IL3

Chr 5

interleukin 3

Also known as: IL-3, MCGF, MULTI-CSF

NCBI Gene: 3562ENSG00000164399UniProt: P08700

The protein encoded by this gene is a potent growth promoting cytokine. This cytokine is capable of supporting the proliferation of a broad range of hematopoietic cell types. It is involved in a variety of cell activities such as cell growth, differentiation and apoptosis. This cytokine has been shown to also possess neurotrophic activity, and it may be associated with neurologic disorders. [provided by RefSeq, Jul 2008]

41
ClinVar variants
16
Pathogenic / LP
0.00
pLI score
2
Active trials
Clinical Summary— IL3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
16 Pathogenic / Likely Pathogenic· 14 VUS of 41 total submissions
💊
Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.93LOEUF
pLI 0.000
Z-score -1.28
OE 1.51 (0.91–1.93)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.23Z-score
OE missense 0.93 (0.78–1.11)
86 obs / 92.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.51 (0.91–1.93)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.93 (0.78–1.11)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.96
0≤1.21.6
LoF obs/exp: 11 / 7.3Missense obs/exp: 86 / 92.3Syn Z: 0.20

ClinVar Variant Classifications

41 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14
Likely Pathogenic2
VUS14
Likely Benign8
Benign3
14
Pathogenic
2
Likely Pathogenic
14
VUS
8
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
14
0
14
Likely Pathogenic
0
0
2
0
2
VUS
0
12
2
0
14
Likely Benign
0
7
1
0
8
Benign
0
1
1
1
3
Total02020141

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

IL3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
INTERLEUKIN 3; IL3
MIM #147740 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
GM-CSF, IL-3, and IL-5 Family of Cytokines: Regulators of Inflammation.
Dougan M et al.·Immunity
2019Review
Mast Cell Biology at Molecular Level: a Comprehensive Review.
Elieh Ali Komi D et al.·Clin Rev Allergy Immunol
2020Review
Control of acute myeloid leukemia by a trifunctional NKp46-CD16a-NK cell engager targeting CD123.
Gauthier L et al.·Nat Biotechnol
2023Functional
Interleukin-11.
Kobayashi S et al.·Leuk Lymphoma
1994Review
HTLV-I uveitis.
Mochizuki M et al.·J Acquir Immune Defic Syndr Hum Retrovirol
1996Review
Human cell surface-AAV interactomes identify LRP6 as blood-brain barrier transcytosis receptor and immune cytokine IL3 as AAV9 binder.
Shay TF et al.·Nat Commun
2024
CD123-targeting immunotherapeutic approaches in acute myeloid leukaemia.
Dreyzin A et al.·Br J Haematol
2025Review
[Cytokines and hematopoiesis].
Wickenhauser C et al.·Pathologe
1995Review
Hypereosinophilic syndrome: an update.
Wilkins HJ et al.·Am J Hematol
2005Review
ETV6::ACSL6 translocation-driven super-enhancer activation leads to eosinophilia in acute lymphoblastic leukemia through IL-3 overexpression.
Xu W et al.·Haematologica
2024
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Adult Acute Myeloid Leukemia in RemissionAcute Biphenotypic LeukemiaEarly Relapse of Acute Myeloid Leukemia

Genetically Modified T-cell Immunotherapy in Treating Patients With Relapsed/Refractory Acute Myeloid Leukemia and Persistent/Recurrent Blastic Plasmacytoid Dendritic Cell Neoplasm

ACTIVE NOT RECRUITING
NCT02159495Phase PHASE1City of Hope Medical CenterStarted 2015-12-15
cyclophosphamideAutologous CD123CAR-CD28-CD3zeta-EGFRt-expressing T Lymphocyteslaboratory biomarker analysis
Healthy AdultsHigh AltitudeIsolation, Social

Human Milk Oligosaccharides (HMOs) and Gut Microbiota, Immune System in Antarctica

ENROLLING BY INVITATION
NCT06133530Phase NAIU University of Applied SciencesStarted 2023-09-24
Human milk oligosaccharidesMaltose

External Resources

Links to major genomics databases and tools