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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SCUBE3
signal peptide, CUB domain and EGF like domain containing 3
Chromosome 6 Β· 6p21.31
NCBI Gene: 222663Ensembl: ENSG00000146197.10HGNC: HGNC:13655UniProt: Q8IX30
30PubMed Papers
21Diseases
0Drugs
11Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of osteoblast differentiationcell surfaceplasma membraneidentical protein bindingshort stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2Abnormal facial shapeAbnormality of the skeletal systemShort stature
✦AI Summary

SCUBE3 is a secreted multifunctional glycoprotein that functions as a critical positive regulator of skeletal development and tissue regeneration. Mechanistically, SCUBE3 acts as a BMP2/BMP4 co-receptor that recruits BMP receptor complexes into lipid raft microdomains, facilitating interactions between BMPs and BMP type I receptors to enhance signaling 1. It also binds to TGFBR2 and activates TGF-Ξ² signaling 2. During osteogenic differentiation, SCUBE3 levels increase significantly and promote osteogenesis through BMP2/TGF-Ξ² pathway activation and mitophagy induction 3. In dental development, epithelium-derived SCUBE3 translocates paracrine to mesenchymal cells where it enhances odontoblastic differentiation and pulp regeneration 2. Hair follicle development also depends on SCUBE3 secretion by dermal papilla fibroblasts; microinjection of SCUBE3 protein alone is sufficient to induce new hair growth 4. Biallelic SCUBE3 inactivation causes a syndromic disorder with short stature, skeletal anomalies, craniofacial dysmorphism, and dental defects 1. Clinically, SCUBE3 is pathologically elevated in multiple cancers where it promotes tumor progression through EGFR and TGFΞ²RI/II interactions, supporting oncogenic signaling, therapy resistance, and immunosuppression 567. High SCUBE3 expression correlates with poor prognosis in osteosarcoma and ovarian cancer patients 86.

Sources cited
1
Mechanistically, SCUBE3 acts as a BMP2/BMP4 co-receptor that recruits BMP receptor complexes into lipid raft microdomains, facilitating interactions between BMPs and BMP type I receptors to enhance signaling .
PMID: 33308444
2
It also binds to TGFBR2 and activates TGF-Ξ² signaling .
PMID: 37189178
3
During osteogenic differentiation, SCUBE3 levels increase significantly and promote osteogenesis through BMP2/TGF-Ξ² pathway activation and mitophagy induction .
PMID: 39250278
4
Hair follicle development also depends on SCUBE3 secretion by dermal papilla fibroblasts; microinjection of SCUBE3 protein alone is sufficient to induce new hair growth .
PMID: 35777353
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2Open Targets
0.78Strong
Abnormal facial shapeOpen Targets
0.52Moderate
Abnormality of the dentitionOpen Targets
0.52Moderate
Abnormality of the skeletal systemOpen Targets
0.52Moderate
Short statureOpen Targets
0.52Moderate
short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomaliesOpen Targets
0.51Moderate
systemic lupus erythematosusOpen Targets
0.40Weak
developmental disorder of mental healthOpen Targets
0.37Weak
placenta praeviaOpen Targets
0.31Weak
type 1 diabetes mellitusOpen Targets
0.31Weak
ankylosing spondylitisOpen Targets
0.23Weak
celiac diseaseOpen Targets
0.20Weak
genetic disorderOpen Targets
0.19Weak
rheumatoid arthritisOpen Targets
0.19Weak
Abnormality of the integumentOpen Targets
0.18Weak
asthmaOpen Targets
0.15Weak
iridocyclitisOpen Targets
0.13Weak
gastroesophageal reflux diseaseOpen Targets
0.12Weak
esophageal diseaseOpen Targets
0.12Weak
prostate cancerOpen Targets
0.11Weak
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2UniProt
Pathogenic Variants11
NM_152753.4(SCUBE3):c.2444T>C (p.Ile815Thr)Pathogenic
Abnormality of the dentition;Abnormal facial shape;Short stature;Abnormality of the skeletal system|Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2
β˜…β˜…β˜†β˜†2022β†’ Residue 815
NM_152753.4(SCUBE3):c.222C>A (p.Cys74Ter)Likely pathogenic
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2
β˜…β˜†β˜†β˜†2024β†’ Residue 74
NM_152753.4(SCUBE3):c.1909+1G>ALikely pathogenic
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2
β˜…β˜†β˜†β˜†2023
NM_152753.4(SCUBE3):c.1557C>A (p.Cys519Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 519
NM_152753.4(SCUBE3):c.2599+2T>CPathogenic
Abnormality of the dentition;Abnormal facial shape;Short stature;Abnormality of the skeletal system
β˜…β˜†β˜†β˜†2020
NM_152753.4(SCUBE3):c.2785C>T (p.Arg929Ter)Pathogenic
Abnormality of the dentition;Abnormal facial shape;Short stature;Abnormality of the skeletal system|Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2
β˜…β˜†β˜†β˜†2020β†’ Residue 929
NM_152753.4(SCUBE3):c.829+3_952+2delPathogenic
Abnormality of the dentition;Abnormal facial shape;Short stature;Abnormality of the skeletal system
β˜…β˜†β˜†β˜†2020
NM_152753.4(SCUBE3):c.291C>G (p.Cys97Trp)Pathogenic
Abnormality of the dentition;Abnormal facial shape;Short stature;Abnormality of the skeletal system|Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2
β˜…β˜†β˜†β˜†2020β†’ Residue 97
NM_152753.4(SCUBE3):c.611G>A (p.Gly204Asp)Pathogenic
Abnormality of the dentition;Abnormal facial shape;Short stature;Abnormality of the skeletal system
β˜…β˜†β˜†β˜†2020β†’ Residue 204
NM_152753.4(SCUBE3):c.2239+1G>APathogenic
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2|Abnormality of the dentition;Abnormal facial shape;Short stature;Abnormality of the skeletal system
β˜…β˜†β˜†β˜†2020
NM_152753.4(SCUBE3):c.2419G>T (p.Glu807Ter)Likely pathogenic
Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2
β˜…β˜†β˜†β˜†β†’ Residue 807
View on ClinVar β†—
Related Genes
MMP9Protein interaction92%TGFBR2Protein interaction88%MMP2Protein interaction83%SCUBE1Protein interaction76%KCPShared pathway33%ZHX3Shared pathway33%
Tissue Expression6 tissues
Heart
100%
Brain
24%
Ovary
21%
Lung
19%
Liver
5%
Bone Marrow
3%
Gene Interaction Network
Click a node to explore
SCUBE3MMP9TGFBR2MMP2SCUBE1KCPZHX3
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q8IX30
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.40Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.30 [0.22–0.40]
RankingsWhere SCUBE3 stands among ~20K protein-coding genes
  • #12,030of 20,598
    Most Researched30
  • #2,800of 5,498
    Most Pathogenic Variants11
  • #2,024of 17,882
    Most Constrained (LOEUF)0.40 Β· top quartile
Genes detectedSCUBE3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state.
PMID: 35777353
Dev Cell Β· 2022
1.00
2
PMID: 37237303
0.90
3
SCUBE3 promotes osteogenic differentiation and mitophagy in human bone marrow mesenchymal stem cells through the BMP2/TGF-Ξ² signaling pathway.
PMID: 39250278
FASEB J Β· 2024
0.80
4
Epithelium-derived SCUBE3 promotes polarized odontoblastic differentiation of dental mesenchymal stem cells and pulp regeneration.
PMID: 37189178
Stem Cell Res Ther Β· 2023
0.70
5
SCUBE3 loss-of-function causes a recognizable recessive developmental disorder due to defective bone morphogenetic protein signaling.
PMID: 33308444
Am J Hum Genet Β· 2021
0.60