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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SUPT3H
SPT3 homolog, SAGA and STAGA complex component
Chromosome 6 · 6p21.1
NCBI Gene: 8464Ensembl: ENSG00000196284.19HGNC: HGNC:11466UniProt: B4E1H0
74PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Hub GeneTranscription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
transcription coactivator activityregulation of transcription by RNA polymerase IInucleusnucleoplasmAbnormality of the skeletal systemosteoarthritis, hipcleidocranial dysplasia 1skin aging
✦AI Summary

SUPT3H is a transcriptional coactivator and core component of the SAGA (Spt-Ada-Gcn5 Acetyltransferase) complex, conserved from yeast to humans 1. As a histone-fold domain-containing protein, SUPT3H contributes one histone-fold pair to the SAGA complex's octamer-like scaffold structure 2. While SUPT3H's yeast ortholog Spt3 interacts with TATA-binding protein (TBP) and regulates global RNA polymerase II transcription 2, mammalian SUPT3H functions distinctly. In mouse embryonic stem cells, SUPT3H is dispensable for SAGA assembly and global Pol II transcription but essential for cell growth and self-renewal, affecting only a specific subset of genes 2. Beyond transcription, SUPT3H variants associate with facial morphology variation in Eurasian populations 3 and knee osteoarthritis progression risk 4. SUPT3H also participates in bone metabolism: a long noncoding RNA derived from SUPT3H (lnc-SUPT3H-1:16) acts as a competing endogenous RNA regulating parathyroid hormone-stimulated osteoblast differentiation through miRNA-6797-5p sponging 5. Additionally, SUPT3H variants associate with ADAMTS13 activity levels 6, and the SUPT3H promoter physically interacts with the RUNX2-P1 bone-specific promoter during osteoblast differentiation 7. These findings demonstrate SUPT3H's multifaceted roles in transcriptional regulation and development beyond its SAGA complex function.

Sources cited
1
SUPT3H is a histone-fold domain-containing protein in SAGA complex; not required for assembly, TBP recruitment, or global Pol II transcription in mammals but essential for mESC growth and self-renewal
PMID: 35871303
2
SUPT3H is the human homologue of yeast Spt3 transcription factor with conserved functional domains
PMID: 9787080
3
SUPT3H rs227833 SNP is associated with facial shape variation in Eurasian populations
PMID: 31025105
4
SUPT3H rs10948172 SNP is a genetic biomarker for predicting knee osteoarthritis structural progression
PMID: 36089590
5
Long noncoding RNA lnc-SUPT3H-1:16 acts as competing endogenous RNA sponging miR-6797-5p to regulate Runx2 expression and PTH-stimulated osteoblast differentiation
PMID: 30562548
6
SUPT3H promoter physically interacts with RUNX2-P1 bone-specific promoter and can modulate its activity during osteoblast differentiation
PMID: 25120271
7
SUPT3H rs10456544 variant is associated with ADAMTS13 activity levels
PMID: 25934476
8
SUPT3H is identified as a hub protein in protein-protein interaction network associated with USP22 in hepatocellular carcinoma
PMID: 40814554
Disease Associationsⓘ20
Abnormality of the skeletal systemOpen Targets
0.44Moderate
osteoarthritis, hipOpen Targets
0.40Weak
cleidocranial dysplasia 1Open Targets
0.38Weak
skin agingOpen Targets
0.34Weak
Metaphyseal dysplasia - maxillary hypoplasia - brachydactyOpen Targets
0.33Weak
metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndromeOpen Targets
0.33Weak
total hip arthroplastyOpen Targets
0.30Weak
otosclerosisOpen Targets
0.29Weak
osteoarthritis, kneeOpen Targets
0.28Weak
bone diseaseOpen Targets
0.28Weak
glaucomaOpen Targets
0.28Weak
osteoarthritis, handOpen Targets
0.28Weak
osteoarthritisOpen Targets
0.27Weak
Inguinal herniaOpen Targets
0.26Weak
facial morphologyOpen Targets
0.24Weak
medical procedureOpen Targets
0.24Weak
total joint arthroplastyOpen Targets
0.23Weak
complicationOpen Targets
0.22Weak
trauma complicationOpen Targets
0.22Weak
Abnormality of the gastrointestinal tractOpen Targets
0.21Weak
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
DR1Protein interaction100%KAT2AProtein interaction100%GPS2Protein interaction100%SARS1Protein interaction100%TADA2AProtein interaction100%TAF2Protein interaction100%
Tissue Expression6 tissues
Ovary
100%
Brain
76%
Bone Marrow
52%
Lung
33%
Heart
27%
Liver
23%
Gene Interaction Network
Click a node to explore
SUPT3HDR1KAT2AGPS2SARS1TADA2ATAF2
PROTEIN STRUCTURE
Preparing viewer…
PDB7KTR · 2.93 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.34LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.89 [0.61–1.34]
RankingsWhere SUPT3H stands among ~20K protein-coding genes
  • #6,433of 20,598
    Most Researched74
  • #14,044of 17,882
    Most Constrained (LOEUF)1.34
Genes detectedSUPT3H
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population.
PMID: 31025105
Hum Genet · 2019
1.00
2
SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells.
PMID: 35871303
Nucleic Acids Res · 2022
0.90
3
Single nucleotide polymorphism genes and mitochondrial DNA haplogroups as biomarkers for early prediction of knee osteoarthritis structural progressors: use of supervised machine learning classifiers.
PMID: 36089590
BMC Med · 2022
0.80
4
Parathyroid hormone-stimulation of Runx2 during osteoblast differentiation via the regulation of lnc-SUPT3H-1:16 (RUNX2-AS1:32) and miR-6797-5p.
PMID: 30562548
Biochimie · 2019
0.70
5
The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter.
PMID: 25120271
Nucleic Acids Res · 2014
0.60