BMP3
Basic information
Region (hg38): 4:81030708-81057627
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 24 | 28 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 24 | 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 |
---|---|---|---|---|
4-81031355-G-T | not specified | Uncertain significance (Jul 15, 2024) | ||
4-81031358-C-G | not specified | Uncertain significance (Nov 08, 2021) | ||
4-81031373-C-A | not specified | Uncertain significance (Dec 09, 2024) | ||
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) | ||
4-81031511-C-T | not specified | Uncertain significance (Nov 11, 2024) | ||
4-81031544-G-T | not specified | Uncertain significance (Mar 11, 2024) | ||
4-81031549-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
4-81045798-A-T | not specified | Uncertain significance (May 02, 2024) | ||
4-81045878-T-C | not specified | Uncertain significance (Jan 23, 2024) | ||
4-81045878-T-G | not specified | Uncertain significance (Sep 30, 2024) | ||
4-81045888-C-T | not specified | Uncertain significance (Aug 30, 2022) | ||
4-81045925-G-T | not specified | Uncertain significance (Oct 21, 2024) | ||
4-81045926-A-T | not specified | Uncertain significance (Oct 21, 2024) | ||
4-81045927-C-G | not specified | Uncertain significance (Oct 12, 2021) | ||
4-81045939-G-T | not specified | Uncertain significance (Mar 15, 2024) | ||
4-81045947-C-A | Benign (May 15, 2018) | |||
4-81045993-A-T | not specified | Uncertain significance (Dec 07, 2024) | ||
4-81046047-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
4-81046062-A-G | not specified | Uncertain significance (Jul 27, 2024) | ||
4-81046084-T-G | not specified | Uncertain significance (Nov 26, 2024) | ||
4-81046085-A-G | not specified | Uncertain significance (Dec 09, 2023) |
GnomAD
Source:
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:
- 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