JAK2

protein-coding

Janus kinase 2, the group of FERM domain containing|Jak family tyrosine kinases|SH2 domain containing

Gene summary

This gene encodes a non-receptor tyrosine kinase that plays a central role in cytokine and growth factor signalling. The primary isoform of this protein has an N-terminal FERM domain that is required for erythropoietin receptor association, an SH2 domain that binds STAT transcription factors, a pseudokinase domain and a C-terminal tyrosine kinase domain. Cytokine binding induces autophosphorylation and activation of this kinase. This kinase then recruits and phosphorylates signal transducer and activator of transcription (STAT) proteins. Growth factors like TGF-beta 1 also induce phosphorylation and activation of this kinase and translocation of downstream STAT proteins to the nucleus where they influence gene transcription. Mutations in this gene are associated with numerous inflammatory diseases and malignancies. This gene is a downstream target of the pleiotropic cytokine IL6 that is produced by B cells, T cells, dendritic cells and macrophages to produce an immune response or inflammation. Disregulation of the IL6/JAK2/STAT3 signalling pathways produces increased cellular proliferation and myeloproliferative neoplasms of hematopoietic stem cells. A nonsynonymous mutation in the pseudokinase domain of this gene disrupts the domains inhibitory effect and results in constitutive tyrosine phosphorylation activity and hypersensitivity to cytokine signalling. This gene and the IL6/JAK2/STAT3 signalling pathway is a therapeutic target for the treatment of excessive inflammatory responses to viral infections. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2020]

MANE transcript

NM_004972.4

Inheritance

AD

ClinVar variants

P:10U:320B:126

Top phenotype

Thrombocythemia 3

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr9:4,984,390-5,129,948

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~145.6 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

thrombocythemia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013794

Submitter: Genomics England PanelApp

thrombocythemia 3MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0013794

Submitter: PanelApp Australia

familial thrombocytosisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019111

Submitter: Orphanet

thrombocythemia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013794

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Thrombocythemia 3AD

Manifestation: Hematologic

Intervention: Hematologic

Rationale: Individuals may be at high risk of thrombosis, and preventive measures and early treatment of manifestations may be beneficial

Refs: 16762626; 16707754; 17989398; 19036091; 19287384; 19287385; 19338077; 19847199; 22397670; 22696908; 22571758Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JAK2 variants in ClinVar

21 Conditions Cataloged
not providedTotal: 445
Inborn genetic diseasesTotal: 80
JAK2-related disorderTotal: 47
not specifiedTotal: 37
Thrombocythemia 3Total: 28
Acquired polycythemia veraTotal: 15
Acute myeloid leukemiaTotal: 11
Budd-Chiari syndromeTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004972.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
7
clinvar
90
clinvar
11
clinvar
108
missense
3
clinvar
6
clinvar
294
clinvar
24
clinvar
1
clinvar
328
nonsense
4
clinvar
4
start loss
0
frameshift
6
clinvar
6
splice donor/acceptor (+/-2bp)
1
clinvar
9
clinvar
10
Total3732011412456

Highest pathogenic variant AF is 0.00029329018

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004972.4RefSeqNP_004963.123MANE Select
ENST00000381652.4EnsemblENSP00000371067.423MANE Select
NM_001322194.2RefSeqNP_001309123.123Standard
NM_001322195.2RefSeqNP_001309124.123Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
jak2aDanio rerio

Structure: nucleate erythrocyte

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • Adipocytokine signaling pathway - Homo sapiens (human)
  • Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
  • AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human)
  • Jak-STAT signaling pathway - Homo sapiens (human)

Biological Process

  • MAPK cascade
  • activation of MAPKK activity
  • adaptive immune response
  • protein phosphorylation
  • apoptotic process

Molecular Function

  • protein kinase activity
  • protein tyrosine kinase activity
  • non-membrane spanning protein tyrosine kinase activity
  • Ras guanyl-nucleotide exchange factor activity
  • signaling receptor binding

Cellular Component

  • nucleus
  • nucleoplasm
  • cytoplasm
  • cytosol
  • cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000381652
Coding exons
23
Length
143151
Individuals with no LoFs
125717
Homozygous LoFs
0
Heterozygous LoFs
29
Defined
125746
p
0.000115
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8965185790.8950.00002887523
Missense (PolyPhen)146215.620.67712887
Synonymous-1.212101891.110.000009161997
Loss of Function5.661360.60.2150.00000337763

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.000190.00017rare
Ashkenazi Jewish0.000100.000099rare
East Asian0.000280.00027rare
Finnish00.0absent
European (Non-Finnish)0.000140.00013rare
South Asian0.0000330.000033rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Non-receptor tyrosine kinase involved in various processes such as cell growth, development, differentiation or histone modifications. Mediates essential signaling events in both innate and adaptive immunity. In the cytoplasm, plays a pivotal role in signal transduction via its association with type I receptors such as growth hormone (GHR), prolactin (PRLR), leptin (LEPR), erythropoietin (EPOR), thrombopoietin (THPO); or type II receptors including IFN-alpha, IFN-beta, IFN-gamma and multiple interleukins (PubMed:7615558). Following ligand-binding to cell surface receptors, phosphorylates specific tyrosine residues on the cytoplasmic tails of the receptor, creating docking sites for STATs proteins (PubMed:9618263). Subsequently, phosphorylates the STATs proteins once they are recruited to the receptor. Phosphorylated STATs then form homodimer or heterodimers and translocate to the nucleus to activate gene transcription. For example, cell stimulation with erythropoietin (EPO) during erythropoiesis leads to JAK2 autophosphorylation, activation, and its association with erythropoietin receptor (EPOR) that becomes phosphorylated in its cytoplasmic domain. Then, STAT5 (STAT5A or STAT5B) is recruited, phosphorylated and activated by JAK2. Once activated, dimerized STAT5 translocates into the nucleus and promotes the transcription of several essential genes involved in the modulation of erythropoiesis. Part of a signaling cascade that is activated by increased cellular retinol and that leads to the activation of STAT5 (STAT5A or STAT5B) (PubMed:21368206). In addition, JAK2 mediates angiotensin-2-induced ARHGEF1 phosphorylation (PubMed:20098430). Plays a role in cell cycle by phosphorylating CDKN1B (PubMed:21423214). Cooperates with TEC through reciprocal phosphorylation to mediate cytokine-driven activation of FOS transcription. In the nucleus, plays a key role in chromatin by specifically mediating phosphorylation of 'Tyr-41' of histone H3 (H3Y41ph), a specific tag that promotes exclusion of CBX5 (HP1 alpha) from chromatin (PubMed:19783980). {ECO:0000269|PubMed:12023369, ECO:0000269|PubMed:19783980, ECO:0000269|PubMed:20098430, ECO:0000269|PubMed:21368206, ECO:0000269|PubMed:21423214, ECO:0000269|PubMed:7615558, ECO:0000269|PubMed:9618263}.;
Disease
DISEASE: Note=Chromosomal aberrations involving JAK2 are found in both chronic and acute forms of eosinophilic, lymphoblastic and myeloid leukemia. Translocation t(8;9)(p22;p24) with PCM1 links the protein kinase domain of JAK2 to the major portion of PCM1. Translocation t(9;12)(p24;p13) with ETV6.; DISEASE: Budd-Chiari syndrome (BDCHS) [MIM:600880]: A syndrome caused by obstruction of hepatic venous outflow involving either the hepatic veins or the terminal segment of the inferior vena cava. Obstructions are generally caused by thrombosis and lead to hepatic congestion and ischemic necrosis. Clinical manifestations observed in the majority of patients include hepatomegaly, right upper quadrant pain and abdominal ascites. Budd-Chiari syndrome is associated with a combination of disease states including primary myeloproliferative syndromes and thrombophilia due to factor V Leiden, protein C deficiency and antithrombin III deficiency. Budd-Chiari syndrome is a rare but typical complication in patients with polycythemia vera. {ECO:0000269|PubMed:16707754}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Polycythemia vera (PV) [MIM:263300]: A myeloproliferative disorder characterized by abnormal proliferation of all hematopoietic bone marrow elements, erythroid hyperplasia, an absolute increase in total blood volume, but also by myeloid leukocytosis, thrombocytosis and splenomegaly. {ECO:0000269|PubMed:15781101, ECO:0000269|PubMed:15793561, ECO:0000269|PubMed:15858187, ECO:0000269|PubMed:16603627}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thrombocythemia 3 (THCYT3) [MIM:614521]: A myeloproliferative disorder characterized by excessive platelet production, resulting in increased numbers of circulating platelets. It can be associated with spontaneous hemorrhages and thrombotic episodes. {ECO:0000269|PubMed:16325696, ECO:0000269|PubMed:22397670}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; DISEASE: Myelofibrosis (MYELOF) [MIM:254450]: A disorder characterized by replacement of the bone marrow by fibrous tissue, occurring in association with a myeloproliferative disorder. Clinical manifestations may include anemia, pallor, splenomegaly, hypermetabolic state, petechiae, ecchymosis, bleeding, lymphadenopathy, hepatomegaly, portal hypertension. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leukemia, acute myelogenous (AML) [MIM:601626]: A subtype of acute leukemia, a cancer of the white blood cells. AML is a malignant disease of bone marrow characterized by maturational arrest of hematopoietic precursors at an early stage of development. Clonal expansion of myeloid blasts occurs in bone marrow, blood, and other tissue. Myelogenous leukemias develop from changes in cells that normally produce neutrophils, basophils, eosinophils and monocytes. {ECO:0000269|PubMed:16247455}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.934

Intolerance Scores

LoFtool
0.189
RVIS EVS
-0.37
RVIS percentile EVS
28.22

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.991

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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