LTBP3

protein-coding

latent 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]

Previous symbols:
  • LTBP2

MANE transcript

NM_001130144.3

Inheritance

AD, AR

ClinVar variants

P:98U:967B:568

Top phenotype

Geleophysic dysplasia 3; Dental anomalies and short stature

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr11:65,538,559-65,558,930

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~20.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

geleophysic dysplasia 3LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0054722

Submitter: Ambry Genetics

geleophysic dysplasiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0000127

Submitter: Orphanet

brachyolmia-amelogenesis imperfecta syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011018

Submitter: Orphanet

brachyolmia-amelogenesis imperfecta syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0011018

Submitter: Ambry Genetics

brachyolmia-amelogenesis imperfecta syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011018

Submitter: Labcorp Genetics (formerly Invitae)

geleophysic dysplasia 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0054722

Submitter: PanelApp Australia

geleophysic dysplasia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0054722

Submitter: PanelApp Australia

geleophysic dysplasia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0054722

Submitter: Labcorp Genetics (formerly Invitae)

Acromicric dysplasiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007055

Submitter: Orphanet

brachyolmia-amelogenesis imperfecta syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011018

Submitter: G2P

Clinical Genomic Database (CGD)

Geleophysic dysplasia 3; Dental anomalies and short statureAD/AR

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

Refs: 19344874; 25669657; 25899461; 27068007Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LTBP3 variants in ClinVar

12 Conditions Cataloged
Brachyolmia-amelogenesis imperfecta syndromeTotal: 1510
Inborn genetic diseasesTotal: 920
not providedTotal: 122
LTBP3-related disorderTotal: 99
not specifiedTotal: 70
Geleophysic dysplasia 3Total: 27
Heritable Thoracic Aortic DiseaseTotal: 3
Amelogenesis imperfectaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
17
clinvar
541
clinvar
4
clinvar
562
missense
1
clinvar
3
clinvar
932
clinvar
23
clinvar
959
nonsense
12
clinvar
2
clinvar
4
clinvar
18
start loss
0
frameshift
38
clinvar
12
clinvar
5
clinvar
55
splice donor/acceptor (+/-2bp)
3
clinvar
27
clinvar
9
clinvar
39
Total544496756441633

Highest pathogenic variant AF is 0.00023667759

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001130144.3RefSeqNP_001123616.128MANE Select
ENST00000301873.11EnsemblENSP00000301873.528MANE Select
NM_001164266.1RefSeqNP_001157738.126Standard
NM_021070.4RefSeqNP_066548.227Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ltbp3Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.855537760.7120.00004898339
Missense (PolyPhen)162287.770.562943044
Synonymous0.8923163370.9380.00002392553
Loss of Function5.891465.40.2140.00000303743

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish0.000100.000099rare
East Asian0.000170.00016rare
Finnish0.000270.00023rare
European (Non-Finnish)0.000220.00021rare
South Asian0.0000680.000065rare
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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