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GeneE
50 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.
SOX9
SRY-box transcription factor 9
Chromosome 17 Β· 17q24.3
NCBI Gene: 6662Ensembl: ENSG00000125398.9HGNC: HGNC:11204UniProt: P48436
567PubMed Papers
23Diseases
0Drugs
137Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
Highly StudiedVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of cell population proliferationmale gonad developmentcellular response to interleukin-1regulation of cell cycle processcampomelic dysplasiaPierre-Robin sequenceneurodegenerative diseasecolorectal adenocarcinoma
✦AI Summary

SOX9 is a transcription factor that serves as a master regulator of chondrocyte differentiation and skeletal development 1. It binds the 5'-ACAAAG-3' DNA motif to promote expression of cartilage matrix genes including COL2A1, COL9A1, and ACAN 2. SOX9 is absolutely required for precartilaginous condensation and works with SOX5/SOX6 during early chondrogenesis, while also directing hypertrophic maturation by suppressing osteoblast differentiation through reduced Ξ²-catenin signaling 3. Beyond skeletal development, SOX9 functions in other tissues: it promotes astrocyte differentiation from pluripotent stem cells 4, regulates alternative splicing in pancreatic beta cells to maintain insulin secretion 5, and maintains lung progenitor proliferation by amplifying WNT and RTK signaling 6. SOX9 exhibits context-dependent roles in cancer: it acts as a tumor suppressor in colorectal cancer by inhibiting epithelial-mesenchymal transition and SOX2 induction, with low SOX9 expression correlating with poor prognosis 7. Therapeutically, SOX9 gene delivery via rAAV vectors in alginate hydrogels promotes cartilage regeneration by increasing extracellular matrix deposition in osteoarthritic chondrocytes 8. Mutations in SOX9 cause campomelic dysplasia and sex reversal disorders, underscoring its critical developmental roles.

Sources cited
1
SOX9 plays a key role in chondrocyte differentiation and skeletal development
PMID: 24038782
2
SOX9 binds the 5'-ACAAAG-3' DNA motif and promotes expression of cartilage matrix genes including COL2A1, COL9A1, and ACAN
PMID: 8640233
3
SOX9+ progenitors recapitulate endochondral ossification stages including condensation, chondrocyte hypertrophy, vascular invasion, and bone formation
PMID: 40118845
4
SOX9 overexpression rapidly and efficiently induces functional astrocytes from human pluripotent stem cells
PMID: 30127505
5
SOX9 regulates alternative splicing in mature pancreatic beta cells to maintain insulin secretion; loss of SOX9 causes defective insulin secretion and glucose intolerance
PMID: 38238288
6
SOX9 promotes lung progenitor proliferation and maintains progenitor state by amplifying WNT and RTK signaling
PMID: 36121125
7
SOX9 acts as a tumor suppressor in colorectal cancer; low SOX9 expression correlates with higher tumor grade, poor survival, and increased metastatic potential
PMID: 40179020
8
SOX9 gene delivery via rAAV/alginate hydrogel increases extracellular matrix deposition in osteoarthritic cartilage for therapeutic regeneration
PMID: 41520176
Disease Associationsβ“˜23
campomelic dysplasiaOpen Targets
0.86Strong
Pierre-Robin sequenceOpen Targets
0.56Moderate
neurodegenerative diseaseOpen Targets
0.55Moderate
colorectal adenocarcinomaOpen Targets
0.51Moderate
genetic disorderOpen Targets
0.50Moderate
46,XY complete gonadal dysgenesisOpen Targets
0.47Moderate
connective tissue diseaseOpen Targets
0.47Moderate
46,XX testicular disorder of sex developmentOpen Targets
0.47Moderate
isolated Pierre-Robin syndromeOpen Targets
0.46Moderate
colorectal cancerOpen Targets
0.42Moderate
kidney diseaseOpen Targets
0.40Moderate
nontoxic goiterOpen Targets
0.38Weak
46,XX ovotesticular disorder of sex developmentOpen Targets
0.38Weak
cleft palateOpen Targets
0.37Weak
46,XY partial gonadal dysgenesisOpen Targets
0.37Weak
Varicose veinsOpen Targets
0.34Weak
osteoarthritis, kneeOpen Targets
0.33Weak
colon adenocarcinomaOpen Targets
0.33Weak
pancreatitisOpen Targets
0.33Weak
prostate carcinomaOpen Targets
0.33Weak
46,XX sex reversal 2UniProt
46,XY sex reversal 10UniProt
Campomelic dysplasiaUniProt
Pathogenic Variants137
NM_000346.4(SOX9):c.1320C>A (p.Tyr440Ter)Pathogenic
Camptomelic dysplasia|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 440
NM_000346.4(SOX9):c.1320C>G (p.Tyr440Ter)Pathogenic
CAMPOMELIC DYSPLASIA WITH AUTOSOMAL SEX REVERSAL|Camptomelic dysplasia|not provided|Connective tissue disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 440
NM_000346.4(SOX9):c.788dup (p.Arg264fs)Pathogenic
CAMPOMELIC DYSPLASIA WITH AUTOSOMAL SEX REVERSAL|not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 264
NM_000346.4(SOX9):c.1180C>T (p.Arg394Ter)Pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2024β†’ Residue 394
NM_000346.4(SOX9):c.509C>G (p.Pro170Arg)Pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2024β†’ Residue 170
NM_000346.4(SOX9):c.442G>T (p.Glu148Ter)Pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2023β†’ Residue 148
NM_000346.4(SOX9):c.508C>A (p.Pro170Thr)Pathogenic
Camptomelic dysplasia|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 170
NM_000346.4(SOX9):c.508C>T (p.Pro170Ser)Pathogenic
Camptomelic dysplasia|CAMPOMELIC DYSPLASIA WITH AUTOSOMAL SEX REVERSAL|not provided|See cases
β˜…β˜…β˜†β˜†2023β†’ Residue 170
NM_000346.4(SOX9):c.337A>G (p.Met113Val)Pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2023β†’ Residue 113
NM_000346.4(SOX9):c.473C>T (p.Ala158Val)Pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2023β†’ Residue 158
NM_000346.4(SOX9):c.455G>C (p.Arg152Pro)Pathogenic
Camptomelic dysplasia|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 152
NM_000346.4(SOX9):c.331G>A (p.Ala111Thr)Pathogenic
Inborn genetic diseases|SOX9-related disorder
β˜…β˜…β˜†β˜†2022β†’ Residue 111
NM_000346.4(SOX9):c.508C>G (p.Pro170Ala)Pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2022β†’ Residue 170
NM_000346.4(SOX9):c.1018C>T (p.Gln340Ter)Pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2022β†’ Residue 340
NM_000346.4(SOX9):c.432-2A>TPathogenic
Camptomelic dysplasia
β˜…β˜…β˜†β˜†2021
NM_000346.4(SOX9):c.527C>G (p.Pro176Arg)Likely pathogenic
not provided|Camptomelic dysplasia
β˜…β˜…β˜†β˜†2020β†’ Residue 176
NM_000346.4(SOX9):c.498G>C (p.Lys166Asn)Likely pathogenic
Camptomelic dysplasia
β˜…β˜†β˜†β˜†2026β†’ Residue 166
NM_000346.4(SOX9):c.685+2T>CPathogenic
Camptomelic dysplasia
β˜…β˜†β˜†β˜†2025
NM_000346.4(SOX9):c.339G>A (p.Met113Ile)Likely pathogenic
Camptomelic dysplasia
β˜…β˜†β˜†β˜†2025β†’ Residue 113
NM_000346.4(SOX9):c.1224_1251dup (p.Ile418fs)Pathogenic
Camptomelic dysplasia
β˜…β˜†β˜†β˜†2025β†’ Residue 418
View on ClinVar β†—
Related Genes
TWIST1Protein interaction95%PRKACAProtein interaction93%PRKACBProtein interaction93%CDH1Protein interaction93%PRKACGProtein interaction93%NR0B1Protein interaction92%
Tissue Expression6 tissues
Brain
100%
Heart
59%
Liver
10%
Lung
5%
Bone Marrow
1%
Ovary
0%
Gene Interaction Network
Click a node to explore
SOX9TWIST1PRKACAPRKACBCDH1PRKACGNR0B1
PROTEIN STRUCTURE
Preparing viewer…
PDB4EUW Β· 2.77 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.15Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.05 [0.02–0.15]
RankingsWhere SOX9 stands among ~20K protein-coding genes
  • #422of 20,598
    Most Researched567 Β· top 5%
  • #561of 5,498
    Most Pathogenic Variants137 Β· top quartile
  • #224of 17,882
    Most Constrained (LOEUF)0.15 Β· top 5%
Genes detectedSOX9
Sources retrieved50 papers
Response timeβ€”
πŸ“„ Sources
50β–Ό
1
Rapid and efficient induction of functional astrocytes from human pluripotent stem cells.
PMID: 30127505
Nat Methods Β· 2018
1.00
2
Sox9 regulates alternative splicing and pancreatic beta cell function.
PMID: 38238288
Nat Commun Β· 2024
0.90
3
SOX9: an important factor in regulating breast cancer.
PMID: 40826431
Eur J Med Res Β· 2025
0.84
4
Recapitulation of endochondral ossification by hPSC-derived SOX9
PMID: 40118845
Nat Commun Β· 2025
0.80
5
SOX9 Induces Orbital Fibroblast Activation in Thyroid Eye Disease Via MAPK/ERK1/2 Pathway.
PMID: 38345552
Invest Ophthalmol Vis Sci Β· 2024
0.80