BMP3 bone morphogenetic protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: BMP3provided by HGNC
Official Full Name: bone morphogenetic protein 3provided by HGNC
Primary source: HGNC:HGNC:1070
See related: Ensembl:ENSG00000152785 MIM:112263; AllianceGenome:HGNC:1070
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BMP-3A
Summary: 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]
Expression: Biased expression in urinary bladder (RPKM 12.1), colon (RPKM 5.2) and 5 other tissues See more
Orthologs: all
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Genomic context

Location:: 4q21.21

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (81030708..81057627)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (84360741..84387664)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (81951862..81978781)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overexpression of lncRNA A2M-AS1 inhibits cell growth and aggressiveness via regulating the miR-587/bone morphogenetic protein 3 axis in lung adenocarcinoma.
Title: Overexpression of lncRNA A2M-AS1 inhibits cell growth and aggressiveness via regulating the miR-587/bone morphogenetic protein 3 axis in lung adenocarcinoma.
LncRNA SNHG3 regulates the BMSC osteogenic differentiation in bone metastasis of breast cancer by modulating the miR-1273g-3p/BMP3 axis.
Title: LncRNA SNHG3 regulates the BMSC osteogenic differentiation in bone metastasis of breast cancer by modulating the miR-1273g-3p/BMP3 axis.
USF2 reduces BMP3 expression via transcriptional activation of miR-34a, thus promoting osteogenic differentiation of BMSCs.
Title: USF2 reduces BMP3 expression via transcriptional activation of miR-34a, thus promoting osteogenic differentiation of BMSCs.
Inhibition of BMP3 increases the inflammatory response of fibroblast-like synoviocytes in rheumatoid arthritis.
Title: Inhibition of BMP3 increases the inflammatory response of fibroblast-like synoviocytes in rheumatoid arthritis.
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.
Title: BMP3 suppresses colon tumorigenesis via ActRIIB/SMAD2-dependent and TAK1/JNK signaling pathways.
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.
Title: miR-450b Promotes Osteogenic Differentiation In Vitro and Enhances Bone Formation In Vivo by Targeting BMP3.
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.
Title: BMP3 promoter hypermethylation in plasma-derived cell-free DNA in colorectal cancer patients.
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.
Title: Genetic Biomarker Prevalence Is Similar in Fecal Immunochemical Test Positive and Negative Colorectal Cancer Tissue.
Methylation level in stool decreases dramatically following colorectal cancer resection
Title: Stool methylated DNA markers decrease following colorectal cancer resection--implications for surveillance.
Bone morphogenic protein 3 signaling in the regulation of osteogenesis.
Title: Bone morphogenic protein 3 signaling in the regulation of osteogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Many sequence variants affecting diversity of adult human height. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:481606

STS-M22491 (e-PCR)
- UniSTS:5734

RH66829 (e-PCR)
- UniSTS:38038

SHGC-51737 (e-PCR)
- UniSTS:66046

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables BMP receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables cytokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables growth factor activity	IEA Inferred from Electronic Annotation more info
enables signaling receptor binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in cell surface receptor protein serine/threonine kinase signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of ossification	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of ossification	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in skeletal system development	IEA Inferred from Electronic Annotation more info
involved_in skeletal system development	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
is_active_in extracellular region	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: bone morphogenetic protein 3

Names: bone morphogenetic protein 3 (osteogenic); bone morphogenetic protein 3A; osteogenin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001201.5 → NP_001192.4 bone morphogenetic protein 3 preproprotein

Status: REVIEWED

Source sequence(s)

AC093883

Consensus CDS

CCDS3588.1

UniProtKB/Swiss-Prot

P12645, Q4VAS5

Related

ENSP00000282701.2, ENST00000282701.4

Conserved Domains (1) summary

cd19393
Location:363 → 472

TGF_beta_BMP3; transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 3 (BMP-3) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

81030708..81057627

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006714291.4 → XP_006714354.1 bone morphogenetic protein 3 isoform X1

UniProtKB/TrEMBL

A0ACI8SG74

Related

ENSP00000579168.1, ENST00000909109.2

Conserved Domains (1) summary

cl02510
Location:370 → 439

TGF_beta; Transforming growth factor beta like domain