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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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RAB39A
RAB39A, member RAS oncogene family
Chromosome 11 · 11q22.3
NCBI Gene: 54734Ensembl: ENSG00000179331.3HGNC: HGNC:16521UniProt: Q14964
47PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transporter
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
lysosomal membranephagocytic vesicleprotein bindingphagosome acidificationanemia (phenotype)cancerAbruptio Placentaebreast carcinoma
✦AI Summary

RAB39A is a small GTPase that functions as a key regulator of intracellular membrane trafficking by cycling between GDP-bound inactive and GTP-bound active states to recruit downstream effectors 1. Its primary role involves regulating autophagosome-lysosome fusion through recruitment of the HOPS endosomal tethering complex onto lysosomes, where lysosomal RAB39A and autophagosomal RAB2A coordinate HOPS subcomplexes to mediate membrane tethering and SNARE-driven fusion 2. RAB39A localizes to the late endocytic pathway at multivesicular bodies and controls trafficking of sphingomyelin, phospholipids, and lysobisphosphatidic acid 3. It negatively regulates LPS-induced autophagosome formation in macrophages through PI3K interaction 4, and facilitates caspase-1-dependent IL-1β secretion by serving as a trafficking adaptor 5. RAB39A plays roles in phagosome maturation and pathogen handling. Clinically, RAB39A exhibits context-dependent effects in cancer: it promotes cancer stemness and tumorigenesis through the RAB39A-RXRB axis in sarcomas and lymphoid malignancies 6, yet acts as an epigenetically silenced tumor suppressor in cervical cancer by inhibiting AKT-mediated EMT 7. Dysregulation implicates RAB39A in neurodevelopmental disorders, as defective DENND5B variants affecting RAB39A interaction cause cognitive impairment and white matter abnormalities 8.

Sources cited
1
RAB39A functions as a small GTPase regulating intracellular membrane trafficking through GDP/GTP cycling
PMID: 21255211
2
RAB39A regulates autophagosome-lysosome fusion via HOPS endosomal tethering complex recruitment
PMID: 37821429
3
RAB39A localizes to late endocytic pathway and controls sphingolipid and phospholipid trafficking
PMID: 30987349
4
RAB39A negatively regulates LPS-induced autophagy in macrophages through PI3K interaction
PMID: 24349490
5
RAB39A binds caspase-1 and is required for IL-1β secretion
PMID: 19833722
6
RAB39A promotes cancer stemness and tumorigenesis through RXRB axis in multiple cancer types
PMID: 29515775
7
RAB39A acts as tumor suppressor in cervical cancer by inhibiting AKT-mediated EMT
PMID: 30826396
8
Defective DENND5B variants affecting RAB39A interaction cause neurodevelopmental disorder with cognitive impairment
PMID: 38387458
Disease Associationsⓘ20
anemia (phenotype)Open Targets
0.27Weak
cancerOpen Targets
0.08Suggestive
Abruptio PlacentaeOpen Targets
0.03Suggestive
breast carcinomaOpen Targets
0.03Suggestive
neoplasmOpen Targets
0.02Suggestive
cervical cancerOpen Targets
0.02Suggestive
sarcomaOpen Targets
0.01Suggestive
osteosarcomaOpen Targets
0.01Suggestive
ataxia telangiectasiaOpen Targets
0.01Suggestive
Parkinson diseaseOpen Targets
0.00Suggestive
infectionOpen Targets
0.00Suggestive
Chlamydia trachomatis infectious diseaseOpen Targets
0.00Suggestive
glioblastomaOpen Targets
0.00Suggestive
gliomaOpen Targets
0.00Suggestive
Invasive Breast CarcinomaOpen Targets
0.00Suggestive
leukemiaOpen Targets
0.00Suggestive
lymphomaOpen Targets
0.00Suggestive
ParkinsonismOpen Targets
0.00Suggestive
pheochromocytomaOpen Targets
0.00Suggestive
Testicular Germ Cell TumorOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
RABGGTAProtein interaction72%RAB4AShared pathway29%RAB30Shared pathway29%RAB39BShared pathway29%RAB20Shared pathway29%RAB2AShared pathway25%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
34%
Lung
7%
Heart
6%
Liver
2%
Ovary
1%
Gene Interaction Network
Click a node to explore
RAB39ARABGGTARAB4ARAB30RAB39BRAB20RAB2A
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q14964
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.19LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.79 [0.54–1.19]
RankingsWhere RAB39A stands among ~20K protein-coding genes
  • #9,262of 20,598
    Most Researched47
  • #12,509of 17,882
    Most Constrained (LOEUF)1.19
Genes detectedRAB39A
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
De novo variants in DENND5B cause a neurodevelopmental disorder.
PMID: 38387458
Am J Hum Genet · 2024
1.00
2
RAB39A: a Rab small GTPase with a prominent role in cancer stemness.
PMID: 29648608
J Biochem · 2018
0.90
3
Rab39a and Rab39b Display Different Intracellular Distribution and Function in Sphingolipids and Phospholipids Transport.
PMID: 30987349
Int J Mol Sci · 2019
0.80
4
Drosophila Rab39 Attenuates Lysosomal Degradation.
PMID: 34638976
Int J Mol Sci · 2021
0.70
5
Prominent role of RAB39A-RXRB axis in cancer development and stemness.
PMID: 29515775
Oncotarget · 2018
0.60