BMPR1B
protein-codingbone morphogenetic protein receptor type 1B, the group of CD molecules|Type 1 receptor serine/threonine kinases
Gene summary
This gene encodes a member of the bone morphogenetic protein (BMP) receptor family of transmembrane serine/threonine kinases. The ligands of this receptor are BMPs, which are members of the TGF-beta superfamily. BMPs are involved in endochondral bone formation and embryogenesis. These proteins transduce their signals through the formation of heteromeric complexes of 2 different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Type II receptors bind ligands in the absence of type I receptors, but they require their respective type I receptors for signaling, whereas type I receptors require their respective type II receptors for ligand binding. Mutations in this gene have been associated with primary pulmonary hypertension. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~400.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012274
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007215
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012274
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007216
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0021004
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007216
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0012274
Submitter: PanelApp Australia
Inheritance Pattern: Unknown
Disease ID:MONDO:0015924
Submitter: ClinGen
After a comprehensive literature review, the gene-disease relationship of BMPR1B and pulmonary arterial hypertension is disputed. Despite experimental evidence including function in biochemical pathways, protien interaction with BMPR2, and expression evidence in pumonary artery smooth muscle cells, there is insufficient proband level genetic evidence to classify the relationship as limited despite years of studies investigating the relationship between PAH and BMPR1B. Classification approved by Pulmonary Hypertension GCEP panel on 8/30/2022.
Inheritance Pattern: AD
Disease ID:MONDO:0014798
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0007216
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0012274
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014798
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0015924
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007216
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009231
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0008703
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0001476
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Genitourinary; Musculoskeletal
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
Comments: In Acromesomelic dysplasia, Demirhan type, interventions may be beneficial to allow reproductive capacity
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BMPR1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001203.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 52 | 2 | 56 | ||
| missense | 5 | 5 | 168 | 35 | 4 | 217 |
| nonsense | 2 | 1 | 1 | 4 | ||
| start loss | 0 | |||||
| frameshift | 2 | 1 | 3 | |||
| splice donor/acceptor (+/-2bp) | 2 | 2 | 3 | 1 | 8 | |
| Total | 11 | 8 | 175 | 88 | 6 | 288 |
Highest pathogenic variant AF is 0.000013147688
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001194.1 | 10 | MANE Select | |
| Ensembl | ENSP00000426617.1 | 10 | MANE Select | |
| RefSeq | NP_001243721.1 | 10 | Standard | |
| RefSeq | NP_001243722.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| bmpr1ba | Danio rerio | Structure: skeletal muscle cell Quality: differentiated abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- TGF-beta signaling pathway - Homo sapiens (human)
- Axon guidance - Homo sapiens (human)
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)
- Hippo signaling pathway - Homo sapiens (human)
- Fluid shear stress and atherosclerosis - Homo sapiens (human)
Biological Process
- skeletal system development
- cartilage condensation
- ovarian cumulus expansion
- eye development
- chondrocyte development
Molecular Function
- protein serine/threonine kinase activity
- transmembrane receptor protein serine/threonine kinase activity
- transforming growth factor beta-activated receptor activity
- transforming growth factor beta receptor activity, type I
- protein binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- dendrite
- neuronal cell body
- receptor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000440890
- Coding exons
- 11
- Length
- 400481
- Individuals with no LoFs
- 125726
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125733
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.270 | 278 | 291 | 0.955 | 0.0000148 | 3490 |
| Missense (PolyPhen) | 115 | 141.81 | 0.81096 | 1653 | ||
| Synonymous | -0.679 | 108 | 99.4 | 1.09 | 0.00000486 | 999 |
| Loss of Function | 4.55 | 2 | 28.0 | 0.0714 | 0.00000145 | 337 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000094 | 0.000092 | rare |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. Receptor for BMP7/OP-1 and GDF5. Positively regulates chondrocyte differentiation through GDF5 interaction. {ECO:0000250|UniProtKB:P36898}.;
- Disease
- DISEASE: Acromesomelic dysplasia, Demirhan type (AMDD) [MIM:609441]: A form of chondrodysplasia. Acromesomelic chondrodysplasias are rare hereditary skeletal disorders characterized by short stature, very short limbs and hand/foot malformations. The severity of limb abnormalities increases from proximal to distal with profoundly affected hands and feet showing brachydactyly and/or rudimentary fingers (knob-like fingers). AMDD inheritance is autosomal recessive. {ECO:0000269|PubMed:15805157, ECO:0000269|PubMed:24129431, ECO:0000269|PubMed:26105076}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brachydactyly A2 (BDA2) [MIM:112600]: A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. In brachydactyly type A2 shortening of the middle phalanges is confined to the index finger and the second toe, all other digits being more or less normal. Because of a rhomboid or triangular shape of the affected middle phalanx, the end of the second finger usually deviates radially. {ECO:0000269|PubMed:14523231, ECO:0000269|PubMed:16957682}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brachydactyly A1, D (BDA1D) [MIM:616849]: A form of brachydactyly type A1. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. Brachydactyly type A1 is characterized by middle phalanges of all the digits rudimentary or fused with the terminal phalanges. The proximal phalanges of the thumbs and big toes are short. BDA1D inheritance is autosomal dominant. {ECO:0000269|PubMed:25758993}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.339
Intolerance Scores
- LoFtool
- 0.100
- RVIS EVS
- -0.76
- RVIS percentile EVS
- 13.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |