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TBC1D20 TBC1 domain family member 20 [ Homo sapiens (human) ]

Gene ID: 128637, updated on 7-Jun-2020

Summary

Official Symbol
TBC1D20provided by HGNC
Official Full Name
TBC1 domain family member 20provided by HGNC
Primary source
HGNC:HGNC:16133
See related
Ensembl:ENSG00000125875 MIM:611663
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
WARBM4; C20orf140
Summary
This gene encodes a protein that belongs to a family of GTPase activator proteins of Rab-like small GTPases. The encoded protein and its cognate GTPase, Rab1, bind the nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) to mediate viral replication. Depletion of this protein inhibits replication of the virus and HCV infection. Mutations in this gene are associated with Warburg micro syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Expression
Ubiquitous expression in lung (RPKM 14.1), thyroid (RPKM 13.3) and 25 other tissues See more
Orthologs

Genomic context

See TBC1D20 in Genome Data Viewer
Location:
20p13
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (435480..462543, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (416124..443187, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr20.29 Neighboring gene RANBP2-type and C3HC4-type zinc finger containing 1 Neighboring gene casein kinase 2 alpha 1 Neighboring gene transcription factor 15

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env Overexpression of TBC1D20 induces relocalization of HIV-1 Env from detergent-resistant membrane compartments to soluble compartments PubMed
env TBC1D20 overexpression reduces the trafficking of HIV-1 Env towards the assembly sites at the plasma membrane PubMed
env Overexpression of TBC1D20 results in abnormal HIV-1 Env processing and reduces its incorporation into nascent virions, correlating with the reduced infectivity of such particles PubMed
env TBC1D20 overexpression impairs proper HIV-1 Env glycosylation PubMed
Envelope transmembrane glycoprotein gp41 env TBC1D20 overexpression reduces the trafficking of HIV-1 gp41 towards the assembly sites at the plasma membrane PubMed
env Overexpression of TBC1D20 induces relocalization of HIV-1 gp41 from detergent-resistant membrane compartments to soluble compartments PubMed
env Overexpression of TBC1D20, RAB1A, or RAB1B results in abnormal HIV-1 gp41 migration, suggesting that a precise regulation of the RAB1/TBC1D20 axis is necessary for proper HIV-1 gp41 processing PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ45119

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GTPase activator activity IDA
Inferred from Direct Assay
more info
PubMed 
Rab GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Rab GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
COPII vesicle coating TAS
Traceable Author Statement
more info
 
ER to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ER to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
Golgi organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acrosome assembly IEA
Inferred from Electronic Annotation
more info
 
cargo loading into COPII-coated vesicle IMP
Inferred from Mutant Phenotype
more info
PubMed 
lens fiber cell morphogenesis IEA
Inferred from Electronic Annotation
more info
 
lipid droplet organization IEA
Inferred from Electronic Annotation
more info
 
positive regulation by host of viral genome replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation by virus of viral protein levels in host cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of ER to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
seminiferous tubule development IEA
Inferred from Electronic Annotation
more info
 
virion assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum-Golgi intermediate compartment membrane TAS
Traceable Author Statement
more info
 
integral component of Golgi membrane IDA
Inferred from Direct Assay
more info
PubMed 
nuclear membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
TBC1 domain family member 20

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_034082.1 RefSeqGene

    Range
    5021..32074
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_144628.4NP_653229.1  TBC1 domain family member 20

    See identical proteins and their annotated locations for NP_653229.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
    Source sequence(s)
    AF116909, AK291648, AL121747, BC047616, BM984598, DA238706
    Consensus CDS
    CCDS13002.1
    UniProtKB/Swiss-Prot
    Q96BZ9
    UniProtKB/TrEMBL
    Q9Y2V8
    Related
    ENSP00000346139.4, ENST00000354200.5
    Conserved Domains (1) summary
    pfam00566
    Location:63266
    RabGAP-TBC; Rab-GTPase-TBC domain

RNA

  1. NR_111901.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC014983, DA238706

RefSeqs of Annotated Genomes: Homo sapiens Updated 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_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    435480..462543 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005260661.1XP_005260718.1  TBC1 domain family member 20 isoform X1

    See identical proteins and their annotated locations for XP_005260718.1

    UniProtKB/Swiss-Prot
    Q96BZ9
    Related
    ENSP00000432280.1, ENST00000461304.5
    Conserved Domains (1) summary
    pfam00566
    Location:63266
    RabGAP-TBC; Rab-GTPase-TBC domain
  2. XM_006723540.3XP_006723603.1  TBC1 domain family member 20 isoform X2

    Conserved Domains (1) summary
    pfam00566
    Location:74204
    RabGAP-TBC; Rab-GTPase-TBC domain
  3. XM_017027645.1XP_016883134.1  TBC1 domain family member 20 isoform X2

    Conserved Domains (1) summary
    pfam00566
    Location:74204
    RabGAP-TBC; Rab-GTPase-TBC domain
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