testing may also be ordered when a bone marrow biopsy shows atypical megakaryocytic proliferation, fibrosis, or another pattern concerning for an MPN. The mutation can support clonality, particularly when reactive explanations remain possible. In established myelofibrosis, the driver mutation also contributes to prognostic models and can provide useful biologic context.
The specimen is usually peripheral blood or bone marrow. Blood is often adequate because the mutation is present in the hematopoietic clone, not only in marrow tissue. No fasting or special dietary preparation is generally needed.
The test is not intended as population screening for people with a normal blood count. Nor should it be ordered simply because one platelet count is mildly elevated. Clinicians usually confirm persistence, review trends, assess iron stores and inflammation, and consider the clinical context before molecular testing.
A positive driver mutation can be highly informative, but it does not eliminate the need for marrow examination when formal classification requires morphology. ET, prefibrotic PMF, and overt PMF can overlap in blood counts yet differ significantly in marrow architecture and prognosis.
CALR mutations in essential thrombocythemia
Essential thrombocythemia is a clonal myeloproliferative neoplasm characterized by persistent thrombocytosis and a characteristic megakaryocytic pattern in bone marrow after other myeloid neoplasms are excluded. Approximately 80% of patients have one of the three major driver mutations, with JAK2 most common and CALR accounting for a substantial proportion of JAK2-negative cases.
CALR-mutated ET often has a recognizable clinical profile. Compared with JAK2-mutated ET, patients tend to be younger, may have higher platelet counts, and generally have a lower risk of thrombosis. This does not mean thrombosis cannot occur. Age, prior thrombosis, cardiovascular risk factors, and other disease features still matter, and treatment decisions are not based on CALR status alone.
The platelet count itself can be strikingly high in CALR-mutated ET, but the number does not directly measure mutation burden. A platelet count of 900 × 10^9/L does not mean “more CALR” than a count of 600 × 10^9/L. Platelets are the physiologic output of a complex marrow clone, and their level can also be influenced by iron deficiency, inflammation, therapy, and individual biology.
Very high platelet counts can increase bleeding risk in some patients because of acquired von Willebrand syndrome, particularly when platelet levels become extreme. This is one reason a treatment plan may consider both thrombosis and bleeding rather than assuming higher platelets always mean more clotting.
CALR positivity supports the diagnosis but cannot replace marrow morphology. Prefibrotic primary myelofibrosis can present with thrombocytosis and a CALR mutation, yet its marrow megakaryocytes and overall architecture differ from ET. Misclassifying prefibrotic PMF as ET can affect prognostic counseling and follow-up.
Additional somatic mutations may also be present. Genes such as ASXL1, TET2, DNMT3A, spliceosome genes, and others can contribute to the molecular profile. These are not substitutes for the driver mutation, but selected variants can modify risk, particularly in myelofibrosis or when disease evolution is suspected.
CALR mutations in primary myelofibrosis
Primary myelofibrosis is another major disease in which CALR mutations are important. PMF can be diagnosed in a prefibrotic stage, before extensive reticulin or collagen fibrosis develops, or in an overt fibrotic stage. Both forms require characteristic megakaryocytic abnormalities and exclusion of other myeloid neoplasms.
Driver mutation status contributes to the biology and prognosis of PMF. Patients with CALR mutations, especially type 1 or type 1–like variants, have often shown more favorable survival than patients with certain other molecular profiles. By contrast, absence of JAK2, CALR, and MPL—the so-called triple-negative state—is generally associated with higher-risk biology and requires careful molecular assessment to confirm clonality and exclude mimics.
A CALR mutation does not tell how much marrow fibrosis is present. Fibrosis is graded on the biopsy. Nor does it determine whether the person has anemia, constitutional symptoms, splenomegaly, circulating blasts, or other clinical features used in risk scoring. Those findings must be assessed separately.
The mutation also does not remain the only relevant genetic feature as disease evolves. High-risk additional mutations, chromosome abnormalities, blast percentage, blood counts, and symptoms can substantially alter prognosis. Modern risk models may incorporate several of these variables, particularly when deciding whether allogeneic stem-cell transplantation should be considered.
If a patient with longstanding ET later develops anemia, leukoerythroblastosis, increasing spleen size, constitutional symptoms, or progressive marrow fibrosis, the diagnosis may shift to post-ET myelofibrosis. The original CALR mutation commonly remains detectable because it marks the founding clone. Its persistence does not mean the disease has remained biologically unchanged.
The same principle applies to serial variant allele frequency. A changing VAF can reflect clonal dynamics, but clinical progression is not defined by a universal CALR percentage threshold. Blood counts, marrow findings, symptoms, cytogenetics, and additional molecular changes remain central.
How CALR testing is performed and reported
CALR exon 9 mutations can be detected by several molecular methods. Fragment analysis, PCR-based assays, Sanger sequencing, and next-generation sequencing are all used. Each method has different sensitivity and coverage. A targeted PCR assay may detect common insertions and deletions efficiently, while a broader sequencing panel can identify uncommon CALR variants and additional genes in the same test.
Because exon 9 contains many possible insertions and deletions, assay design matters. Laboratories validate which variant sizes and sequence changes they can detect. Rare variants can sometimes challenge purely size-based or allele-specific approaches, which is why sequencing may be used when suspicion remains high despite an initially negative assay.
A positive report should ideally name the DNA-level change and predicted protein consequence and may classify the mutation as type 1, type 2, type 1–like, or type 2–like. If next-generation sequencing is used, the report often includes variant allele frequency.
VAF is the fraction of sequencing reads containing the mutation. For a heterozygous mutation in a pure population of clonal cells, a VAF near 50% might be expected, but real blood samples contain normal cells and can have copy-number changes or subclonal architecture. Therefore, VAF should not be translated directly into “percent cancer cells.”
A negative report means no reportable CALR mutation was identified within the assay’s validated range and sensitivity. It does not exclude ET or PMF. Some patients have JAK2 or MPL mutations; others are triple-negative by the classic drivers but have other clonal markers. A small clone below the detection limit or a rare variant outside assay coverage can also produce a negative result.
There is no reference interval such as 0–10 for CALR. The clinically meaningful categories are mutation detected, not detected, or occasionally indeterminate/insufficient. The exact variant and assay sensitivity provide the nuance.
What positive, negative, and VAF results mean
A positive pathogenic CALR exon 9 mutation in a patient with persistent unexplained thrombocytosis or a compatible marrow strongly supports a clonal myeloproliferative neoplasm. It makes a purely reactive platelet elevation much less likely. The next task is to classify which MPN is present, using marrow morphology and clinical criteria.
In a patient with high platelets, CALR positivity is consistent with ET but can also occur in prefibrotic PMF. In a patient with fibrosis, splenomegaly, anemia, and a characteristic marrow, it supports PMF. The mutation is therefore evidence of clonality, not a disease name by itself.
A negative CALR result has several possible meanings. The patient may have a JAK2- or MPL-mutated MPN, a triple-negative MPN, another myeloid neoplasm, reactive thrombocytosis, or no persistent hematologic disorder at all. The diagnostic pathway depends on the blood count pattern, marrow findings, and what other molecular tests have already been done.
A low VAF positive result can be genuine. Small clones may occur early in disease or coexist with a large background of normal blood cells. However, age-related clonal hematopoiesis complicates interpretation of some myeloid mutations. CALR driver mutations are much more closely linked to MPN biology than common age-related mutations such as DNMT3A or TET2, but a molecular result still needs phenotypic correlation.
A rising VAF on serial tests does not have a standardized treatment trigger in ET. Routine care focuses more on thrombosis risk, blood counts, symptoms, spleen size, and evidence of transformation. In PMF, molecular information may be incorporated into prognostic models, but no single CALR VAF cut point substitutes for comprehensive risk assessment.
If a report labels a CALR variant “uncertain significance,” it should not be interpreted the same way as a classic pathogenic exon 9 frameshift. The laboratory’s classification and the variant’s known mechanism matter.
How CALR results fit into diagnosis and risk
The most useful way to interpret CALR is to place it in a diagnostic sequence. First, confirm that the blood abnormality is persistent. For thrombocytosis, review iron status, inflammation, infection, recent procedures, malignancy, and other reactive causes. Next, evaluate MPN driver mutations and the peripheral blood smear. Then use bone marrow morphology and disease-specific criteria to classify ET, prefibrotic PMF, overt PMF, or another myeloid process.
In ET, mutation status can refine thrombotic risk. JAK2 mutation is incorporated into contemporary thrombosis models, while CALR-mutated, JAK2-wild-type patients often fall into a lower thrombotic-risk category when age and thrombosis history are also favorable. This can influence how clinicians think about aspirin and cytoreductive therapy, although bleeding risk and individual factors remain important.
In PMF, the mutation type can contribute more directly to survival models. Type 1 or type 1–like CALR is generally considered a favorable driver compared with triple-negative disease or certain adverse molecular profiles. The effect is integrated with age, hemoglobin, white blood cell count, blasts, symptoms, cytogenetics, and high-risk mutations.
CALR testing also helps avoid diagnostic shortcuts. A high platelet count plus CALR mutation is not automatically ET. A fibrotic marrow plus CALR mutation is not automatically primary rather than secondary myelofibrosis. Prior history, marrow pattern, and other criteria determine the correct label.
For patients, useful questions include: Which exact CALR variant was found? Is it type 1–like or type 2–like? Were JAK2 and MPL also tested? Does my marrow meet criteria for ET or myelofibrosis? Does this mutation change my thrombosis or survival risk category? Those answers are more informative than simply knowing that CALR is “positive.”
A final practical point is that the mutation usually remains part of the clone even when treatment controls blood counts. A normalized platelet count after cytoreductive therapy does not mean the CALR mutation must disappear. Most current treatments manage the disease phenotype rather than reliably eradicating the founding clone. Molecular response is therefore not interpreted in the same way as BCR::ABL1 monitoring in CML.
References
– CALR-mutated myeloproliferative neoplasms 2025 – Essential thrombocythemia: 2024 update on diagnosis, risk stratification, and management 2024 – Advances in Molecular Understanding of Polycythemia Vera, Essential Thrombocythemia, and Primary Myelofibrosis: Towards Precision Medicine 2024 – Molecular diagnostic criteria of myeloproliferative neoplasms 2023 – International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data 2022
Disclaimer
This article is for general education and is not a substitute for diagnosis or treatment by a hematologist. CALR results must be interpreted with the platelet count, blood smear, bone marrow morphology, other driver mutations, symptoms, and clinical history. Do not change aspirin, cytoreductive treatment, or other MPN therapy based on a mutation report without guidance from the treating team.
