BMP7
bone morphogenetic protein 7, the group of Bone morphogenetic proteins
Basic information
Region (hg38): 20:57168753-57266641
Links
Phenotypes
GenCC
Source:
- multiple congenital anomalies/dysmorphic syndrome (Moderate), mode of inheritance: AD
- hypospadias (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP7 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 | 13 | |||||
| missense | 40 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 21 | 28 | ||||
| Total | 1 | 0 | 40 | 14 | 29 |
Variants in BMP7
This is a list of pathogenic ClinVar variants found in the BMP7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-57171012-C-T | BMP7-related disorder | Uncertain significance (Feb 16, 2023) | ||
| 20-57171040-G-A | Benign (Jan 31, 2024) | |||
| 20-57171051-T-G | not specified | Uncertain significance (Dec 12, 2022) | ||
| 20-57171059-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 20-57171099-T-C | not specified | Uncertain significance (Oct 31, 2023) | ||
| 20-57171260-T-C | Benign (Dec 23, 2018) | |||
| 20-57173008-C-T | Benign (Dec 23, 2018) | |||
| 20-57173048-A-AT | Likely benign (Nov 26, 2019) | |||
| 20-57173150-G-A | Benign (Jun 26, 2018) | |||
| 20-57173242-G-A | BMP7-related disorder | Likely benign (Aug 11, 2020) | ||
| 20-57173256-C-A | Uncertain significance (Jun 05, 2022) | |||
| 20-57173297-G-A | not specified | Uncertain significance (Jul 14, 2022) | ||
| 20-57173302-G-A | Benign (Nov 13, 2023) | |||
| 20-57173646-CATAAA-C | Benign (Jun 29, 2018) | |||
| 20-57174725-A-G | Benign (Jun 29, 2018) | |||
| 20-57174925-C-T | Benign (Jan 31, 2024) | |||
| 20-57174945-C-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 20-57174980-G-C | BMP7-related disorder | Uncertain significance (Jan 06, 2023) | ||
| 20-57174981-C-A | not specified | Uncertain significance (Nov 28, 2023) | ||
| 20-57174993-C-T | not specified | Uncertain significance (Dec 20, 2021) | ||
| 20-57175004-T-C | Congenital total pulmonary venous return anomaly • BMP7-related disorder | Benign (Nov 27, 2023) | ||
| 20-57175148-G-T | Benign (Jun 28, 2018) | |||
| 20-57183425-CT-C | Benign (Jun 26, 2018) | |||
| 20-57183506-C-T | Benign (Aug 03, 2018) | |||
| 20-57183536-A-G | Benign (Aug 03, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BMP7 | protein_coding | protein_coding | ENST00000395863 | 7 | 97882 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.127 | 0.872 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.78 | 190 | 273 | 0.696 | 0.0000182 | 2841 |
| Missense in Polyphen | 56 | 113.52 | 0.49333 | 1196 | ||
| Synonymous | 0.236 | 111 | 114 | 0.972 | 0.00000826 | 807 |
| Loss of Function | 2.90 | 5 | 18.5 | 0.271 | 9.60e-7 | 189 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000128 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000554 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000449 | 0.0000439 |
| Middle Eastern | 0.0000554 | 0.0000544 |
| South Asian | 0.0000680 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Induces cartilage and bone formation. May be the osteoinductive factor responsible for the phenomenon of epithelial osteogenesis. Plays a role in calcium regulation and bone homeostasis.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Axon guidance - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);TGF-Core;Neural Crest Differentiation;Endoderm Differentiation;Mesodermal Commitment Pathway;Differentiation of white and brown adipocyte;Lung fibrosis;Role of Osx and miRNAs in tooth development;Endochondral Ossification;alk in cardiac myocytes;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Extracellular matrix organization;Molecules associated with elastic fibres;Elastic fibre formation;TGF-beta super family signaling pathway canonical;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;BMP receptor signaling;GPCR signaling-G alpha i;BMP2 signaling TGF-beta MV;BMP signaling Dro;ALK2 signaling events
(Consensus)
Recessive Scores
- pRec
- 0.673
Intolerance Scores
- loftool
- 0.123
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.41
Haploinsufficiency Scores
- pHI
- 0.994
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.634
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.958
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bmp7
- Phenotype
- embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; normal 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; hematopoietic system phenotype; pigmentation phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- bmp7a
- Affected structure
- erythroid lineage cell
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- skeletal system development;ossification;metanephros development;ureteric bud development;mesoderm formation;mesonephros development;epithelial to mesenchymal transition;endocardial cushion formation;pericardium morphogenesis;axon guidance;embryonic pattern specification;regulation of signaling receptor activity;positive regulation of gene expression;negative regulation of striated muscle cell apoptotic process;positive regulation of epithelial to mesenchymal transition;positive regulation of peptidyl-threonine phosphorylation;positive regulation of pathway-restricted SMAD protein phosphorylation;dendrite development;neural fold elevation formation;embryonic limb morphogenesis;positive regulation of bone mineralization;BMP signaling pathway;epithelial cell differentiation;hindbrain development;negative regulation of NF-kappaB transcription factor activity;response to estradiol;response to vitamin D;positive regulation of heterotypic cell-cell adhesion;protein localization to nucleus;negative regulation of phosphorylation;odontogenesis of dentin-containing tooth;regulation of apoptotic process;positive regulation of apoptotic process;steroid hormone mediated signaling pathway;negative regulation of MAP kinase activity;regulation of MAPK cascade;response to peptide hormone;negative regulation of neuron differentiation;positive regulation of osteoblast differentiation;negative regulation of Notch signaling pathway;negative regulation of cell cycle;negative regulation of mitotic nuclear division;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;cell development;embryonic camera-type eye morphogenesis;cardiac muscle tissue development;branching morphogenesis of an epithelial tube;mesenchymal cell differentiation;neuron projection morphogenesis;cartilage development;pharyngeal system development;embryonic skeletal joint morphogenesis;regulation of pathway-restricted SMAD protein phosphorylation;SMAD protein signal transduction;cardiac septum morphogenesis;branching involved in salivary gland morphogenesis;mesenchyme development;negative regulation of cell death;negative regulation of prostatic bud formation;regulation of branching involved in prostate gland morphogenesis;chorio-allantoic fusion;heart trabecula morphogenesis;monocyte aggregation;cellular response to hypoxia;cellular response to BMP stimulus;negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis;negative regulation of glomerular mesangial cell proliferation;metanephric mesenchyme morphogenesis;nephrogenic mesenchyme morphogenesis;metanephric mesenchymal cell proliferation involved in metanephros development;positive regulation of dendrite development;positive regulation of hyaluranon cable assembly;negative regulation of NIK/NF-kappaB signaling;allantois development;positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis;regulation of removal of superoxide radicals
- Cellular component
- extracellular region;extracellular space;vesicle;collagen-containing extracellular matrix
- Molecular function
- cytokine activity;transforming growth factor beta receptor binding;protein binding;growth factor activity;heparin binding;BMP receptor binding