LTBP3
protein-codinglatent transforming growth factor beta binding protein 3, the group of Latent transforming growth factor beta binding proteins
Gene summary
The protein encoded by this gene forms a complex with transforming growth factor beta (TGF-beta) proteins and may be involved in their subcellular localization. Activation of this complex requires removal of the encoded binding protein. This protein also may play a structural role in the extracellular matrix. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]
- LTBP2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0054722
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0000127
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0011018
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0011018
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0011018
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0054722
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0054722
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0054722
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007055
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0011018
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Dental; 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LTBP3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001130144.3. 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 | 17 | 541 | 4 | 562 | ||
| missense | 1 | 3 | 932 | 23 | 959 | |
| nonsense | 12 | 2 | 4 | 18 | ||
| start loss | 0 | |||||
| frameshift | 38 | 12 | 5 | 55 | ||
| splice donor/acceptor (+/-2bp) | 3 | 27 | 9 | 39 | ||
| Total | 54 | 44 | 967 | 564 | 4 | 1633 |
Highest pathogenic variant AF is 0.00023667759
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001123616.1 | 28 | MANE Select | |
| Ensembl | ENSP00000301873.5 | 28 | MANE Select | |
| RefSeq | NP_001157738.1 | 26 | Standard | |
| RefSeq | NP_066548.2 | 27 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ltbp3 | Danio rerio | Structure: pharyngeal vasculature Quality: malformed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Extracellular matrix organization
- Molecules associated with elastic fibres
- Elastic fibre formation
Biological Process
- transforming growth factor beta activation
- positive regulation of mesenchymal stem cell proliferation
- positive regulation of mesenchymal stem cell differentiation
Molecular Function
- calcium ion binding
- transforming growth factor beta binding
Cellular Component
- extracellular region
- collagen-containing extracellular matrix
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301873
- Coding exons
- 28
- Length
- 20126
- Individuals with no LoFs
- 125708
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 40
- Defined
- 125748
- p
- 0.000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.85 | 553 | 776 | 0.712 | 0.0000489 | 8339 |
| Missense (PolyPhen) | 162 | 287.77 | 0.56294 | 3044 | ||
| Synonymous | 0.892 | 316 | 337 | 0.938 | 0.0000239 | 2553 |
| Loss of Function | 5.89 | 14 | 65.4 | 0.214 | 0.00000303 | 743 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.00027 | 0.00023 | rare |
| European (Non-Finnish) | 0.00022 | 0.00021 | rare |
| South Asian | 0.000068 | 0.000065 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Key regulator of transforming growth factor beta (TGFB1, TGFB2 and TGFB3) that controls TGF-beta activation by maintaining it in a latent state during storage in extracellular space. Associates specifically via disulfide bonds with the Latency- associated peptide (LAP), which is the regulatory chain of TGF- beta, and regulates integrin-dependent activation of TGF-beta. {ECO:0000303|PubMed:10743502, ECO:0000303|PubMed:11104663}.;
- Disease
- DISEASE: Dental anomalies and short stature (DASS) [MIM:601216]: A disorder characterized by hypoplastic amelogenesis imperfecta, significant short stature, brachyolmia-like anomalies including platyspondyly with short pedicles, narrow intervertebral and interpedicular distances, rectangular-shaped vertebrae with posterior scalloping and herniation of the nuclei, and broad femoral necks. Dental anomalies include widely spaced, small, yellow teeth, oligodontia, and severely reduced to absent enamel. {ECO:0000269|PubMed:19344874}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Geleophysic dysplasia 3 (GPHYSD3) [MIM:617809]: A form of geleophysic dysplasia, a rare skeletal disease characterized by severe short stature, short hands and feet, and joint limitations. Radiologic features include delayed bone age, cone-shaped epiphyses, shortened long tubular bones, and ovoid vertebral bodies. Affected individuals have characteristic facial features including a 'happy' face with full cheeks, shortened nose, hypertelorism, long and flat philtrum, and thin upper lip. Other distinctive features include skin thickening, progressive cardiac valvular thickening often leading to an early death, toe walking, tracheal stenosis, respiratory insufficiency, and lysosomal-like storage vacuoles in various tissues. GPHYSD3 inheritance is autosomal dominant. {ECO:0000269|PubMed:27068007}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- LoFtool
- 0.0559
- RVIS EVS
- -0.93
- RVIS percentile EVS
- 9.61
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.646
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |