BMPR1B

protein-coding

bone 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

NM_001203.3

Inheritance

AR, AD

ClinVar variants

P:19U:175B:94

Top phenotype

Acromesomelic dysplasia 3; Brachydactyly, type A1, D; Brachydactyly, type A2; Brachydactyly C/Symphalangism-like phenotype

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr4:94,757,955-95,158,448

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~400.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

acromesomelic dysplasia 3MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012274

Submitter: Ambry Genetics

brachydactyly type A1SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007215

Submitter: Orphanet

acromesomelic dysplasia 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012274

Submitter: Labcorp Genetics (formerly Invitae)

brachydactyly type A2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007216

Submitter: Labcorp Genetics (formerly Invitae)

brachydactylyMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0021004

Submitter: Ambry Genetics

brachydactyly type A2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007216

Submitter: PanelApp Australia

acromesomelic dysplasia 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012274

Submitter: PanelApp Australia

pulmonary arterial hypertensionNO_KNOWN

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.

brachydactyly type A1DSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014798

Submitter: PanelApp Australia

brachydactyly type A2DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0007216

Submitter: G2P

acromesomelic dysplasia 3MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012274

Submitter: Ambry Genetics

brachydactyly type A1DMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014798

Submitter: Ambry Genetics

pulmonary arterial hypertensionMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0015924

Submitter: PanelApp Australia

brachydactyly type A2SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007216

Submitter: Orphanet

acromesomelic dysplasia 2BSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009231

Submitter: Orphanet

acromesomelic dysplasia 2ASUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008703

Submitter: Orphanet

colobomaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0001476

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Acromesomelic dysplasia 3; Brachydactyly, type A1, D; Brachydactyly, type A2; Brachydactyly C/Symphalangism-like phenotypeAD/AR

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

Refs: 14523231; 15805157; 16957682; 24129431; 25758993; 26105076Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BMPR1B variants in ClinVar

15 Conditions Cataloged
Acromesomelic dysplasia 3Total: 245
Type A2 brachydactylyTotal: 239
not providedTotal: 60
Inborn genetic diseasesTotal: 60
BrachydactylyTotal: 28
not specifiedTotal: 21
BMPR1B-related disorderTotal: 21
Brachydactyly type A1DTotal: 9

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
52
clinvar
2
clinvar
56
missense
5
clinvar
5
clinvar
168
clinvar
35
clinvar
4
clinvar
217
nonsense
2
clinvar
1
clinvar
1
clinvar
4
start loss
0
frameshift
2
clinvar
1
clinvar
3
splice donor/acceptor (+/-2bp)
2
clinvar
2
clinvar
3
clinvar
1
clinvar
8
Total118175886288

Highest pathogenic variant AF is 0.000013147688

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001203.3RefSeqNP_001194.110MANE Select
ENST00000515059.6EnsemblENSP00000426617.110MANE Select
NM_001256792.2RefSeqNP_001243721.110Standard
NM_001256793.2RefSeqNP_001243722.111Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
bmpr1baDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2702782910.9550.00001483490
Missense (PolyPhen)115141.810.810961653
Synonymous-0.67910899.41.090.00000486999
Loss of Function4.55228.00.07140.00000145337

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000940.000092rare
European (Non-Finnish)0.00000880.0000088rare
South Asian0.0000330.000033rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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