BMP5
bone morphogenetic protein 5, the group of Bone morphogenetic proteins
Basic information
Region (hg38): 6:55753653-55875590
Links
Phenotypes
GenCC
Source:
- dysostosis (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (61 variants)
- BMP5-related_disorder (11 variants)
- not_provided (4 variants)
- Patellar_aplasia (2 variants)
- Hypoplastic_ischiopubic_ramus (2 variants)
- Microtia (2 variants)
- Atrioventricular_canal_defect (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021073.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | |||||
| missense | 59 | 64 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 2 | 59 | 5 | 5 |
Highest pathogenic variant AF is 0.000006581632
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BMP5 | protein_coding | protein_coding | ENST00000370830 | 7 | 121920 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000901 | 0.997 | 125728 | 0 | 17 | 125745 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.625 | 228 | 256 | 0.890 | 0.0000144 | 2993 |
| Missense in Polyphen | 63 | 94.471 | 0.66687 | 1131 | ||
| Synonymous | 0.0172 | 87 | 87.2 | 0.998 | 0.00000468 | 863 |
| Loss of Function | 2.64 | 9 | 22.5 | 0.400 | 0.00000136 | 241 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000301 | 0.000300 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000793 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Induces cartilage and bone formation.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);alk in cardiac myocytes;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
- 0.260
Intolerance Scores
- loftool
- 0.465
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.49
Haploinsufficiency Scores
- pHI
- 0.929
- hipred
- N
- hipred_score
- 0.495
- ghis
- 0.419
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.406
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bmp5
- Phenotype
- embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- bmp5
- Affected structure
- perineuronal satellite cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- skeletal system development;ossification;endocardial cushion formation;type B pancreatic cell development;pericardium morphogenesis;pattern specification process;positive regulation of cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;negative regulation of epithelial to mesenchymal transition;positive regulation of pathway-restricted SMAD protein phosphorylation;negative regulation of steroid biosynthetic process;neural fold elevation formation;BMP signaling pathway;male genitalia development;hindbrain development;negative regulation of aldosterone biosynthetic process;regulation of apoptotic process;regulation of MAPK cascade;negative regulation of insulin-like growth factor receptor signaling pathway;ear development;positive regulation of transcription by RNA polymerase II;cell development;cardiac muscle tissue development;positive regulation of epithelial cell proliferation;cartilage development;pharyngeal system development;SMAD protein signal transduction;cardiac septum morphogenesis;chorio-allantoic fusion;heart trabecula morphogenesis;negative regulation of mononuclear cell migration;anterior head development;positive regulation of dendrite development;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;allantois development;negative regulation of cortisol biosynthetic process
- Cellular component
- cellular_component;extracellular space;vesicle
- Molecular function
- cytokine activity;transforming growth factor beta receptor binding;growth factor activity;BMP receptor binding