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

    Gene ID: 9392, updated on 10-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TGFBRAP1 in Genome Data Viewer
    Location:
    2q12.1-q12.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (105249404..105329735, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (105710521..105790921, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (105865861..105946192, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373528 Neighboring gene NANOG hESC enhancer GRCh37_chr2:105813700-105814274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:105866724-105867602 Neighboring gene G protein-coupled receptor 45 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16313 Neighboring gene Sharpr-MPRA regulatory region 6730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16315 Neighboring gene C2orf49 divergent transcript Neighboring gene chromosome 2 open reading frame 49 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:105985867-105986368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:105986369-105986868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16316 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 Functions

    What's a GeneRIF?

    Phenotypes

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ21394, FLJ22294

    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

    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)

    NEW Try the new Transcript table

    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
      4980..70301
      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, 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: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_001328646.3NP_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 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: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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      105249404..105329735 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      105710521..105790921 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_137328.2: Suppressed sequence

      Description
      NR_137328.2: This RefSeq was removed because it is not a nonsense-mediated mRNA decay (NMD) candidate but rather represents indel variation and is a protein coding transcript.