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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
TFE3
transcription factor binding to IGHM enhancer 3
Chromosome X Β· Xp11.23
NCBI Gene: 7030Ensembl: ENSG00000068323.18HGNC: HGNC:11752UniProt: B4DIA5
222PubMed Papers
2Diseases
0Drugs
20Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedOncogeneTranscription Factor
RESEARCH IMPACT
Trending
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of cell adhesionpositive regulation of DNA-templated transcriptionpositive regulation of transcription by RNA polymerase IIprotein bindingIntellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse faciesRenal cell carcinoma Xp11-associated
✦AI Summary

TFE3 is a master transcriptional regulator of lysosomal biogenesis and autophagy that functions downstream of mTORC1 signaling 1. Under nutrient-rich conditions, mTORC1-mediated phosphorylation promotes TFE3 cytoplasmic retention and inactivation, while starvation or lysosomal stress leads to TFE3 dephosphorylation and nuclear translocation 1. TFE3 recognizes and binds E-box and CLEAR-box sequences to activate lysosomal gene expression 1. Additionally, AMPK phosphorylates TFE3 on serine residues to enhance its transcriptional activity during metabolic stress, creating a dual regulatory mechanism where mTORC1 controls subcellular localization while AMPK modulates transcriptional function 1. Clinically, TFE3 is highly relevant in cancer biology through chrX translocations that create oncogenic fusion proteins. TFE3 translocations drive aggressive renal cell carcinomas (tRCC) and perivascular epithelioid cell tumors (PEComas), with ASPSCR1-TFE3 fusions associated with particularly poor outcomes 23. These fusion proteins form liquid-like condensates that enhance transcriptional activity, alter chrX accessibility, and drive tumor progression 4. Notably, TFE3-rearranged PEComas show association with prior chemotherapy exposure and demonstrate resistance to mTOR inhibitor therapy, highlighting the clinical importance of understanding TFE3 dysregulation in cancer 3.

Sources cited
1
AMPK phosphorylates TFE3 for transcriptional activation while mTORC1 controls cytoplasmic retention
PMID: 33734022
2
TFE3 translocations drive aggressive renal cell carcinomas with ASPSCR1-TFE3 fusions showing poor outcomes
PMID: 34489456
3
TFE3-rearranged PEComas associate with prior chemotherapy exposure and show resistance to mTOR inhibitors
PMID: 38597260
4
TFE3 fusion proteins form condensates that enhance transcriptional activity and drive tumor progression
PMID: 40222010
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜2
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse faciesUniProt
Renal cell carcinoma Xp11-associatedUniProt
Pathogenic Variants20
NM_006521.6(TFE3):c.560C>T (p.Thr187Met)Pathogenic
Inborn genetic diseases|Neurodevelopmental abnormality|Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies|Renal cell carcinoma|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 187
NM_006521.6(TFE3):c.350G>A (p.Arg117Gln)Pathogenic
Neurodevelopmental disorder|not provided|Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜…β˜†β˜†2024β†’ Residue 117
NM_006521.6(TFE3):c.350_358del (p.Arg117_Gln119del)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 117
NM_006521.6(TFE3):c.572T>C (p.Leu191Pro)Pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2024β†’ Residue 191
NM_006521.6(TFE3):c.338G>A (p.Arg113Lys)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 113
NM_006521.6(TFE3):c.608T>C (p.Leu203Pro)Likely pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2023β†’ Residue 203
NM_006521.6(TFE3):c.556C>A (p.Pro186Thr)Likely pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2023β†’ Residue 186
NM_006521.6(TFE3):c.560C>A (p.Thr187Lys)Pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2023β†’ Residue 187
NM_006521.6(TFE3):c.554A>G (p.Asn185Ser)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 185
NM_006521.6(TFE3):c.556C>T (p.Pro186Ser)Likely pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2022β†’ Residue 186
NM_006521.6(TFE3):c.349C>T (p.Arg117Trp)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 117
NM_006521.6(TFE3):c.569A>G (p.His190Arg)Likely pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2021β†’ Residue 190
NM_006521.6(TFE3):c.559A>G (p.Thr187Ala)Pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2021β†’ Residue 187
NM_006521.6(TFE3):c.374_379del (p.123AQ[1])Likely pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†2021
NM_006521.6(TFE3):c.566A>G (p.Tyr189Cys)Likely pathogenic
Intellectual disability
β˜…β˜†β˜†β˜†2020β†’ Residue 189
NM_006521.6(TFE3):c.557C>T (p.Pro186Leu)Likely pathogenic
not provided|Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜…β˜†β˜†β˜†β†’ Residue 186
NM_006521.6(TFE3):c.780+1G>APathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies|Thyroid cancer, nonmedullary, 1
β˜†β˜†β˜†β˜†2021
NM_006521.6(TFE3):c.560C>G (p.Thr187Arg)Pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜†β˜†β˜†β˜†2021β†’ Residue 187
NM_006521.6(TFE3):c.602A>C (p.Gln201Pro)Pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜†β˜†β˜†β˜†2021β†’ Residue 201
NM_006521.6(TFE3):c.356A>C (p.Gln119Pro)Pathogenic
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
β˜†β˜†β˜†β˜†2021β†’ Residue 119
View on ClinVar β†—
Related Genes
TBC1D25Protein interaction97%PRCCProtein interaction97%E2F3Protein interaction88%CLTCProtein interaction82%SMAD3Protein interaction76%SFPQProtein interaction75%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
Click a node to explore
TFE3TBC1D25PRCCE2F3CLTCSMAD3SFPQ
PROTEIN STRUCTURE
Preparing viewer…
PDB7F09 Β· 2.60 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.30Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.14 [0.07–0.30]
RankingsWhere TFE3 stands among ~20K protein-coding genes
  • #1,850of 20,598
    Most Researched222 Β· top 10%
  • #2,180of 5,498
    Most Pathogenic Variants20
  • #1,154of 17,882
    Most Constrained (LOEUF)0.30 Β· top 10%
Genes detectedTFE3
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
AMPK-dependent phosphorylation is required for transcriptional activation of TFEB and TFE3.
PMID: 33734022
Autophagy Β· 2021
1.00
2
Integrated exome and RNA sequencing of TFE3-translocation renal cell carcinoma.
PMID: 34489456
Nat Commun Β· 2021
0.90
3
PEComa-its clinical features, histopathology, and current therapy.
PMID: 40336169
Jpn J Clin Oncol Β· 2025
0.80
4
GPNMB expression identifies TSC1/2/mTOR-associated and MiT family translocation-driven renal neoplasms.
PMID: 35072947
J Pathol Β· 2022
0.70
5
MITF, TFEB, and TFE3 drive distinct adaptive gene expression programs and immune infiltration in melanoma.
PMID: 41275493
Cell Rep Β· 2025
0.64