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Aliases for TBC1D20 Gene

Aliases for TBC1D20 Gene

  • TBC1 Domain Family Member 20 2 3 5
  • C20orf140 3 4
  • Chromosome 20 Open Reading Frame 140 2
  • TBC1 Domain Family, Member 20 2
  • WARBM4 3

External Ids for TBC1D20 Gene

Previous HGNC Symbols for TBC1D20 Gene

  • C20orf140

Previous GeneCards Identifiers for TBC1D20 Gene

  • GC20M000367

Summaries for TBC1D20 Gene

Entrez Gene Summary for TBC1D20 Gene

  • 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]

GeneCards Summary for TBC1D20 Gene

TBC1D20 (TBC1 Domain Family Member 20) is a Protein Coding gene. Diseases associated with TBC1D20 include Warburg Micro Syndrome 4 and Warburg Micro Syndrome. Among its related pathways are Metabolism of proteins and Transport to the Golgi and subsequent modification. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and Rab GTPase binding.

UniProtKB/Swiss-Prot for TBC1D20 Gene

  • GTPase-activating protein specific for Rab1 and Rab2 small GTPase families for which it can accelerate the intrinsic GTP hydrolysis rate by more than five orders of magnitude.

Additional gene information for TBC1D20 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TBC1D20 Gene

Genomics for TBC1D20 Gene

GeneHancer (GH) Regulatory Elements for TBC1D20 Gene

Promoters and enhancers for TBC1D20 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I000460 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 561.7 +0.7 745 3.2 PKNOX1 FOXA2 SMAD1 MLX ARID4B SIN3A ZNF2 YY1 ZNF213 ZNF143 TBC1D20 GC20P000462 TRIB3 PIR53425
GH20I000360 Enhancer 1.5 Ensembl ENCODE dbSUPER 51.2 +98.6 98623 7.8 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 TRIB3 TBC1D20 RBCK1 ACTG1P3 ENSG00000206797 ENSG00000229728 CSNK2A1 C20orf96 SLC52A3 GC20P000385
GH20I001185 Promoter/Enhancer 1.8 Ensembl ENCODE 41.2 -724.3 -724331 3.8 HDGF ARNT ARID4B YBX1 DMAP1 YY1 SLC30A9 POLR2B CBX5 E2F8 TMEM74B ENSG00000274269 LOC105372496 TBC1D20 ACTG1P3 RBCK1 ENSG00000229728 SDCBP2-AS1 PSMF1
GH20I000368 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 39.7 +90.0 90033 8 MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF548 SP3 PPARGC1A MEF2D TBC1D20 TRIB3 RBCK1 SRXN1 ENSG00000206797 ACTG1P3 CSNK2A1 FAM110A GC20P000385 GC20P000387
GH20I000651 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 27.8 -190.5 -190486 2.7 HDGF PKNOX1 SMAD1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 SRXN1 GC20P000653 TBC1D20 ACTG1P3 RBCK1 ENSG00000229728 GC20M000621 ENSG00000270299
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TBC1D20 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TBC1D20 gene promoter:

Genomic Locations for TBC1D20 Gene

Genomic Locations for TBC1D20 Gene
chr20:435,477-462,553
(GRCh38/hg38)
Size:
27,077 bases
Orientation:
Minus strand
chr20:416,124-443,197
(GRCh37/hg19)

Genomic View for TBC1D20 Gene

Genes around TBC1D20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBC1D20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBC1D20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBC1D20 Gene

Proteins for TBC1D20 Gene

  • Protein details for TBC1D20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96BZ9-TBC20_HUMAN
    Recommended name:
    TBC1 domain family member 20
    Protein Accession:
    Q96BZ9
    Secondary Accessions:
    • A8K6I3
    • B9A6M1
    • Q5JWQ7
    • Q6ZSY8
    • Q96NE1
    • Q9BYM7
    • Q9H140

    Protein attributes for TBC1D20 Gene

    Size:
    403 amino acids
    Molecular mass:
    45855 Da
    Quaternary structure:
    • Directly interacts with the N-terminal amphipathic helix of hepatitis C virus (HCV) NS5A.

    Three dimensional structures from OCA and Proteopedia for TBC1D20 Gene

    Alternative splice isoforms for TBC1D20 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D20 Gene

Post-translational modifications for TBC1D20 Gene

No Post-translational modifications

Other Protein References for TBC1D20 Gene

No data available for DME Specific Peptides for TBC1D20 Gene

Domains & Families for TBC1D20 Gene

Gene Families for TBC1D20 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for TBC1D20 Gene

Suggested Antigen Peptide Sequences for TBC1D20 Gene

Graphical View of Domain Structure for InterPro Entry

Q96BZ9

UniProtKB/Swiss-Prot:

TBC20_HUMAN :
  • The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rabs switch 2 glutamine and insert in Rabs active site.
Domain:
  • The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rabs switch 2 glutamine and insert in Rabs active site.
genes like me logo Genes that share domains with TBC1D20: view

Function for TBC1D20 Gene

Molecular function for TBC1D20 Gene

UniProtKB/Swiss-Prot Function:
GTPase-activating protein specific for Rab1 and Rab2 small GTPase families for which it can accelerate the intrinsic GTP hydrolysis rate by more than five orders of magnitude.

Phenotypes From GWAS Catalog for TBC1D20 Gene

Gene Ontology (GO) - Molecular Function for TBC1D20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA,IDA 17684057
GO:0005515 protein binding IPI 17684057
GO:0017137 Rab GTPase binding IPI 17684057
genes like me logo Genes that share ontologies with TBC1D20: view
genes like me logo Genes that share phenotypes with TBC1D20: view

Human Phenotype Ontology for TBC1D20 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TBC1D20 Gene

Localization for TBC1D20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBC1D20 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBC1D20 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 3
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for TBC1D20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA 22491470
GO:0005789 endoplasmic reticulum membrane IDA 17684057
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030173 integral component of Golgi membrane IDA 17684057
genes like me logo Genes that share ontologies with TBC1D20: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TBC1D20 Gene

Pathways & Interactions for TBC1D20 Gene

genes like me logo Genes that share pathways with TBC1D20: view

Gene Ontology (GO) - Biological Process for TBC1D20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001675 acrosome assembly IEA --
GO:0002088 lens development in camera-type eye IEA --
GO:0006888 ER to Golgi vesicle-mediated transport IMP 21680502
GO:0007030 Golgi organization IMP,IEA 17684057
GO:0007283 spermatogenesis IEA --
genes like me logo Genes that share ontologies with TBC1D20: view

No data available for SIGNOR curated interactions for TBC1D20 Gene

Drugs & Compounds for TBC1D20 Gene

No Compound Related Data Available

Transcripts for TBC1D20 Gene

Unigene Clusters for TBC1D20 Gene

TBC1 domain family, member 20:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D20 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11
SP1: - - - - -
SP2: - - -
SP3: - -
SP4: - - -
SP5: -
SP6:
SP7: - - -
SP8: -
SP9:
SP10:

Relevant External Links for TBC1D20 Gene

GeneLoc Exon Structure for
TBC1D20
ECgene alternative splicing isoforms for
TBC1D20

Expression for TBC1D20 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TBC1D20 Gene

Protein differential expression in normal tissues from HIPED for TBC1D20 Gene

This gene is overexpressed in Bone (28.2) and Peripheral blood mononuclear cells (17.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TBC1D20 Gene



Protein tissue co-expression partners for TBC1D20 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TBC1D20 Gene:

TBC1D20

SOURCE GeneReport for Unigene cluster for TBC1D20 Gene:

Hs.590876

Evidence on tissue expression from TISSUES for TBC1D20 Gene

  • Nervous system(4.7)
  • Lung(4.3)
  • Skin(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TBC1D20 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • scalp
  • skull
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
Pelvis:
  • pelvis
  • penis
  • testicle
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with TBC1D20: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TBC1D20 Gene

Orthologs for TBC1D20 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TBC1D20 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TBC1D20 33 34
  • 99.01 (n)
dog
(Canis familiaris)
Mammalia TBC1D20 33 34
  • 92.8 (n)
cow
(Bos Taurus)
Mammalia TBC1D20 33 34
  • 92.72 (n)
mouse
(Mus musculus)
Mammalia Tbc1d20 33 16 34
  • 89.3 (n)
rat
(Rattus norvegicus)
Mammalia Tbc1d20 33
  • 88.89 (n)
oppossum
(Monodelphis domestica)
Mammalia TBC1D20 34
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 57 (a)
OneToMany
-- 34
  • 35 (a)
OneToMany
chicken
(Gallus gallus)
Aves TBC1D20 33 34
  • 80.38 (n)
lizard
(Anolis carolinensis)
Reptilia TBC1D20 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tbc1d20.1 33
  • 73.89 (n)
Str.10618 33
African clawed frog
(Xenopus laevis)
Amphibia MGC52691 33
zebrafish
(Danio rerio)
Actinopterygii tbc1d20 33 34
  • 70.61 (n)
zgc63863 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008312 33
  • 54.2 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG17883 33 34
  • 49.88 (n)
worm
(Caenorhabditis elegans)
Secernentea tbc-20 33 34
  • 49.6 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GYP8 34
  • 16 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU05272 33
  • 44.1 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gyp10 33
  • 41.7 (n)
Species where no ortholog for TBC1D20 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TBC1D20 Gene

ENSEMBL:
Gene Tree for TBC1D20 (if available)
TreeFam:
Gene Tree for TBC1D20 (if available)

Paralogs for TBC1D20 Gene

No data available for Paralogs for TBC1D20 Gene

Variants for TBC1D20 Gene

Sequence variations from dbSNP and Humsavar for TBC1D20 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs587777157 pathogenic, Warburg micro syndrome 4 447,946(-) G/A coding_sequence_variant, intron_variant, non_coding_transcript_variant, stop_gained
rs587777158 pathogenic, Warburg micro syndrome 4 445,095(-) G/A coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs587777159 pathogenic, Warburg micro syndrome 4 442,028(-) TGT/T coding_sequence_variant, frameshift, non_coding_transcript_variant
rs587777160 pathogenic, Warburg micro syndrome 4 440,344(-) C/T coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs141648576 conflicting-interpretations-of-pathogenicity, not specified 438,655(-) C/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for TBC1D20 Gene

Variant ID Type Subtype PubMed ID
nsv9774 CNV gain 18304495
nsv585171 CNV loss 21841781
nsv469833 CNV gain 16826518
nsv458842 CNV loss 19166990
nsv1109347 CNV deletion 24896259
nsv1066598 CNV gain 25217958
nsv1056266 CNV gain 25217958
esv3644956 CNV gain 21293372
esv3644953 CNV gain 21293372
esv3644952 CNV gain 21293372
esv3556706 CNV deletion 23714750
esv2677224 CNV deletion 23128226
esv2535181 CNV deletion 19546169
esv1050414 CNV deletion 17803354
dgv4221n100 CNV gain 25217958
dgv4219n100 CNV gain 25217958

Variation tolerance for TBC1D20 Gene

Residual Variation Intolerance Score: 23.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.38; 54.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBC1D20 Gene

Human Gene Mutation Database (HGMD)
TBC1D20
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBC1D20

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBC1D20 Gene

Disorders for TBC1D20 Gene

MalaCards: The human disease database

(7) MalaCards diseases for TBC1D20 Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
warburg micro syndrome 4
  • warbm4
warburg micro syndrome
  • micro syndrome
warburg micro syndrome 1
  • warbm1
hepatitis c virus
  • hepatitis c virus, susceptibility to
warburg micro syndrome 2
  • warbm2
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TBC20_HUMAN
  • Warburg micro syndrome 4 (WARBM4) [MIM:615663]: A form of Warburg micro syndrome, a rare syndrome characterized by microcephaly, microphthalmia, microcornia, congenital cataracts, optic atrophy, cortical dysplasia, in particular corpus callosum hypoplasia, severe mental retardation, spastic diplegia, and hypogonadism. {ECO:0000269 PubMed:24239381}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TBC1D20

genes like me logo Genes that share disorders with TBC1D20: view

No data available for Genatlas for TBC1D20 Gene

Publications for TBC1D20 Gene

  1. Loss-of-function mutations in TBC1D20 cause cataracts and male infertility in blind sterile mice and Warburg micro syndrome in humans. (PMID: 24239381) Liegel RP … Sidjanin DJ (American journal of human genetics 2013) 3 4 58
  2. Catalytic mechanism of a mammalian Rab·RabGAP complex in atomic detail. (PMID: 23236136) Gavriljuk K … Gerwert K (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 4 58
  3. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PMID: 19077034) Ishibashi K … Fukuda M (Genes to cells : devoted to molecular & cellular mechanisms 2009) 3 4 58
  4. TBC1D20 is a Rab1 GTPase-activating protein that mediates hepatitis C virus replication. (PMID: 17901050) Sklan EH … Glenn JS (The Journal of biological chemistry 2007) 2 3 58
  5. A Rab-GAP TBC domain protein binds hepatitis C virus NS5A and mediates viral replication. (PMID: 17686842) Sklan EH … Glenn JS (Journal of virology 2007) 3 4 58

Products for TBC1D20 Gene

Sources for TBC1D20 Gene

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