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

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; AllianceGenome:HGNC:16133
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: mouse all
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Genomic context

Location:: 20p13

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (435480..462533, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (479231..506260, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (416124..443177, complement)

Chromosome 20 - NC_000020.11 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?

Micro and Martsolf syndromes in 34 new patients: Refining the phenotypic spectrum and further molecular insights.
Title: Micro and Martsolf syndromes in 34 new patients: Refining the phenotypic spectrum and further molecular insights.
Martsolf syndrome with novel mutation in the TBC1D20 gene in a family from Iran.
Title: Martsolf syndrome with novel mutation in the TBC1D20 gene in a family from Iran.
Warburg Micro syndrome is caused by TBC1D20 deficiency.
Title: Warburg Micro syndrome is caused by RAB18 deficiency or dysregulation.
Loss-of-function mutations in TBC1D20 cause cataracts and male infertility in blind sterile mice and Warburg micro syndrome in humans.
Title: Loss-of-function mutations in TBC1D20 cause cataracts and male infertility in blind sterile mice and Warburg micro syndrome in humans.
The detailed molecular reaction mechanism of a complex between human Rab and RabGAP at the highest possible spatiotemporal resolution and in atomic detail, is described.
Title: Catalytic mechanism of a mammalian Rab·RabGAP complex in atomic detail.
The NS5A interaction with TBC1D20 and Rab1 is essential for the viral life cycle.
Title: Role for TBC1D20 and Rab1 in hepatitis C virus replication via interaction with lipid droplet-bound nonstructural protein 5A.
These findings add TBC1D20 to the network of host factors regulating HIV replication cycle.
Title: Human immunodeficiency virus type 1 envelope proteins traffic toward virion assembly sites via a TBC1D20/Rab1-regulated pathway.
TBC1D20 was found to be the first known GAP for Rab1, which is implicated in the regulation of anterograde traffic between the endoplasmic reticulum and the Golgi complex
Title: TBC1D20 is a Rab1 GTPase-activating protein that mediates hepatitis C virus replication.

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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

Associated conditions

Description	Tests
Warburg micro syndrome 4 MedGen: C3810265 OMIM: 615663 GeneReviews: RAB18 Deficiency	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

RH66094 (e-PCR)
- UniSTS:53006

G09312 (e-PCR)
- UniSTS:8978

SHGC-132609 (e-PCR)
- UniSTS:185366

WI-21992 (e-PCR)
- UniSTS:7461

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-56964 (e-PCR)
- UniSTS:66877

RH16324 (e-PCR)
- UniSTS:3414

D1S1423 (e-PCR)
- UniSTS:149619

G19838 (e-PCR)
- UniSTS:45266

A002A04 (e-PCR)
- UniSTS:45267

STS-Z41706 (e-PCR)
- UniSTS:15833

SHGC-36522 (e-PCR)
- UniSTS:16380

SHGC-36460 (e-PCR)
- UniSTS:16381

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activator activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle cargo loading	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in Golgi organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in acrosome assembly	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lens fiber cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in lipid droplet organization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by host of viral genome replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation by virus of viral protein levels in host cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ER to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of GTPase activity	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in seminiferous tubule development	IEA Inferred from Electronic Annotation more info
involved_in virion assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum-Golgi intermediate compartment membrane	TAS Traceable Author Statement more info
located_in nuclear membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: TBC1 domain family member 20

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_034082.1 RefSeqGene

Range

5021..32074

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_144628.4 → NP_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

A8K6I3, B9A6M1, Q5JWQ7, Q6ZSY8, Q96BZ9, Q96NE1, Q9BYM7, Q9H140

UniProtKB/TrEMBL

A0A7P0TBI8

Related

ENSP00000346139.4, ENST00000354200.5

Conserved Domains (1) summary

pfam00566
Location:63 → 266

RabGAP-TBC; Rab-GTPase-TBC domain

RNA

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