TGFBRAP1 transforming growth factor beta receptor associated protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TGFBRAP1provided by HGNC
Official Full Name: transforming growth factor beta receptor associated protein 1provided by HGNC
Primary source: HGNC:HGNC:16836
See related: Ensembl:ENSG00000135966 MIM:606237; AllianceGenome:HGNC:16836
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: VPS3; TRAP1; TRAP-1
Summary: This gene encodes a protein that binds to transforming growth factor-beta (TGF-beta) receptors and plays a role in TGF-beta signaling. The encoded protein acts as a chaprone in signaling downstream of TGF-beta. It is involved in signal-dependent association with SMAD4. The protein is also a component of mammalian CORVET, a multisubunit tethering protein complex that is involved in fusion of early endosomes. [provided by RefSeq, Jun 2016]
Expression: Ubiquitous expression in bone marrow (RPKM 7.3), thyroid (RPKM 6.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q12.1-q12.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (105249404..105329735, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (105710521..105790921, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (105865861..105946192, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

Findings suggest that genetic polymorphisms of TGF-beta1 receptor-associated protein 1 (TGFBRAP1) may contribute to the genetic susceptibility of type 2 diabetes mellitus (T2DM) by mediating diabetes-related miRNA expression.
Title: The variant at TGFBRAP1 is significantly associated with type 2 diabetes mellitus and affects diabetes-related miRNA expression.
Vps3 and Vps8 are required for recycling of beta1 integrins.
Title: Vps3 and Vps8 control integrin trafficking from early to recycling endosomes and regulate integrin-dependent functions.
MFSD2B, CCL20 and STAT1, or STARD7 and ZNF512 genes may be risk or protect factors in prognosis of ADC; HTR2B, DPP4, and TGFBRAP1 genes may be risk factors in prognosis of SQC.
Title: Variations of chromosome 2 gene expressions among patients with lung cancer or non-cancer.
the association of rs2679860 polymorphisms of TGFBRAP1 and DBP variation as well as plasma levels of TGF-beta1
Title: Polymorphisms of the TGFBRAP1 gene in relation to blood pressure variability and plasma TGF-β1.
In the absence of Langerhans cells (LC), contact hypersensitivity (CHS) reactions in langerin-positive dendritic cell-specific TGF-betaR1-deficient mice are diminished, providing further evidence against a regulatory role for LC in CHS.
Title: Conditional deletion of TGF-βR1 using Langerin-Cre mice results in Langerhans cell deficiency and reduced contact hypersensitivity.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03).
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Genetic predisposition of responsiveness to therapy for chronic hepatitis C.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of pre-eclampsia detects novel maternal single nucleotide polymorphisms and copy-number variants in subsets of the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study cohort. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03). EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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

L29730 (e-PCR)
- UniSTS:40882

TGFBRAP1_7945 (e-PCR)
- UniSTS:467936

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SMAD binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transforming growth factor beta receptor binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosomal vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosomal vesicle fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosomal vesicle fusion	NAS Non-traceable Author Statement more info	PubMed
involved_in endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of SNARE complex assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in transforming growth factor beta receptor signaling pathway	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of CORVET complex	NAS Non-traceable Author Statement more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: transforming growth factor-beta receptor-associated protein 1

Names: TGF-beta receptor-associated protein 1; VPS3 CORVET complex subunit

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_050952.1 RefSeqGene

Range

4980..70301

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001142621.3 → NP_001136093.1 transforming growth factor-beta receptor-associated protein 1 isoform 1

See identical proteins and their annotated locations for NP_001136093.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 5, and 6 all encode the same isoform (1).

Source sequence(s)

AC012360, AK291382, BC019841

Consensus CDS

CCDS2067.1

UniProtKB/Swiss-Prot

A8K5R7, D3DVJ8, O60466, Q8WUH2

Conserved Domains (4) summary

pfam00637
Location:585 → 699

Clathrin; Region in Clathrin and VPS

pfam10366
Location:448 → 550

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:738 → 846

Vps39_2; Vacuolar sorting protein 39 domain 2

cl02434
Location:87 → 283

CNH; CNH domain
NM_001328646.3 → NP_001315575.1 transforming growth factor-beta receptor-associated protein 1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 3' terminal exon, resulting in novel 3' coding region and 3' UTR. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC012360

Conserved Domains (5) summary

smart00299
Location:586 → 700

CLH; Clathrin heavy chain repeat homology

pfam00637
Location:571 → 700

Clathrin; Region in Clathrin and VPS

pfam10366
Location:448 → 550

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:738 → 804

Vps39_2; Vacuolar sorting protein 39 domain 2

cl02434
Location:87 → 283

CNH; CNH domain
NM_001426428.1 → NP_001413357.1 transforming growth factor-beta receptor-associated protein 1 isoform 1

Status: REVIEWED

Source sequence(s)

CP068276
NM_001426429.1 → NP_001413358.1 transforming growth factor-beta receptor-associated protein 1 isoform 1

Status: REVIEWED

Source sequence(s)

CP068276
NM_004257.6 → NP_004248.2 transforming growth factor-beta receptor-associated protein 1 isoform 1

See identical proteins and their annotated locations for NP_004248.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 5, and 6 all encode the same isoform (1).

Source sequence(s)

AC012360, BC019841, BC020548

Consensus CDS

CCDS2067.1

UniProtKB/Swiss-Prot

A8K5R7, D3DVJ8, O60466, Q8WUH2

Related

ENSP00000377027.2, ENST00000393359.7

Conserved Domains (4) summary

pfam00637
Location:585 → 699

Clathrin; Region in Clathrin and VPS

pfam10366
Location:448 → 550

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:738 → 846

Vps39_2; Vacuolar sorting protein 39 domain 2

cl02434
Location:87 → 283

CNH; CNH domain

RNA

NR_137328.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains alternate splice sites in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC012360, BM672953

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

105249404..105329735 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047446424.1 → XP_047302380.1 transforming growth factor-beta receptor-associated protein 1 isoform X2
XM_047446422.1 → XP_047302378.1 transforming growth factor-beta receptor-associated protein 1 isoform X1

UniProtKB/Swiss-Prot

A8K5R7, D3DVJ8, O60466, Q8WUH2
XM_047446423.1 → XP_047302379.1 transforming growth factor-beta receptor-associated protein 1 isoform X1

UniProtKB/Swiss-Prot

A8K5R7, D3DVJ8, O60466, Q8WUH2