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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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CLIP3
CAP-Gly domain containing linker protein 3
Chromosome 19 · 19q13.12
NCBI Gene: 25999Ensembl: ENSG00000105270.16HGNC: HGNC:24314UniProt: Q96DZ5
21PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingpeptidyl-L-cysteine S-palmitoylationnegative regulation of microtubule polymerizationganglioside bindingneurodegenerative diseaseglioblastoma multiformeatrial fibrillationschizophrenia
✦AI Summary

CLIP3 (CAP-Gly domain containing linker protein 3) is a cytoplasmic linker protein primarily involved in regulating glucose metabolism and membrane trafficking. The protein functions as a trans-Golgi network (TGN) cytoplasmic linker that localizes to the trans-Golgi apparatus and early/recycling endosomes 1. CLIP3 regulates glucose transport in adipocytes by modulating AKT kinase compartmentalization and promoting its membrane localization, which facilitates GLUT4 trafficking to the cell surface 2. This process is controlled by DHHC17-mediated palmitoylation at specific cysteine residues, which regulates CLIP3's plasma membrane association 2. CLIP3 also plays a role in insulin-regulated glucose metabolism, where insulin downregulates miR-593-3p to increase CLIP3 expression and promote glycolysis 3. Beyond metabolic functions, CLIP3 regulates TNF-α-induced apoptosis by controlling RIP1 ubiquitination through interaction with the deubiquitinating enzyme CYLD 4. Clinically, CLIP3 expression is frequently downregulated in glioblastoma, where its loss enhances stemness and glycolytic activity, promoting radioresistance 5. Additionally, altered DNA methylation at the CLIP3 locus is associated with cardiovascular disease risk in smokers 6, and CLIP3 serves as a prognostic marker in stomach adenocarcinoma 7.

Sources cited
1
CLIP3 (CLIPR-59) is a CLIP-170-related protein localized to trans-Golgi apparatus with functional microtubule-binding domains; overexpression perturbs early/recycling endosome-TGN dynamics
PMID: 11854307
2
CLIP3 (ClipR-59) interacts with Akt and regulates Glut4 membrane trafficking; DHHC17 palmitoylates CLIP3 at Cys534/535 to promote plasma membrane association
PMID: 24001771
3
CLIP3 mediates insulin-regulated glucose metabolism; insulin downregulates miR-593-3p to increase CLIP3 expression and promote glycolysis
PMID: 27613819
4
CLIP3 (CLIPR-59) regulates TNF-α-induced apoptosis by controlling RIP1 ubiquitination through association with CYLD deubiquitinating enzyme
PMID: 22297296
5
CLIP3 downregulation in glioblastoma enhances stemness and glycolytic flux; Spy1-CLIP3 axis regulates GLUT3 trafficking; glimepiride restores CLIP3 to overcome radioresistance
PMID: 34488821
6
DNA methylation at CLIP3 locus (cg21647257) is associated with atrial fibrillation risk in smokers through epigenetic mechanisms
PMID: 39748436
7
CLIP3 is identified as a hub gene in stomach adenocarcinoma with prognostic significance; low CLIP3 levels associated with better survival and immunotherapy responsiveness
PMID: 39885324
8
miR-145 induces m6A loss of CLIP3 mRNA through FTO/AGO1/ILF3 complex formation, increasing CLIP3 nascent translation during glioma stem cell differentiation
PMID: 33684100
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.26Weak
glioblastoma multiformeOpen Targets
0.07Suggestive
atrial fibrillationOpen Targets
0.04Suggestive
schizophreniaOpen Targets
0.03Suggestive
chronic lymphocytic leukemiaOpen Targets
0.02Suggestive
periodontitisOpen Targets
0.01Suggestive
glioblastomaOpen Targets
0.01Suggestive
endometrial carcinomaOpen Targets
0.01Suggestive
cholangiocarcinomaOpen Targets
0.01Suggestive
Alzheimer diseaseOpen Targets
0.01Suggestive
esophageal squamous cell carcinomaOpen Targets
0.01Suggestive
neoplasmOpen Targets
0.01Suggestive
cancerOpen Targets
0.01Suggestive
acute lymphoblastic leukemiaOpen Targets
0.01Suggestive
acute myeloid leukemiaOpen Targets
0.01Suggestive
gastric adenocarcinomaOpen Targets
0.01Suggestive
coronary atherosclerosisOpen Targets
0.01Suggestive
myocardial infarctionOpen Targets
0.01Suggestive
gliomaOpen Targets
0.00Suggestive
dilated cardiomyopathyOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
CYLDProtein interaction92%ZDHHC8Shared pathway14%HOOK1Shared pathway13%KATNB1Shared pathway13%HOOK2Shared pathway12%AKTIPShared pathway11%
Tissue Expression6 tissues
Brain
100%
Ovary
32%
Heart
5%
Lung
4%
Liver
2%
Bone Marrow
1%
Gene Interaction Network
Click a node to explore
CLIP3CYLDZDHHC8HOOK1KATNB1HOOK2AKTIP
PROTEIN STRUCTURE
Preparing viewer…
PDB2CP0 · NMR
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.40Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.25 [0.17–0.40]
RankingsWhere CLIP3 stands among ~20K protein-coding genes
  • #13,870of 20,598
    Most Researched21
  • #1,984of 17,882
    Most Constrained (LOEUF)0.40 · top quartile
Genes detectedCLIP3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Unraveling the causal impact of smoking and its DNA methylation signatures on cardiovascular disease: Mendelian randomization and colocalization analysis.
PMID: 39748436
Clin Epigenetics · 2025
1.00
2
MicroRNA-593-3p regulates insulin-promoted glucose consumption by targeting Slc38a1 and CLIP3.
PMID: 27613819
J Mol Endocrinol · 2016
0.90
3
miRNA-mediated loss of m6A increases nascent translation in glioblastoma.
PMID: 33684100
PLoS Genet · 2021
0.80
4
Downregulated CLIP3 induces radioresistance by enhancing stemness and glycolytic flux in glioblastoma.
PMID: 34488821
J Exp Clin Cancer Res · 2021
0.70
5
Integrating multiomics analysis and machine learning to refine the molecular subtyping and prognostic analysis of stomach adenocarcinoma.
PMID: 39885324
Sci Rep · 2025
0.60