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 homo... See more...

Aliases for BMP3 Gene

Aliases for BMP3 Gene

  • Bone Morphogenetic Protein 3 2 3 4 5
  • Osteogenin 2 3 4
  • Bone Morphogenetic Protein 3 (Osteogenic) 2 3
  • Bone Morphogenetic Protein 3A 3 4
  • BMP-3A 3 4
  • BMP3A 4
  • BMP-3 4
  • BMP3 5

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 Renal Artery Atheroma and Refractive Error. Among its related pathways are Nanog in Mammalian ESC Pluripotency and PEDF Induced 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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for BMP3 Gene

Genomics for BMP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for BMP3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
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 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.4 357 2 FEZF1 ZNF341 ZBTB48 ZNF189 NRF1 ZNF362 GLIS1 ZNF398 ZNF548 ZNF366 BMP3 HSALNG0035480 PRKG2
GH04J081029 Enhancer 0.3 Ensembl 250.7 -1.0 -1007 0.2 NFIB BMP3 HSALNG0035480 HSALNG0035475 CFAP299
GH04J081052 Enhancer 1 Ensembl ENCODE 10.9 +21.7 21663 0.7 BCLAF1 ZNF654 BCL11A TRIM22 CTCF RAD21 SMC3 IRF4 EZH2 EBF1 BMP3 HSALNG0035480 piR-37895-116 PRKG2
GH04J081002 Enhancer 0.9 Ensembl ENCODE 11.7 -27.0 -27000 1.7 BCL11A TRIM22 NR2C1 BHLHE40 ELF1 ZNF24 IKZF1 BMI1 RB1 NR2F1 BMP3 HSALNG0035475 RF00017-3906 CFAP299
GH04J080990 Enhancer 0.5 ENCODE 10.9 -40.6 -40576 0.1 REST TRIM22 CTCF ELF1 RAD21 SMC3 MAFK ELF3 BMP3 RF00017-3906 HSALNG0035471 CFAP299
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BMP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for BMP3

Top Transcription factor binding sites by QIAGEN in the BMP3 gene promoter:
  • AP-1
  • AREB6
  • ATF-2
  • c-Jun
  • Evi-1
  • GATA-1
  • GATA-2
  • MIF-1
  • MZF-1

Genomic Locations for BMP3 Gene

Latest Assembly
chr4:81,030,708-81,057,627
(GRCh38/hg38)
Size:
26,920 bases
Orientation:
Plus strand

Previous Assembly
chr4:81,951,862-81,978,781
(GRCh37/hg19 by Entrez Gene)
Size:
26,920 bases
Orientation:
Plus strand

chr4:81,952,119-81,978,685
(GRCh37/hg19 by Ensembl)
Size:
26,567 bases
Orientation:
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:
    P12645-BMP3_HUMAN
    Recommended name:
    Bone morphogenetic protein 3
    Protein Accession:
    P12645
    Secondary Accessions:
    • Q4VAS5

    Protein attributes for BMP3 Gene

    Size:
    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 Ser68, Thr69, Thr75, Ser83, Asn117, Asn141, Asn175, Asn220, and Asn463
  • 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

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

Protein Domains for BMP3 Gene

InterPro:
Blocks:
  • Transforming growth factor beta (TGFb)
  • Growth factor cystine knot superfamily signature

Suggested Antigen Peptide Sequences for BMP3 Gene

GenScript: Design optimal peptide antigens:
  • Osteogenin (BMP3_HUMAN)
  • Bone morphogenetic protein 3 (D7NT62_HUMAN)
  • Bone morphogenetic protein 3 (D7NTB8_HUMAN)
  • Bone morphogenetic protein 3 (D7NTD1_HUMAN)
  • Bone morphogenetic protein 3 (D7NTG9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P12645

UniProtKB/Swiss-Prot:

BMP3_HUMAN :
  • Belongs to the TGF-beta family.
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 21873635
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:

miRNA for BMP3 Gene

miRTarBase miRNAs that target BMP3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BMP3

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

Secreted.

Subcellular locations from

COMPARTMENTS
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
plasma membrane 2
cytoskeleton 2
nucleus 2
cytosol 2
mitochondrion 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1
peroxisome 0

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 21873635
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

PathCards logo

SuperPathways for BMP3 Gene

SuperPathway Contained pathways
1 Apoptotic Pathways in Synovial Fibroblasts
.85
.85
.84
.84
.74
.72
.66
.65
.64
.62
.61
.60
.57
.57
2 PEDF Induced Signaling
.94
.94
.73
.71
.62
.61
.57
.51
.47
.46
.43
3 GPCR Pathway
.73
.73
.62
.59
.58
.58
.55
4 TGF-Beta Pathway
.60
.60
.57
.51
.43
.40
5 ERK Signaling
.61
.61
.58
.51
.49
genes like me logo Genes that share pathways with BMP3: view

Pathways by source for BMP3 Gene

1 BioSystems pathway for BMP3 Gene
1 KEGG pathway for BMP3 Gene
71 Qiagen pathways for BMP3 Gene
  • 14-3-3 Induced Intracellular Signaling
  • Actin-Based Motility by Rho Family GTPases
  • Activation of cAMP-Dependent PKA
  • Activation of PKA through GPCR
  • Activation of PKC through GPCR

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

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BMP3

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

No ASD Table

Relevant External Links for BMP3 Gene

GeneLoc Exon Structure for
BMP3

Expression for BMP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for BMP3

SOURCE GeneReport for Unigene cluster for BMP3 Gene:

Hs.387411

mRNA Expression by UniProt/SwissProt for BMP3 Gene:

P12645-BMP3_HUMAN
Tissue specificity: Expressed in adult and fetal cartilage.

Evidence on tissue expression from TISSUES for BMP3 Gene

  • Liver(4.4)
  • Intestine(2.4)
  • Muscle(2.4)
  • Bone(2.3)
  • Nervous system(2.3)
  • Heart(2.1)
  • Kidney(2)
genes like me logo Genes that share expression patterns with BMP3: view

Primer products for research

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
Chimpanzee
(Pan troglodytes)
Mammalia BMP3 29 30
  • 98.73 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia BMP3 29 30
  • 85.45 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia BMP3 29 30
  • 84.82 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Bmp3 29 16 30
  • 81.72 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Bmp3 29
  • 81 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia BMP3 30
  • 73 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia BMP3 30
  • 72 (a)
OneToOne
Chicken
(Gallus gallus)
Aves BMP3 29 30
  • 68.78 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia BMP3 30
  • 71 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia bmp3 29
  • 63.86 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.26502 29
Zebrafish
(Danio rerio)
Actinopterygii bmp3 29 30
  • 60.59 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea unc-129 30
  • 20 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 20 (a)
OneToMany
Species where no ortholog for BMP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for BMP3 (if available)
TreeFam:
Gene Tree for BMP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for BMP3: view image
Alliance of Genome Resources:
Additional Orthologs for BMP3

Paralogs for BMP3 Gene

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

  • BMP3_HUMAN
  • D7NT62_HUMAN
  • D7NTB8_HUMAN
  • D7NTD1_HUMAN
  • D7NTG9_HUMAN
  • D7NTK7_HUMAN
  • D7NTK8_HUMAN
  • D7NTK9_HUMAN
  • D7NTP6_HUMAN
  • D7NTR3_HUMAN
  • D7NTU0_HUMAN
  • D7NTU1_HUMAN
  • D7NTU5_HUMAN
  • D7NTV0_HUMAN
  • D7NU02_HUMAN

Pseudogenes.org Pseudogenes for BMP3 Gene

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

Variants for BMP3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for BMP3 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs145297209 Benign: not provided 81,046,464(+) C/T
NM_001201.4(BMP3):c.1043C>T (p.Thr348Met)
MISSENSE
rs34213771 Benign: not provided 81,045,947(+) C/Ap.Gln176Lys
NM_001201.4(BMP3):c.526C>A (p.Gln176Lys)
MISSENSE
rs34505126 Benign: not provided 81,046,086(+) C/Tp.Thr222Met
NM_001201.4(BMP3):c.665C>T (p.Thr222Met)
MISSENSE
rs61729826 Benign: not provided 81,046,456(+) G/C
NM_001201.4(BMP3):c.1035G>C (p.Lys345Asn)
MISSENSE
rs34847147 -- p.Gln176Leu

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for BMP3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)
BMP3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
BMP3
Leiden Open Variation Database (LOVD)
BMP3

SNP Genotyping and Copy Number Assays for research

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

Disorders for BMP3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for BMP3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
renal artery atheroma
  • atherosclerosis of renal artery
refractive error
  • refractive errors
brachydactyly, type a2
  • bda2
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

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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
  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
  3. BMP signaling components are expressed in human fracture callus. (PMID: 13678778) Kloen P … Goumans MJ (Bone 2003) 3 4 22
  4. 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
  5. 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 40

Products for BMP3 Gene

Sources for BMP3 Gene