Free for academic non-profit institutions. Other users need a Commercial license

Aliases for BMP3 Gene

Aliases for BMP3 Gene

  • Bone Morphogenetic Protein 3 2 3 3 5
  • Osteogenin 2 3 4
  • Bone Morphogenetic Protein 3 (Osteogenic) 2 3
  • Bone Morphogenetic Protein 3A 3 4
  • BMP-3A 3 4
  • BMP-3 4
  • BMP3A 4

External Ids for BMP3 Gene

Previous GeneCards Identifiers for BMP3 Gene

  • GC04P081849
  • GC04P082247
  • GC04P082410
  • GC04P082309
  • GC04P081952
  • GC04P077696

Summaries for BMP3 Gene

Entrez Gene Summary for BMP3 Gene

  • This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein suppresses osteoblast differentiation, and negatively regulates bone density, by modulating TGF-beta receptor availability to other ligands. [provided by RefSeq, Jul 2016]

GeneCards Summary for BMP3 Gene

BMP3 (Bone Morphogenetic Protein 3) is a Protein Coding gene. Diseases associated with BMP3 include Dentine Erosion and Chromosome 4Q21 Deletion Syndrome. Among its related pathways are ERK Signaling and Akt Signaling. Gene Ontology (GO) annotations related to this gene include signaling receptor binding and growth factor activity. An important paralog of this gene is GDF10.

UniProtKB/Swiss-Prot for BMP3 Gene

  • Negatively regulates bone density. Antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentitation and ossification.

Gene Wiki entry for BMP3 Gene

Additional gene information for BMP3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BMP3 Gene

Genomics for BMP3 Gene

GeneHancer (GH) Regulatory Elements for BMP3 Gene

Promoters and enhancers for BMP3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J081030 Promoter/Enhancer 1.2 EPDnew ENCODE 650.7 +0.4 443 2 LEF1 ZSCAN4 FEZF1 ZNF335 GLIS2 POLR2A ZNF366 ZBTB48 SCRT2 PRDM10 BMP3 LOC101928942
GH04J081052 Enhancer 0.8 ENCODE 10.9 +21.9 21868 0.5 SMAD1 RB1 STAT5A BMI1 BATF IRF4 RAD21 ZNF143 ATF7 ETV6 BMP3 LOC101928942
GH04J081002 Enhancer 0.7 ENCODE 11.7 -26.9 -26914 1.7 SMAD1 RB1 BACH1 EBF1 BMI1 ATF7 ZSCAN29 IKZF2 NR2F1 TRIM22 BMP3 GC04P080708
GH04J080471 Enhancer 0.8 Ensembl ENCODE 10.1 -558.8 -558802 0.8 IRF2 FOXA2 FOXA3 FOXA1 YY1 ZNF148 POLR2A VEZF1 ZFP36 BMP3 CFAP299 GC04M080460 LOC105377305
GH04J080990 Enhancer 0.5 ENCODE 10.9 -40.5 -40490 0.1 ELF3 CTCF TRIM22 SMC3 REST ELF1 RAD21 BMP3 GC04P080708
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around BMP3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BMP3 gene promoter:

Genomic Locations for BMP3 Gene

Genomic Locations for BMP3 Gene
26,910 bases
Plus strand

Genomic View for BMP3 Gene

Genes around BMP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BMP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BMP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BMP3 Gene

Proteins for BMP3 Gene

  • Protein details for BMP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Bone morphogenetic protein 3
    Protein Accession:
    Secondary Accessions:
    • Q4VAS5

    Protein attributes for BMP3 Gene

    472 amino acids
    Molecular mass:
    53372 Da
    Quaternary structure:
    • Homodimer; disulfide-linked.

    Three dimensional structures from OCA and Proteopedia for BMP3 Gene

neXtProt entry for BMP3 Gene

Post-translational modifications for BMP3 Gene

  • Glycosylation at posLast=463463, Asn220, Asn175, posLast=141141, Asn117, posLast=7575, and posLast=6868
  • Modification sites at PhosphoSitePlus

Other Protein References for BMP3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for BMP3 Gene

Domains & Families for BMP3 Gene

Gene Families for BMP3 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TGF-beta family.
  • Belongs to the TGF-beta family.
genes like me logo Genes that share domains with BMP3: view

Function for BMP3 Gene

Molecular function for BMP3 Gene

UniProtKB/Swiss-Prot Function:
Negatively regulates bone density. Antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentitation and ossification.
UniProtKB/Swiss-Prot Induction:
Highly expressed in fracture tissue, particularly in osteoblasts, osteoclasts and chondroblasts.
GENATLAS Biochemistry:
bone morphogenetic protein 3 (Drosophila decapentaplegic-Vg-related,DVR family;TGFB superfamily)

Phenotypes From GWAS Catalog for BMP3 Gene

Gene Ontology (GO) - Molecular Function for BMP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding TAS 3201241
GO:0005125 cytokine activity IBA --
GO:0005160 transforming growth factor beta receptor binding IBA --
GO:0008083 growth factor activity IEA --
GO:0070700 BMP receptor binding IDA 7811286
genes like me logo Genes that share ontologies with BMP3: view
genes like me logo Genes that share phenotypes with BMP3: view

Animal Models for BMP3 Gene

MGI Knock Outs for BMP3:

Animal Model Products

miRNA for BMP3 Gene

miRTarBase miRNAs that target BMP3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for BMP3 Gene

Localization for BMP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BMP3 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BMP3 gene
Compartment Confidence
extracellular 5
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for BMP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA --
GO:0070062 extracellular exosome HDA 19199708
genes like me logo Genes that share ontologies with BMP3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for BMP3 Gene

Pathways & Interactions for BMP3 Gene

genes like me logo Genes that share pathways with BMP3: view

Gene Ontology (GO) - Biological Process for BMP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 3201241
GO:0001503 ossification IEA --
GO:0001649 osteoblast differentiation IEA --
GO:0007267 cell-cell signaling TAS 3201241
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with BMP3: view

No data available for SIGNOR curated interactions for BMP3 Gene

Drugs & Compounds for BMP3 Gene

(3) Drugs for BMP3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for BMP3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with BMP3: view

Transcripts for BMP3 Gene

mRNA/cDNA for BMP3 Gene

(5) Additional mRNA sequences :
(2) REFSEQ mRNAs :
(10) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for BMP3 Gene

Bone morphogenetic protein 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BMP3 Gene

No ASD Table

Relevant External Links for BMP3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BMP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BMP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BMP3 Gene

This gene is overexpressed in Colon - Sigmoid (x8.6), Colon - Transverse (x7.3), Esophagus - Muscularis (x4.8), Nerve - Tibial (x4.5), and Bladder (x4.2).

Protein differential expression in normal tissues from HIPED for BMP3 Gene

This gene is overexpressed in Bone (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for BMP3 Gene

Protein tissue co-expression partners for BMP3 Gene

NURSA nuclear receptor signaling pathways regulating expression of BMP3 Gene:


SOURCE GeneReport for Unigene cluster for BMP3 Gene:


mRNA Expression by UniProt/SwissProt for BMP3 Gene:

Tissue specificity: Expressed in adult and fetal cartilage.

Evidence on tissue expression from TISSUES for BMP3 Gene

  • Liver(4.2)
  • Bone(2.4)
  • Muscle(2)
genes like me logo Genes that share expression patterns with BMP3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for BMP3 Gene

Orthologs for BMP3 Gene

This gene was present in the common ancestor of animals.

Orthologs for BMP3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BMP3 34 33
  • 98.73 (n)
(Canis familiaris)
Mammalia BMP3 34 33
  • 85.45 (n)
(Bos Taurus)
Mammalia BMP3 34 33
  • 84.82 (n)
(Mus musculus)
Mammalia Bmp3 16 34 33
  • 81.72 (n)
(Rattus norvegicus)
Mammalia Bmp3 33
  • 81 (n)
(Ornithorhynchus anatinus)
Mammalia BMP3 34
  • 73 (a)
(Monodelphis domestica)
Mammalia BMP3 34
  • 72 (a)
(Gallus gallus)
Aves BMP3 34 33
  • 68.78 (n)
(Anolis carolinensis)
Reptilia BMP3 34
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bmp3 33
  • 63.86 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.26502 33
(Danio rerio)
Actinopterygii bmp3 34 33
  • 60.59 (n)
(Caenorhabditis elegans)
Secernentea unc-129 34
  • 20 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 20 (a)
Species where no ortholog for BMP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for BMP3 Gene

Gene Tree for BMP3 (if available)
Gene Tree for BMP3 (if available)
Evolutionary constrained regions (ECRs) for BMP3: view image

Paralogs for BMP3 Gene

(11) SIMAP similar genes for BMP3 Gene using alignment to 15 proteins:

  • D7NT62_HUMAN
  • D7NU02_HUMAN Pseudogenes for BMP3 Gene

genes like me logo Genes that share paralogs with BMP3: view

Variants for BMP3 Gene

Sequence variations from dbSNP and Humsavar for BMP3 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000156707 -- 81,043,278(+) C/T intron_variant
rs10002189 -- 81,040,543(+) A/C intron_variant
rs1000572561 -- 81,034,006(+) T/C intron_variant
rs10005851 -- 81,050,816(+) C/A intron_variant
rs1000591139 -- 81,040,647(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BMP3 Gene

Variant ID Type Subtype PubMed ID
dgv1010e214 CNV loss 21293372
esv3601143 CNV gain 21293372
esv3601147 CNV gain 21293372

Variation tolerance for BMP3 Gene

Residual Variation Intolerance Score: 60.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.94; 79.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BMP3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BMP3 Gene

Disorders for BMP3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for BMP3 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
dentine erosion
chromosome 4q21 deletion syndrome
  • 4q21 microdeletion syndrome
maturity-onset diabetes of the young
  • mody
- elite association - COSMIC cancer census association via MalaCards
Search BMP3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BMP3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with BMP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BMP3 Gene

Publications for BMP3 Gene

  1. BMP-3 and BMP-6 structures illuminate the nature of binding specificity with receptors. (PMID: 17924656) Allendorph GP … Choe S (Biochemistry 2007) 3 4 22 58
  2. Expression of bone morphogenetic proteins, receptors, and tissue inhibitors in human fetal, adult, and osteoarthritic articular cartilage. (PMID: 15475196) Chen AL … Di Cesare PE (Journal of orthopaedic research : official publication of the Orthopaedic Research Society 2004) 3 4 22 58
  3. BMP signaling components are expressed in human fracture callus. (PMID: 13678778) Kloen P … Goumans MJ (Bone 2003) 3 4 22 58
  4. A large-scale candidate gene association study of age at menarche and age at natural menopause. (PMID: 20734064) He C … Hunter DJ (Human genetics 2010) 3 44 58
  5. BMP-3 promotes mesenchymal stem cell proliferation through the TGF-beta/activin signaling pathway. (PMID: 20143330) Stewart A … Yang K (Journal of cellular physiology 2010) 3 22 58

Products for BMP3 Gene

Sources for BMP3 Gene

Loading form....