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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
DENND3
DENN domain containing 3
Chromosome 8 Β· 8q24.3
NCBI Gene: 22898Ensembl: ENSG00000105339.11HGNC: HGNC:29134UniProt: A2RUS2
18PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
guanyl-nucleotide exchange factor activityendosome to lysosome transportprotein catabolic processregulation of Rab protein signal transductionOculomotor palsyliver diseaseLower limb painJaundice
✦AI Summary

DENND3 is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RAB12 by promoting GDP-to-GTP exchange 1. The protein contains a unique PHenn domain with both actin-binding and pleckstrin homology-like properties that are essential for its biological function 2. DENND3 regulates autophagy initiation during starvation through RAB12 activation, with GEF activity controlled by intramolecular interactions involving key residues like tyrosine 940 3. Beyond autophagy, DENND3 mediates protein trafficking from recycling endosomes to lysosomes, affecting degradation of cargo proteins like transferrin receptor and amino acid transporters 1. Clinically, DENND3 variants have emerged as genetic modifiers in multiple disease contexts: a missense variant (p.R534S) disrupts cardiac ion channel trafficking, increasing arrhythmogenicity through altered RAB5 distribution 4; loss-of-function mutations impair enteric nervous system development in Hirschsprung disease 5; and variants associate with hereditary hemochromatosis and primary sclerosing cholangitis in Asian populations 67. DENND3 also shows potential involvement in prostatic basal cell carcinoma pathogenesis 8. These findings establish DENND3 as a multifunctional regulator of membrane trafficking with broad disease relevance.

Sources cited
1
DENND3 is a GEF activating RAB12 and regulates autophagy and endosome-to-lysosome transport
PMID: 20937701
2
DENND3 contains a PHenn domain with actin-binding capability required for autophagy function
PMID: 29352104
3
DENND3 GEF activity is regulated through intramolecular interactions controlled by tyrosine 940
PMID: 28249939
4
DENND3-p.R534S variant disrupts cardiac ion channel trafficking and increases arrhythmogenic risk
PMID: 40423607
5
DENND3 loss-of-function mutations impair enteric nervous system development in Hirschsprung disease
PMID: 28274275
6
DENND3 variants are identified in hereditary hemochromatosis in Asian populations
PMID: 34583728
7
DENND3 upregulation associates with primary sclerosing cholangitis and immune dysregulation
PMID: 39496776
8
DENND3 alterations identified in prostatic basal cell carcinoma genomics
PMID: 36309102
Disease Associationsβ“˜20
Oculomotor palsyOpen Targets
0.31Weak
liver diseaseOpen Targets
0.30Weak
Lower limb painOpen Targets
0.30Weak
JaundiceOpen Targets
0.30Weak
Alzheimer diseaseOpen Targets
0.28Weak
color vision disorderOpen Targets
0.28Weak
psoriatic arthritisOpen Targets
0.27Weak
skull disorderOpen Targets
0.26Weak
placenta praeviaOpen Targets
0.25Weak
vascular diseaseOpen Targets
0.25Weak
post term pregnancyOpen Targets
0.24Weak
Hirschsprung diseaseOpen Targets
0.22Weak
angina pectorisOpen Targets
0.21Weak
humerus fractureOpen Targets
0.20Weak
Aganglionic megacolonOpen Targets
0.14Weak
smoking initiationOpen Targets
0.09Suggestive
Abnormality of refractionOpen Targets
0.05Suggestive
lung adenocarcinomaOpen Targets
0.03Suggestive
Abnormality of the skeletal systemOpen Targets
0.03Suggestive
mathematical abilityOpen Targets
0.03Suggestive
Pathogenic Variants1
NM_001352890.3(DENND3):c.2160del (p.Lys720fs)Likely pathogenic
Hirschsprung disease, susceptibility to, 1
β˜†β˜†β˜†β˜†2016β†’ Residue 720
View on ClinVar β†—
Related Genes
RAB12Protein interaction65%DENND4AShared pathway33%DENND4BShared pathway33%GPRASP1Shared pathway33%PLEKHF2Shared pathway25%PGPEP1Shared pathway25%
Tissue Expression6 tissues
Lung
100%
Bone Marrow
76%
Ovary
18%
Heart
14%
Brain
11%
Liver
7%
Gene Interaction Network
Click a node to explore
DENND3RAB12DENND4ADENND4BGPRASP1PLEKHF2PGPEP1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt A2RUS2
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.81LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.66 [0.55–0.81]
RankingsWhere DENND3 stands among ~20K protein-coding genes
  • #14,681of 20,598
    Most Researched18
  • #5,396of 5,498
    Most Pathogenic Variants1
  • #6,727of 17,882
    Most Constrained (LOEUF)0.81
Genes detectedDENND3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Molecular and functional characterization of DENND3 as a novel regulator of ion channel trafficking.
PMID: 40423607
Heart Rhythm Β· 2026
1.00
2
Genomic Characterization of Prostatic Basal Cell Carcinoma.
PMID: 36309102
Am J Pathol Β· 2023
0.90
3
Regulatory T cells-related gene in primary sclerosing cholangitis: evidence from Mendelian randomization and transcriptome data.
PMID: 39496776
Genes Immun Β· 2024
0.80
4
DENND3: a signaling/trafficking interface in autophagy.
PMID: 26177209
Cell Cycle Β· 2015
0.70
5
Correlation of genotype and phenotype in 32 patients with hereditary hemochromatosis in China.
PMID: 34583728
Orphanet J Rare Dis Β· 2021
0.60