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GeneE
25 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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YBX3
Y-box binding protein 3
Chromosome 12 · 12p13.2
NCBI Gene: 8531Ensembl: ENSG00000060138.14HGNC: HGNC:2428UniProt: P16989
228PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
Trending
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingRNA bindingnegative regulation of intrinsic apoptotic signaling pathway in response to osmotic stressnegative regulation of necroptotic processcoronary artery diseaseAbnormality of refractionneurodegenerative diseasemenopause
✦AI Summary

YBX3 (Y-box binding protein 3) is an RNA-binding protein that functions primarily as a regulator of mRNA stability and translation. YBX3 contains a highly conserved cold-shock domain and binds to specific RNA sequences, particularly the 3'-UTR regions of target mRNAs 1. The protein exhibits dual functions in cellular regulation: it can enhance mRNA stability and translation of certain targets like SPRED1 through direct binding to CACAUC motifs 2, while also promoting degradation of others such as SLC7A11 3. YBX3 expression varies significantly across cancer types and is associated with tumor progression through multiple mechanisms 1. In B cell development, YBX3 expression reciprocally correlates with transcription factor EBF1 during pre-BCR-dependent proliferative phases 4. The protein plays critical roles in immune evasion, with depletion leading to enhanced antigen presentation and pro-inflammatory gene expression 5. YBX3 is regulated by various mechanisms including protein stabilization through TTC36 binding that prevents proteasomal degradation 2, and interaction with long non-coding RNAs like HEIH and PIG13-DT that affect its stability and function 16. Clinically, YBX3 expression correlates with tumor grading, immune therapy responses, and drug resistance patterns across multiple cancer types.

Sources cited
1
YBX3 expression reciprocally correlates with EBF1 during B cell development pre-BCR stages
PMID: 34824268
2
YBX3 encodes a protein with conserved cold-shock domain and varies significantly across cancer types
PMID: 36059530
3
YBX3 depletion leads to derepression of pro-inflammatory genes and enhanced antigen presentation
PMID: 41025501
4
YBX3 interacts with lncRNA PIG13-DT and promotes USP15 mRNA translation and stability
PMID: 41065761
5
YBX3 promotes degradation of SLC7A11 and regulates ferroptosis in colorectal cancer
PMID: 41213937
6
YBX3 enhances SPRED1 mRNA stability by binding CACAUC motifs in 3'-UTR and is stabilized by TTC36
PMID: 41208883
Disease Associationsⓘ20
coronary artery diseaseOpen Targets
0.42Moderate
Abnormality of refractionOpen Targets
0.31Weak
neurodegenerative diseaseOpen Targets
0.31Weak
menopauseOpen Targets
0.31Weak
brain injuryOpen Targets
0.17Weak
azoospermiaOpen Targets
0.10Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.08Suggestive
colorectal carcinomaOpen Targets
0.08Suggestive
partial chromosome Y deletionOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.08Suggestive
cancerOpen Targets
0.08Suggestive
nasopharyngeal carcinomaOpen Targets
0.08Suggestive
chronic myelogenous leukemiaOpen Targets
0.07Suggestive
spermatogenic failure 25Open Targets
0.07Suggestive
spermatogenic failure 57Open Targets
0.07Suggestive
spermatogenic failure 50Open Targets
0.07Suggestive
neoplasmOpen Targets
0.07Suggestive
spermatogenic failure 71Open Targets
0.06Suggestive
spermatogenic failure, X-linked, 2Open Targets
0.06Suggestive
spermatogenic failure 63Open Targets
0.06Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
TJP1Protein interaction100%DCNProtein interaction99%YBX1Protein interaction99%CCND1Protein interaction96%CDK4Protein interaction96%SYMPKProtein interaction96%
Tissue Expression6 tissues
Heart
100%
Lung
90%
Ovary
41%
Bone Marrow
13%
Brain
11%
Liver
9%
Gene Interaction Network
Click a node to explore
YBX3TJP1DCNYBX1CCND1CDK4SYMPK
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt P16989
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.01LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.73 [0.54–1.01]
RankingsWhere YBX3 stands among ~20K protein-coding genes
  • #1,776of 20,598
    Most Researched228 · top 10%
  • #9,853of 17,882
    Most Constrained (LOEUF)1.01
Genes detectedYBX3
Sources retrieved25 papers
Response time—
📄 Sources
25▼
1
Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation.
PMID: 34824268
Nat Commun · 2021
1.00
2
Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer.
PMID: 36059530
Front Immunol · 2022
0.90
3
Protein-level mutant p53 reporters identify druggable rare precancerous clones in noncancerous tissues.
PMID: 37537298
Nat Cancer · 2023
0.80
4
A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m
PMID: 40615396
Nat Commun · 2025
0.76
5
YBX1&YBX3 as novel targets to potentiate immune checkpoint blockade response in gliomas.
PMID: 41025501
Neuro Oncol · 2026
0.70