BMP3

gene
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Summary

BMP3 (bone morphogenetic protein 3, HGNC:1070) is a protein-coding gene on chromosome 4q21.21, encoding Bone morphogenetic protein 3 (P12645). Growth factor of the TGF-beta superfamily that plays an essential role in developmental process by inducing and patterning early skeletal formation and by negatively regulating bone density.

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.

Source: NCBI Gene 651 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): coloboma (Moderate, GenCC)
  • GWAS associations: 12
  • Clinical variants (ClinVar): 83 total
  • MANE Select transcript: NM_001201

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1070
Approved symbolBMP3
Namebone morphogenetic protein 3
Location4q21.21
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000152785
Ensembl biotypeprotein_coding
OMIM112263
Entrez651

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000282701, ENST00000909109

RefSeq mRNA: 1 — MANE Select: NM_001201 NM_001201

CCDS: CCDS3588

Canonical transcript exons

ENST00000282701 — 3 exons

ExonStartEnd
ENSE000010071138103070881031600
ENSE000010071158104573881046648
ENSE000015490558105334581057627

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 79.85.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4027 / max 28.5608, expressed in 129 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
485400.175371
485390.166869
485380.060625

Top tissues by expression

275 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
muscle layer of sigmoid colonUBERON:003580579.85gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.20gold quality
rectumUBERON:000105277.84gold quality
transverse colonUBERON:000115776.66gold quality
mucosa of transverse colonUBERON:000499174.15gold quality
sigmoid colonUBERON:000115973.32gold quality
colonUBERON:000115573.07gold quality
lower esophagus muscularis layerUBERON:003583372.57gold quality
lower esophagusUBERON:001347372.41gold quality
large intestineUBERON:000005972.16gold quality
intestineUBERON:000016071.39gold quality
tibial nerveUBERON:000132370.93gold quality
small intestine Peyer’s patchUBERON:000345470.61gold quality
esophagogastric junction muscularis propriaUBERON:003584169.25gold quality
small intestineUBERON:000210868.96gold quality
olfactory segment of nasal mucosaUBERON:000538667.82gold quality
palpebral conjunctivaUBERON:000181267.08silver quality
gall bladderUBERON:000211065.41gold quality
colonic epitheliumUBERON:000039764.85gold quality
ileal mucosaUBERON:000033162.47silver quality
cortical plateUBERON:000534361.54gold quality
right uterine tubeUBERON:000130261.28gold quality
pancreatic ductal cellCL:000207959.81silver quality
duodenumUBERON:000211459.68gold quality
ganglionic eminenceUBERON:000402359.33gold quality
minor salivary glandUBERON:000183058.63gold quality
urinary bladderUBERON:000125558.46gold quality
bone marrow cellCL:000209258.09silver quality
left ovaryUBERON:000211956.65gold quality
deciduaUBERON:000245056.55gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes11.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

222 targeting BMP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4476100.0068.182030
HSA-MIR-4795-3P100.0074.624024
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-3646100.0073.565283
HSA-MIR-126-5P100.0072.713180
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4262100.0073.263931
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-8485100.0077.574731
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-548AW99.9972.573559
HSA-MIR-186-5P99.9970.833707
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-366299.9973.825684

Literature-anchored findings (GeneRIF, showing 19)

  • The expression signals of BMP3 mRNA in malignant schwannoma were relatively lower than in benign lesions (PMID:11642720)
  • BMP-3 receptor specificity is controlled by the interaction of Lys-30 of BMP-3 with Glu-76 of ActRIIb (PMID:17924656)
  • BMP3 silencing is an early and frequent event in colorectal tumors progressing via the serrated and traditional pathways. (PMID:18311777)
  • These results demonstrate that BMP-3 stimulates mesenchymal stem cell proliferation via the TGF-beta/activin signaling pathway. (PMID:20143330)
  • Data suggest that promotor region methylation of the BMP3 gene may cause gastric carcinoma in Chinese people. (PMID:20238409)
  • Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality (PMID:20532035)
  • Circulating bone morphogenetic protein 1-3 isoform increases renal fibrosis. (PMID:21415150)
  • a critical link between HNF1A-MODY-induced alterations in Bmp-3 expression and insulin gene levels (PMID:21628466)
  • As an addition to PRKG2 and RASGEFIB genes, we propose to include BMP3 gene as the principal determinant of the observed common phenotype. (PMID:22303795)
  • Bone morphogenic protein 3 signaling in the regulation of osteogenesis. (PMID:23127436)
  • Methylation level in stool decreases dramatically following colorectal cancer resection (PMID:24993691)
  • BMP3 - the biomarker of a currently in-use multi-target stool DNA test was commonly expressed in tumor tissue specimens, independent of Fecal Immunochemical Test result. (PMID:28044229)
  • a novel microRNA miR-450b was essential for adipose-derived mesenchymal stem cell differentiation, which could promote osteogenic differentiation in vitro and enhance bone formation in vivo by directly suppressing BMP3. (PMID:29649414)
  • This study demonstrated that there was a significantly higher frequency of BMP3 methylated DNA in plasma in patients with polyps versus healthy controls with a sensitivity and specificity of 40 and 94%, respectively. (PMID:29892846)
  • Results found that BMP3 gene was extensively hypermethylated and downregulated in colorectal cancer (CRC) and suggest that BMP3 acts as a tumor suppressor or has a growth rate-limiting role in CRC development and progression. (PMID:31665064)
  • Inhibition of BMP3 increases the inflammatory response of fibroblast-like synoviocytes in rheumatoid arthritis. (PMID:32568738)
  • USF2 reduces BMP3 expression via transcriptional activation of miR-34a, thus promoting osteogenic differentiation of BMSCs. (PMID:34350522)
  • LncRNA SNHG3 regulates the BMSC osteogenic differentiation in bone metastasis of breast cancer by modulating the miR-1273g-3p/BMP3 axis. (PMID:35081500)
  • Overexpression of lncRNA A2M-AS1 inhibits cell growth and aggressiveness via regulating the miR-587/bone morphogenetic protein 3 axis in lung adenocarcinoma. (PMID:36461613)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriobmp3ENSDARG00000060526
mus_musculusBmp3ENSMUSG00000029335
rattus_norvegicusBmp3ENSRNOG00000002381

Paralogs (31): TGFB2 (ENSG00000092969), BMP7 (ENSG00000101144), TGFB1 (ENSG00000105329), BMP5 (ENSG00000112175), BMP8B (ENSG00000116985), TGFB3 (ENSG00000119699), INHBA (ENSG00000122641), INHA (ENSG00000123999), BMP4 (ENSG00000125378), BMP2 (ENSG00000125845), GDF5 (ENSG00000125965), GDF1 (ENSG00000130283), BMP15 (ENSG00000130385), GDF15 (ENSG00000130513), GDF11 (ENSG00000135414), MSTN (ENSG00000138379), INHBE (ENSG00000139269), LEFTY2 (ENSG00000143768), GDF7 (ENSG00000143869), BMP6 (ENSG00000153162), GDF6 (ENSG00000156466), NODAL (ENSG00000156574), INHBB (ENSG00000163083), BMP10 (ENSG00000163217), GDF9 (ENSG00000164404), INHBC (ENSG00000175189), BMP8A (ENSG00000183682), GDF3 (ENSG00000184344), LEFTY1 (ENSG00000243709), GDF2 (ENSG00000263761), GDF10 (ENSG00000266524)

Protein

Protein identifiers

Bone morphogenetic protein 3P12645 (reviewed: P12645)

Alternative names: Bone morphogenetic protein 3A, Osteogenin

All UniProt accessions (1): P12645

UniProt curated annotations — full annotation on UniProt →

Function. Growth factor of the TGF-beta superfamily that plays an essential role in developmental process by inducing and patterning early skeletal formation and by negatively regulating bone density. Antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentiation and ossification. Initiates signaling cascades by associating with type II receptor ACVR2B to activate SMAD2-dependent and SMAD-independent signaling cascades including TAK1 and JNK pathways.

Subunit / interactions. Homodimer; disulfide-linked. Interacts with type II receptor ACVR2B.

Subcellular location. Secreted.

Tissue specificity. Expressed in adult and fetal cartilage.

Induction. Highly expressed in fracture tissue, particularly in osteoblasts, osteoclasts and chondroblasts.

Similarity. Belongs to the TGF-beta family.

RefSeq proteins (1): NP_001192* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001839TGF-b_CDomain
IPR015615TGF-beta-likeFamily
IPR017197BMP3/BMP3BFamily
IPR017948TGFb_CSConserved_site
IPR029034Cystine-knot_cytokineHomologous_superfamily

Pfam: PF00019

UniProt features (34 total): strand 9, glycosylation site 5, sequence variant 5, disulfide bond 4, turn 2, helix 2, region of interest 2, compositionally biased region 2, signal peptide 1, propeptide 1, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2QCQX-RAY DIFFRACTION2.21

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P12645-F165.110.24

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (4): 370–437, 399–469, 403–471, 436

Glycosylation sites (5): 220, 463, 117, 141, 175

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): RNGTGGGC_UNKNOWN, GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_OSTEOBLAST_DIFFERENTIATION, GOMF_GROWTH_FACTOR_ACTIVITY, GOBP_CELL_CELL_SIGNALING, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_OSSIFICATION, GOMF_CYTOKINE_ACTIVITY, SABATES_COLORECTAL_ADENOMA_DN, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_OSSIFICATION, GOMF_SIGNALING_RECEPTOR_BINDING

GO Biological Process (9): skeletal system development (GO:0001501), osteoblast differentiation (GO:0001649), cell surface receptor protein serine/threonine kinase signaling pathway (GO:0007178), cell-cell signaling (GO:0007267), negative regulation of ossification (GO:0030279), positive regulation of transcription by RNA polymerase II (GO:0045944), cartilage development (GO:0051216), ossification (GO:0001503), cell differentiation (GO:0030154)

GO Molecular Function (4): signaling receptor binding (GO:0005102), cytokine activity (GO:0005125), growth factor activity (GO:0008083), BMP receptor binding (GO:0070700)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), extracellular exosome (GO:0070062), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ossification2
receptor ligand activity2
system development1
cell differentiation1
enzyme-linked receptor protein signaling pathway1
cell communication1
signaling1
regulation of ossification1
negative regulation of multicellular organismal process1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
skeletal system development1
animal organ development1
connective tissue development1
multicellular organismal process1
cellular developmental process1
protein binding1
transmembrane receptor protein serine/threonine kinase binding1
extracellular vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

1278 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BMP3ACVR2BQ13705887
BMP3NDRG4Q9ULP0840
BMP3AMBNQ9NP70779
BMP3ACVR2AP27037726
BMP3TFPI2P48307695
BMP3BMPR1BP78366691
BMP3IBSPP21815677
BMP3BMPR1AP36894670
BMP3BMPR2Q13873635
BMP3SMAD4Q13485626
BMP3SEPTIN9Q9UHD8620
BMP3BMP1P13497615
BMP3SPP1P10451609
BMP3VIMP08670575
BMP3FSTP19883574

IntAct

6 interactions, top by confidence:

ABTypeScore
BMP3WFIKKN1psi-mi:“MI:0407”(direct interaction)0.440
BMP3WFIKKN2psi-mi:“MI:0407”(direct interaction)0.440
BMP2KBMP3psi-mi:“MI:0915”(physical association)0.370
BMP3KDM1Apsi-mi:“MI:0915”(physical association)0.370
BMP3PRMT6psi-mi:“MI:0915”(physical association)0.370

BioGRID (4): BMP3 (Affinity Capture-MS), YBX3 (Cross-Linking-MS (XL-MS)), KDM1A (Two-hybrid), PRMT6 (Two-hybrid)

ESM2 similar proteins: A2VDJ0, A9CB18, O13048, O18752, O18753, O60383, O70183, O77681, O95813, O95972, P09529, P12645, P14082, P17491, P20722, P21237, P22003, P22004, P22444, P23363, P25429, P27093, P49002, P49003, Q04906, Q04999, Q07105, Q08DV9, Q0EAB7, Q28GB8, Q3SAT7, Q3U3D7, Q66NC0, Q6PX77, Q7T2X6, Q7T2X7, Q7YRB4, Q800B9, Q8BHE5, Q8QG74

Diamond homologs: A1C2U3, A1C2U6, A1C2U7, A1C2V0, A1C2V5, A8E7N9, G5EEL5, O08689, O14793, O18828, O18830, O18831, O18836, O35312, O42220, O42221, O42222, O46576, O61643, O95390, O95393, P09534, P12644, P12645, P17491, P18075, P20722, P20863, P22003, P22004, P22444, P23359, P27091, P27539, P35621, P43026, P43027, P43028, P43029, P48970

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

83 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance72
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

476 predictions. Top by Δscore:

VariantEffectΔscore
4:81045733:CCTAG:Cacceptor_loss1.0000
4:81045734:CTA:Cacceptor_loss1.0000
4:81045735:TAG:Tacceptor_loss1.0000
4:81045736:A:AGacceptor_gain1.0000
4:81045736:A:Tacceptor_loss1.0000
4:81045737:G:GGacceptor_gain1.0000
4:81045737:GAA:Gacceptor_gain1.0000
4:81045737:GAAA:Gacceptor_gain1.0000
4:81031597:GCAG:Gdonor_gain0.9900
4:81031598:CAG:Cdonor_loss0.9900
4:81031599:AGG:Adonor_loss0.9900
4:81031600:GGTG:Gdonor_loss0.9900
4:81045737:GA:Gacceptor_gain0.9900
4:81045737:GAAAC:Gacceptor_gain0.9900
4:81053453:A:AGdonor_gain0.9900
4:81053454:G:GGdonor_gain0.9900
4:81031603:GAGT:Gdonor_loss0.9800
4:81031601:G:GGdonor_gain0.9600
4:81045735:TAGAA:Tacceptor_gain0.9600
4:81045736:AGAAA:Aacceptor_gain0.9600
4:81053343:A:AGacceptor_gain0.9600
4:81053344:G:GGacceptor_gain0.9600
4:81045734:CTAG:Cacceptor_gain0.9500
4:81045733:CCTA:Cacceptor_gain0.9300
4:81045732:TCCTA:Tacceptor_gain0.9200
4:81045737:G:Tacceptor_gain0.9100
4:81045739:A:AGacceptor_gain0.9000
4:81045740:A:Gacceptor_gain0.8700
4:81046497:C:Tdonor_gain0.8700
4:81053484:T:TAdonor_gain0.8700

AlphaMissense

3083 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:81046618:C:GC399W1.000
4:81046545:T:CL375P0.999
4:81046556:T:CF379L0.999
4:81046557:T:GF379C0.999
4:81046558:T:AF379L0.999
4:81046558:T:GF379L0.999
4:81046573:G:CW384C0.999
4:81046573:G:TW384C0.999
4:81046616:T:AC399S0.999
4:81046616:T:CC399R0.999
4:81046617:G:AC399Y0.999
4:81046617:G:CC399S0.999
4:81046628:T:CC403R0.999
4:81046629:G:AC403Y0.999
4:81046634:T:CF405L0.999
4:81046635:T:GF405C0.999
4:81046636:C:AF405L0.999
4:81046636:C:GF405L0.999
4:81053426:T:AC437S0.999
4:81053426:T:CC437R0.999
4:81053427:G:AC437Y0.999
4:81053427:G:CC437S0.999
4:81053428:T:GC437W0.999
4:81053523:G:AC469Y0.999
4:81053524:C:GC469W0.999
4:81053528:T:CC471R0.999
4:81046529:T:AC370S0.998
4:81046529:T:CC370R0.998
4:81046530:G:AC370Y0.998
4:81046530:G:CC370S0.998

dbSNP variants (sampled 300 via entrez): RS1000156707 (4:81043278 C>T), RS10002189 (4:81040543 A>C), RS1000572561 (4:81034006 T>A,C), RS10005851 (4:81050816 C>A,G), RS1000591139 (4:81040647 A>G), RS1000622284 (4:81040849 C>A,T), RS1000641037 (4:81032660 G>T), RS1000693240 (4:81039642 T>A), RS10007784 (4:81056536 C>A,G,T), RS1000800991 (4:81044363 T>A,C,G), RS1000814869 (4:81045252 A>G), RS1000901850 (4:81051488 CAG>C), RS1001314165 (4:81044143 T>C), RS1001507304 (4:81034282 A>G), RS1001657466 (4:81033737 A>G)

Disease associations

OMIM: gene MIM:112263 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
colobomaModerateAutosomal dominant

Mondo (1): coloboma (MONDO:0001476)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

12 associations (top):

StudyTraitp-value
GCST000175_43Height2.000000e-06
GCST001858_10Refractive error1.000000e-06
GCST001876_7Pubertal anthropometrics1.000000e-07
GCST003997_27Myopia2.000000e-23
GCST006291_140Spherical equivalent or myopia (age of diagnosis)6.000000e-21
GCST007159_3Corneal astigmatism1.000000e-06
GCST007160_11Refractive astigmatism3.000000e-06
GCST009462_55Optic disc size2.000000e-19
GCST009959_24Retinal detachment or retinal break2.000000e-07
GCST010002_9Refractive error2.000000e-65
GCST012400_40Low myopia vs hyperopia1.000000e-09
GCST90014268_14Cataracts3.000000e-12

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0001382puberty
EFO:0004847age at onset
EFO:1002040Corneal astigmatism
EFO:0010698retinal break

MeSH disease descriptors (1)

DescriptorNameTree numbers
D003103ColobomaC11.250.110; C11.270.147; C16.131.384.282

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects methylation, increases expression2
ethyl-p-hydroxybenzoateincreases expression1
monomethylarsonous acidincreases expression1
bisphenol Saffects cotreatment, decreases methylation1
Fulvestrantaffects cotreatment, decreases methylation1
Air Pollutantsincreases abundance, increases expression1
Arsenicincreases methylation1
Benzo(a)pyreneaffects methylation, increases methylation1
Leadaffects methylation1
Rotenonedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Aciddecreases methylation1
Zearalenonedecreases expression1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1
Particulate Matterincreases expression, increases abundance1

Clinical trials (associated diseases)

4 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00368004Not specifiedTERMINATEDFamily Studies of Uveal Coloboma
NCT01778543Not specifiedRECRUITINGPathogenesis and Genetics of Microphthalmia, Anophthalmia and Uveal Coloboma (MAC)
NCT04833361Not specifiedCOMPLETEDPotential Environmental Causes of Uveal Coloboma
NCT06293560Not specifiedRECRUITINGMicrophthalmia, Anophthalmia, and Coloboma Genetic Epidemiology in Children