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

Gene ID: 9392, updated on 17-Jun-2019

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
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

Genomic context

See TGFBRAP1 in Genome Data Viewer
Location:
2q12.1-q12.2
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (105249408..105329735, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (105865861..105946148, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373528 Neighboring gene G protein-coupled receptor 45 Neighboring gene uncharacterized LOC100506473 Neighboring gene chromosome 2 open reading frame 49 Neighboring gene four and a half LIM domains 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI 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.
NHGRI GWA Catalog
Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03).
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21394, FLJ22294

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SMAD binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SMAD binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transforming growth factor beta receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
endosomal vesicle fusion IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
transforming growth factor beta receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
CORVET complex IEA
Inferred from Electronic Annotation
more info
 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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

  1. NG_050952.1 RefSeqGene

    Range
    5001..70325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142621.3NP_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 and 2 encode the same isoform (1)
    Source sequence(s)
    AC012360, AK291382, BC019841
    Consensus CDS
    CCDS2067.1
    UniProtKB/Swiss-Prot
    Q8WUH2
    Related
    ENSP00000471434.2, ENST00000595531.5
    Conserved Domains (4) summary
    pfam00637
    Location:585699
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:448550
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:738846
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:87283
    CNH; CNH domain
  2. NM_001328646.2NP_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:586700
    CLH; Clathrin heavy chain repeat homology
    pfam00637
    Location:571700
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:448550
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:738804
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:87283
    CNH; CNH domain
  3. NM_004257.6NP_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 longer transcript. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC012360, BC019841, BC020548
    Consensus CDS
    CCDS2067.1
    UniProtKB/Swiss-Prot
    Q8WUH2
    Related
    ENSP00000377027.2, ENST00000393359.7
    Conserved Domains (4) summary
    pfam00637
    Location:585699
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:448550
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:738846
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:87283
    CNH; CNH domain

RNA

  1. NR_137328.1 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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    105249408..105329735 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005339.2XP_016860828.1  transforming growth factor-beta receptor-associated protein 1 isoform X1

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