BMP10
bone morphogenetic protein 10, the group of Bone morphogenetic proteins
Basic information
Region (hg38): 2:68860908-68871397
Links
Phenotypes
GenCC
Source:
- left ventricular noncompaction (Limited), mode of inheritance: AD
- pulmonary arterial hypertension (Limited), mode of inheritance: AD
- congenital heart disease (Limited), mode of inheritance: AD
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 BMP10 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 | 18 | 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 | 18 | 1 | 2 |
Variants in BMP10
This is a list of pathogenic ClinVar variants found in the BMP10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-68865641-C-G | not specified | Uncertain significance (Nov 07, 2022) | ||
| 2-68865915-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
| 2-68866020-C-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 2-68866156-G-T | Benign (Apr 30, 2018) | |||
| 2-68866169-T-C | not specified | Likely benign (Jan 23, 2023) | ||
| 2-68866239-G-A | not specified | Uncertain significance (Jun 05, 2023) | ||
| 2-68866254-G-T | not specified | Uncertain significance (Nov 09, 2022) | ||
| 2-68866257-T-C | not specified | Uncertain significance (Mar 18, 2024) | ||
| 2-68866307-G-C | Bladder exstrophy-epispadias-cloacal extrophy complex | Benign (-) | ||
| 2-68866340-C-G | not specified | Uncertain significance (May 05, 2023) | ||
| 2-68866343-G-A | not specified | Uncertain significance (May 26, 2024) | ||
| 2-68866356-G-T | not specified | Uncertain significance (Sep 26, 2022) | ||
| 2-68866419-G-A | not specified | Uncertain significance (Mar 21, 2023) | ||
| 2-68866442-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
| 2-68866526-G-A | not specified | Uncertain significance (Jul 29, 2023) | ||
| 2-68866536-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 2-68871070-T-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 2-68871072-C-T | not specified | Uncertain significance (Dec 31, 2023) | ||
| 2-68871078-G-C | not specified | Uncertain significance (May 23, 2023) | ||
| 2-68871091-T-C | not specified | Uncertain significance (Apr 13, 2023) | ||
| 2-68871100-C-T | not specified | Uncertain significance (Apr 13, 2023) | ||
| 2-68871102-A-C | not specified | Uncertain significance (May 21, 2024) | ||
| 2-68871138-T-C | not specified | Uncertain significance (Jun 23, 2023) | ||
| 2-68871157-G-A | not specified | Uncertain significance (May 03, 2023) | ||
| 2-68871273-T-G | not specified | Uncertain significance (Jun 21, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BMP10 | protein_coding | protein_coding | ENST00000295379 | 2 | 6037 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.908 | 0.0915 | 125728 | 0 | 4 | 125732 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.02 | 192 | 236 | 0.813 | 0.0000130 | 2815 |
| Missense in Polyphen | 50 | 93.418 | 0.53523 | 1118 | ||
| Synonymous | -0.497 | 101 | 94.8 | 1.06 | 0.00000564 | 813 |
| Loss of Function | 2.96 | 1 | 12.1 | 0.0827 | 6.03e-7 | 161 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for maintaining the proliferative activity of embryonic cardiomyocytes by preventing premature activation of the negative cell cycle regulator CDKN1C/p57KIP and maintaining the required expression levels of cardiogenic factors such as MEF2C and NKX2-5. Acts as a ligand for ACVRL1/ALK1, BMPR1A/ALK3 and BMPR1B/ALK6, leading to activation of SMAD1, SMAD5 and SMAD8 transcription factors. Inhibits endothelial cell migration and growth. May reduce cell migration and cell matrix adhesion in breast cancer cell lines. {ECO:0000269|PubMed:16049014, ECO:0000269|PubMed:17068149, ECO:0000269|PubMed:20608934}.;
- Pathway
- Heart Development;VEGFA-VEGFR2 Signaling Pathway;Signal Transduction;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;GPCR signaling-G alpha i;BMP2 signaling TGF-beta MV;Signaling by BMP;Signaling by TGF-beta family members;BMP signaling Dro
(Consensus)
Recessive Scores
- pRec
- 0.221
Intolerance Scores
- loftool
- 0.0486
- rvis_EVS
- 0.09
- rvis_percentile_EVS
- 60.47
Haploinsufficiency Scores
- pHI
- 0.205
- hipred
- Y
- hipred_score
- 0.644
- ghis
- 0.400
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.310
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bmp10
- Phenotype
- hematopoietic 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); 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); embryo phenotype; immune system phenotype; renal/urinary system phenotype; limbs/digits/tail phenotype; growth/size/body region 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- bmp10
- Affected structure
- endothelial cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- cell adhesion;adult heart development;regulation of signaling receptor activity;negative regulation of endothelial cell migration;positive regulation of cardiac muscle hypertrophy;negative regulation of cardiac muscle hypertrophy;positive regulation of pathway-restricted SMAD protein phosphorylation;negative regulation of cell growth;negative regulation of cell migration;BMP signaling pathway;activin receptor signaling pathway;regulation of apoptotic process;regulation of MAPK cascade;sarcomere organization;positive regulation of transcription, DNA-templated;cell development;atrial cardiac muscle tissue morphogenesis;ventricular cardiac muscle tissue morphogenesis;ventricular cardiac muscle cell development;regulation of cardiac muscle contraction;cardiac muscle cell proliferation;positive regulation of cardiac muscle cell proliferation;positive regulation of sarcomere organization;heart trabecula formation;pathway-restricted SMAD protein phosphorylation;SMAD protein signal transduction;positive regulation of cartilage development;regulation of cardiac muscle hypertrophy in response to stress;positive regulation of cell proliferation involved in heart morphogenesis
- Cellular component
- extracellular region;extracellular space;cytoplasm;cell surface;Z disc
- Molecular function
- cytokine activity;transforming growth factor beta receptor binding;hormone activity;protein binding;growth factor activity;telethonin binding;receptor serine/threonine kinase binding