LTBP3 latent transforming growth factor beta binding protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LTBP3provided by HGNC
Official Full Name: latent transforming growth factor beta binding protein 3provided by HGNC
Primary source: HGNC:HGNC:6716
See related: Ensembl:ENSG00000168056 MIM:602090; AllianceGenome:HGNC:6716
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DASS; LTBP2; LTBP-3; STHAG6; pp6425; GPHYSD3
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]
Annotation information: Note: This gene (GeneID: 4054) was identified as LTBP2 in PMID: 7719025. The official symbol for this gene is now LTBP3. [27 Jan 2017]
Expression: Ubiquitous expression in ovary (RPKM 27.2), fat (RPKM 25.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.1

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (65538559..65558359, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (65532759..65552582, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (65306030..65325830, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[IDENTIFICATION OF A NOVEL LTBP3 GENE PATHOGENIC VARIANT IN DRUZE ARAB PATIENTS PRESENTED WITH SYNDROMIC SHORT STATURE WITH BRACHYOLMIA AND AMELOGENESIS IMPERFECTA].
Title: [IDENTIFICATION OF A NOVEL LTBP3 GENE PATHOGENIC VARIANT IN DRUZE ARAB PATIENTS PRESENTED WITH SYNDROMIC SHORT STATURE WITH BRACHYOLMIA AND AMELOGENESIS IMPERFECTA].
Expanding genotypic and phenotypic spectrums of LTBP3 variants in dental anomalies and short stature syndrome.
Title: Expanding genotypic and phenotypic spectrums of LTBP3 variants in dental anomalies and short stature syndrome.
Latent TGFbeta-binding proteins regulate UCP1 expression and function via TGFbeta2.
Title: Latent TGFβ-binding proteins regulate UCP1 expression and function via TGFβ2.
Novel LTBP3 mutations associated with thoracic aortic aneurysms and dissections.
Title: Novel LTBP3 mutations associated with thoracic aortic aneurysms and dissections.
Bi-allelic loss-of-function novel variants in LTBP3-related skeletal dysplasia: Report of first patient from India.
Title: Bi-allelic loss-of-function novel variants in LTBP3-related skeletal dysplasia: Report of first patient from India.
Common variants in LTBP3 gene contributed to the risk of hip osteoarthritis in Han Chinese population.
Title: Common variants in LTBP3 gene contributed to the risk of hip osteoarthritis in Han Chinese population.
Data indicate that latent transforming growth factor beta binding protein 3 (LTBP3) is a disease gene for acromicric dysplasia (ACMICD) and suggest the genotype-phenotype correlation of LTBP3 mutations.
Title: Genotype-phenotype correlation and expansion of orodental anomalies in LTBP3-related disorders.
A specific role for LTBP3 in cancer progression toward metastatic disease.
Title: LTBP3 promotes early metastatic events during cancer cell dissemination.
homozygous LTBP3 pathogenic variants predispose individuals to thoracic aortic aneurysms and dissections, along with the previously described skeletal and dental abnormalities.
Title: LTBP3 Pathogenic Variants Predispose Individuals to Thoracic Aortic Aneurysms and Dissections.
LTBP3 is a novel component of the microfibrillar network involved in the acromelic dysplasia spectrum.
Title: Mutations in LTBP3 cause acromicric dysplasia and geleophysic dysplasia.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Brachyolmia-amelogenesis imperfecta syndrome MedGen: C1832594 OMIM: 601216 GeneReviews: Not available	not available
Geleophysic dysplasia 3 MedGen: C4540511 OMIM: 617809 GeneReviews: Geleophysic Dysplasia	not available

EBI GWAS Catalog

Description
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH65764 (e-PCR)
- UniSTS:9768

D8S2279 (e-PCR)
- UniSTS:473907

D1S1425 (e-PCR)
- UniSTS:149621

WI-15382 (e-PCR)
- UniSTS:12183

L18006 (e-PCR)
- UniSTS:52735

Clone Names

FLJ33431, FLJ39893, FLJ42533, FLJ44138, FLJ45576, DKFZp586M2123

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transforming growth factor beta binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in bone mineralization	IEA Inferred from Electronic Annotation more info
involved_in bone morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in bone remodeling	IEA Inferred from Electronic Annotation more info
involved_in chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in lung saccule development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of bone mineralization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of bone resorption	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of mesenchymal stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of mesenchymal stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info

General protein information

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Preferred Names: latent-transforming growth factor beta-binding protein 3

Names: latent TGF beta binding protein 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_016437.1 RefSeqGene

Range

4870..24670

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001130144.3 → NP_001123616.1 latent-transforming growth factor beta-binding protein 3 isoform 1 precursor

See identical proteins and their annotated locations for NP_001123616.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AF135960, AF318354, AK024477, AP001362

Consensus CDS

CCDS44647.1

UniProtKB/Swiss-Prot

O15107, Q96HB9, Q9H7K2, Q9NS15, Q9UFN4

UniProtKB/TrEMBL

A0A8I5KYV1

Related

ENSP00000301873.5, ENST00000301873.11

Conserved Domains (3) summary

smart00179
Location:355 → 390

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:660 → 694

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam00683
Location:415 → 450

TB; TB domain
NM_001164266.1 → NP_001157738.1 latent-transforming growth factor beta-binding protein 3 isoform 3

See identical proteins and their annotated locations for NP_001157738.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site, uses a downstream start codon, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks an internal segment near the C-terminus, compared to isoform 1.

Source sequence(s)

AF135960, AF318354, AK024477, BC136277

UniProtKB/TrEMBL

B9EG76, E9PKW1

Conserved Domains (3) summary

smart00179
Location:238 → 273

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:543 → 577

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam00683
Location:298 → 333

TB; TB domain
NM_021070.4 → NP_066548.2 latent-transforming growth factor beta-binding protein 3 isoform 2 precursor

See identical proteins and their annotated locations for NP_066548.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, as compared to variant 1. The resulting isoform (2) lacks an internal segment but has identical N- and C-termini, as compared to isoform 1.

Source sequence(s)

AF135960, AF318354, AK024477

Consensus CDS

CCDS8103.1

UniProtKB/TrEMBL

A0A8I5KYV1

Related

ENSP00000326647.4, ENST00000322147.8

Conserved Domains (3) summary

smart00179
Location:355 → 390

EGF_CA; Calcium-binding EGF-like domain

cd00054
Location:660 → 694

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam00683
Location:415 → 450

TB; TB domain