BMP15
bone morphogenetic protein 15, the group of Bone morphogenetic proteins
Basic information
Region (hg38): X:50910734-50916641
Links
Phenotypes
GenCC
Source:
- ovarian dysgenesis 2 (Moderate), mode of inheritance: AD
- 46 XX gonadal dysgenesis (Supportive), mode of inheritance: AD
- ovarian dysgenesis 2 (Strong), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ovarian dysgenesis 2 | XL | Obstetric | Genetic knowledge may allow reproductive capabilities such as via egg preservation | Endocrine; Genitourinary; Obstetric | 15136966; 16508750; 19263482 |
ClinVar
This is a list of variants' phenotypes submitted to
- Ovarian dysgenesis 2 (24 variants)
- not provided (12 variants)
- Inborn genetic diseases (11 variants)
- not specified (7 variants)
- Premature ovarian failure 4 (3 variants)
- Ovarian dysgenesis (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMP15 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 | 5 | |||||
| missense | 13 | 25 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 3 | |||||
| Total | 5 | 0 | 14 | 8 | 9 |
Highest pathogenic variant AF is 0.0000802
Variants in BMP15
This is a list of pathogenic ClinVar variants found in the BMP15 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BMP15 | protein_coding | protein_coding | ENST00000252677 | 2 | 5824 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000183 | 0.722 | 125707 | 4 | 11 | 125722 | 0.0000597 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0699 | 157 | 159 | 0.984 | 0.0000127 | 2547 |
| Missense in Polyphen | 34 | 36.963 | 0.91984 | 606 | ||
| Synonymous | 0.0609 | 56 | 56.6 | 0.990 | 0.00000405 | 794 |
| Loss of Function | 0.948 | 7 | 10.3 | 0.681 | 8.83e-7 | 143 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000188 | 0.000160 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000137 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000524 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in follicular development. Oocyte- specific growth/differentiation factor that stimulates folliculogenesis and granulosa cell (GC) growth. {ECO:0000269|PubMed:18227435}.;
- Disease
- DISEASE: Ovarian dysgenesis 2 (ODG2) [MIM:300510]: A disorder characterized by lack of spontaneous pubertal development, primary amenorrhea, uterine hypoplasia, and hypergonadotropic hypogonadism as a result of streak gonads. {ECO:0000269|PubMed:15136966}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Premature ovarian failure 4 (POF4) [MIM:300510]: An ovarian disorder defined as the cessation of ovarian function under the age of 40 years. It is characterized by oligomenorrhea or amenorrhea, in the presence of elevated levels of serum gonadotropins and low estradiol. {ECO:0000269|PubMed:16464940, ECO:0000269|PubMed:16508750, ECO:0000269|PubMed:16645022, ECO:0000269|PubMed:19263482, ECO:0000269|PubMed:19438907}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Ovarian steroidogenesis - Homo sapiens (human);TGF-Core;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;TGF-beta super family signaling pathway canonical;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);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
- 0.191
Intolerance Scores
- loftool
- 0.215
- rvis_EVS
- 0.6
- rvis_percentile_EVS
- 82.66
Haploinsufficiency Scores
- pHI
- 0.413
- hipred
- N
- hipred_score
- 0.229
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.223
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bmp15
- Phenotype
- reproductive system phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- bmp15
- Affected structure
- ovarian follicle
- Phenotype tag
- abnormal
- Phenotype quality
- maturity
Gene ontology
- Biological process
- ovarian follicle development;female gamete generation;regulation of signaling receptor activity;positive regulation of pathway-restricted SMAD protein phosphorylation;BMP signaling pathway;regulation of apoptotic process;regulation of MAPK cascade;post-translational protein modification;cellular protein metabolic process;positive regulation of transcription, DNA-templated;cell development;granulosa cell development;SMAD protein signal transduction
- Cellular component
- extracellular space;endoplasmic reticulum lumen
- Molecular function
- cytokine activity;transforming growth factor beta receptor binding;growth factor activity