BMP3

bone morphogenetic protein 3, the group of Bone morphogenetic proteins

Basic information

Region (hg38): 4:81030707-81057627

Links

ENSG00000152785 ∙ NCBI:651 ∙ OMIM:112263 ∙ HGNC:1070 ∙ Uniprot:P12645 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BMP3 gene.

• Inborn genetic diseases (17 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17		4	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	4

Variants in BMP3

This is a list of pathogenic ClinVar variants found in the BMP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-81031358-C-G		not specified	Uncertain significance (Nov 08, 2021)
4-81031390-G-T		not specified	Uncertain significance (Mar 31, 2023)
4-81031391-T-C		not specified	Uncertain significance (Feb 21, 2024)
4-81031397-G-T		not specified	Uncertain significance (Apr 25, 2022)
4-81031403-G-A		not specified	Uncertain significance (Jun 30, 2023)
4-81031482-G-C		not specified	Uncertain significance (Sep 29, 2023)
4-81031544-G-T		not specified	Uncertain significance (Mar 11, 2024)
4-81031549-C-T		not specified	Uncertain significance (Feb 06, 2023)
4-81045878-T-C		not specified	Uncertain significance (Jan 23, 2024)
4-81045888-C-T		not specified	Uncertain significance (Aug 30, 2022)
4-81045927-C-G		not specified	Uncertain significance (Oct 12, 2021)
4-81045947-C-A			Benign (May 15, 2018)
4-81046047-C-T		not specified	Uncertain significance (Dec 03, 2021)
4-81046085-A-G		not specified	Uncertain significance (Dec 09, 2023)
4-81046086-C-T			Benign (May 15, 2018)
4-81046116-G-A		not specified	Uncertain significance (Aug 16, 2022)
4-81046163-G-A		not specified	Uncertain significance (Jun 26, 2023)
4-81046202-G-A		not specified	Uncertain significance (Dec 21, 2023)
4-81046208-C-T		not specified	Uncertain significance (Dec 19, 2022)
4-81046275-G-A		not specified	Uncertain significance (Feb 11, 2022)
4-81046296-G-C		not specified	Uncertain significance (Oct 27, 2022)
4-81046376-A-G		not specified	Uncertain significance (Jun 22, 2023)
4-81046401-A-G		not specified	Uncertain significance (May 24, 2023)
4-81046456-G-C			Benign (Aug 28, 2018)
4-81046464-C-T			Benign (Oct 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMP3	protein_coding	protein_coding	ENST00000282701	3	26567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0564	0.940	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0659	253	256	0.988	0.0000125	3052
Missense in Polyphen		99	100.09	0.98915		1286
Synonymous	-0.725	111	102	1.09	0.00000509	944
Loss of Function	2.56	5	16.1	0.311	7.44e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000623	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates bone density. Antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentitation and ossification. {ECO:0000269|PubMed:11138004, ECO:0000269|PubMed:15269709}.
• Pathway: Adipogenesis;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;TGF-beta super family signaling pathway canonical;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;BMP2 signaling TGF-beta MV;BMP signaling Dro (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.266
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.61

Haploinsufficiency Scores

• pHI: 0.331
• hipred: N
• hipred_score: 0.320
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0860

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bmp3
• Phenotype: skeleton phenotype

Zebrafish Information Network

• Gene name: bmp3
• Affected structure: neurocranium
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: skeletal system development;osteoblast differentiation;cell-cell signaling;regulation of signaling receptor activity;positive regulation of pathway-restricted SMAD protein phosphorylation;regulation of apoptotic process;regulation of MAPK cascade;cell development;cartilage development;SMAD protein signal transduction
• Cellular component: extracellular space;extracellular exosome
• Molecular function: signaling receptor binding;cytokine activity;transforming growth factor beta receptor binding;growth factor activity;BMP receptor binding