Aliases for TBC1D23 Gene

Aliases for TBC1D23 Gene

  • TBC1 Domain Family Member 23 2 3 4 5
  • HCV Non-Structural Protein 4A-Transactivated Protein 1 3 4
  • NS4ATP1 3 4
  • HCV Nonstructural Protein 4A-Transactivated Protein 1 3
  • TBC1 Domain Family, Member 23 2
  • FLJ11046 2
  • TBC1D23 5
  • PCH11 3

External Ids for TBC1D23 Gene

Previous GeneCards Identifiers for TBC1D23 Gene

  • GC03P101463
  • GC03P099979
  • GC03P097347

Summaries for TBC1D23 Gene

GeneCards Summary for TBC1D23 Gene

TBC1D23 (TBC1 Domain Family Member 23) is a Protein Coding gene. Diseases associated with TBC1D23 include Pontocerebellar Hypoplasia, Type 11 and Pontocerebellar Hypoplasia.

UniProtKB/Swiss-Prot Summary for TBC1D23 Gene

  • Putative Rab GTPase-activating protein which plays a role in vesicular trafficking (PubMed:28823707). Involved in endosome-to-Golgi trafficking. Acts as a bridging protein by binding simultaneously to golgins, including GOLGA1 and GOLGA4, located at the trans-Golgi, and to the WASH complex, located on endosome-derived vesicles (PubMed:29084197, PubMed:29426865). Together with WDR11 complex facilitates the golgin-mediated capture of vesicles generated using AP-1 (PubMed:29426865). Plays a role in brain development, including in cortical neuron positioning (By similarity). May also be important for neurite outgrowth, possibly through its involvement in membrane trafficking and cargo delivery, 2 processes that are essential for axonal and dendritic growth (By similarity). May act as a general inhibitor of innate immunity signaling, strongly inhibiting multiple TLR and dectin/CLEC7A-signaling pathways. Does not alter initial activation events, but instead affects maintenance of inflammatory gene expression several hours after bacterial lipopolysaccharide (LPS) challenge (By similarity).

Additional gene information for TBC1D23 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TBC1D23 Gene

Genomics for TBC1D23 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TBC1D23 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
GH03J100259 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 637.8 +0.3 294 4.2 SP1 HNRNPL CREB1 GATAD2A PRDM10 ZNF629 REST SIX5 SOX13 IKZF1 TBC1D23 ENSG00000287378 piR-56229-061 NIT2
GH03J099858 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 35.7 -397.4 -397391 10.8 ZNF221 ZNF174 ZNF300 RELA ZNF776 RBFOX2 IKZF2 ZNF331 POLR2A ZNF311 ENSG00000273374 TBC1D23 FILIP1L DCBLD2 TFG CMSS1 TMEM45A TOMM70 lnc-FILIP1L-2 piR-47830
GH03J100333 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 16.7 +74.4 74403 3.4 PRDM10 REST RFX1 IKZF1 POLR2A BACH1 LARP7 ZNF143 RBFOX2 PKNOX1 NIT2 lnc-TOMM70-4 piR-30963-023 piR-52261-184 LNP1 TOMM70 TBC1D23
GH03J100039 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 21.3 -216.4 -216402 9.8 PRDM10 ZNF629 JUND FOXA1 RELA PATZ1 TCF12 IKZF2 RCOR1 SP1 piR-40358 FILIP1L TBC1D23 CMSS1 TMEM45A LOC105374010
GH03J100000 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 17.1 -255.4 -255417 10.4 CEBPG CREB1 GATAD2A ATF7 PRDM10 ZNF629 IKZF1 ZNF692 TARDBP ZHX2 TBC1D23 FILIP1L LOC105374010 MIR3921 CMSS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBC1D23 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBC1D23

Top Transcription factor binding sites by QIAGEN in the TBC1D23 gene promoter:
  • ATF-2
  • c-Jun
  • c-Myb
  • Cart-1
  • FAC1
  • IRF-1
  • ISGF-3
  • Meis-1
  • Meis-1b

Genomic Locations for TBC1D23 Gene

Genomic Locations for TBC1D23 Gene
chr3:100,260,992-100,325,251
(GRCh38/hg38)
Size:
64,260 bases
Orientation:
Plus strand
chr3:99,979,686-100,044,095
(GRCh37/hg19)
Size:
64,410 bases
Orientation:
Plus strand

Genomic View for TBC1D23 Gene

Genes around TBC1D23 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBC1D23 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBC1D23 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBC1D23 Gene

Proteins for TBC1D23 Gene

  • Protein details for TBC1D23 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUY8-TBC23_HUMAN
    Recommended name:
    TBC1 domain family member 23
    Protein Accession:
    Q9NUY8
    Secondary Accessions:
    • B9A6M5
    • Q8TCN8
    • Q8WUB7
    • Q96D90
    • Q9NV75

    Protein attributes for TBC1D23 Gene

    Size:
    699 amino acids
    Molecular mass:
    78322 Da
    Quaternary structure:
    • Directly interacts with GOLGA1 and GOLGA4 (PubMed:29084197). Interacts with FAM91A1, C17ORF75 and WDR11; the interaction recruits TBC1D23 to AP-1-derived vesicles (PubMed:29084197, PubMed:29426865). Directly interacts with WASHC1 and WASHC2A/FAM21A (PubMed:29084197). Interacts with FKBP15 (PubMed:29084197).
    SequenceCaution:
    • Sequence=AAH10221.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAH20955.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA91881.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TBC1D23 Gene

    Alternative splice isoforms for TBC1D23 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D23 Gene

Post-translational modifications for TBC1D23 Gene

  • Ubiquitination at Lys495
  • Modification sites at PhosphoSitePlus

Other Protein References for TBC1D23 Gene

No data available for DME Specific Peptides for TBC1D23 Gene

Domains & Families for TBC1D23 Gene

Gene Families for TBC1D23 Gene

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

Protein Domains for TBC1D23 Gene

Suggested Antigen Peptide Sequences for TBC1D23 Gene

GenScript: Design optimal peptide antigens:
  • TBC1 domain family, member 23 (B9A6M5_HUMAN)
  • HCV non-structural protein 4A-transactivated protein 1 (TBC23_HUMAN)
genes like me logo Genes that share domains with TBC1D23: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TBC1D23 Gene

Function for TBC1D23 Gene

Molecular function for TBC1D23 Gene

UniProtKB/Swiss-Prot Function:
Putative Rab GTPase-activating protein which plays a role in vesicular trafficking (PubMed:28823707). Involved in endosome-to-Golgi trafficking. Acts as a bridging protein by binding simultaneously to golgins, including GOLGA1 and GOLGA4, located at the trans-Golgi, and to the WASH complex, located on endosome-derived vesicles (PubMed:29084197, PubMed:29426865). Together with WDR11 complex facilitates the golgin-mediated capture of vesicles generated using AP-1 (PubMed:29426865). Plays a role in brain development, including in cortical neuron positioning (By similarity). May also be important for neurite outgrowth, possibly through its involvement in membrane trafficking and cargo delivery, 2 processes that are essential for axonal and dendritic growth (By similarity). May act as a general inhibitor of innate immunity signaling, strongly inhibiting multiple TLR and dectin/CLEC7A-signaling pathways. Does not alter initial activation events, but instead affects maintenance of inflammatory gene expression several hours after bacterial lipopolysaccharide (LPS) challenge (By similarity).

Phenotypes From GWAS Catalog for TBC1D23 Gene

Gene Ontology (GO) - Molecular Function for TBC1D23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with TBC1D23: view
genes like me logo Genes that share phenotypes with TBC1D23: view

Human Phenotype Ontology for TBC1D23 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for TBC1D23 Gene

miRTarBase miRNAs that target TBC1D23

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBC1D23

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TBC1D23 Gene

Localization for TBC1D23 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBC1D23 Gene

Golgi apparatus, trans-Golgi network. Cytoplasmic vesicle. Note=Localization to the trans-Golgi is regulated by ARL1 and ARL5B/ARL8. ARL1 increases Golgi localization, while ARL5B decreases it. Recruitment to the trans-Golgi network requires the presence of GOLGA1 and GOLGA4, but not that of FAM91A1 (PubMed:29084197, PubMed:28823706). Recruited on AP-1-derived vesicles by WDR11 complex (PubMed:29426865). {ECO:0000269 PubMed:28823706, ECO:0000269 PubMed:29084197, ECO:0000269 PubMed:29426865}.

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 TBC1D23 gene
Compartment Confidence
golgi apparatus 5
cytosol 3
endosome 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
lysosome 1
extracellular 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TBC1D23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005794 Golgi apparatus IDA --
GO:0005802 trans-Golgi network IDA 28823706
GO:0005829 cytosol IEA --
GO:0031410 cytoplasmic vesicle IEA,IDA 29426865
genes like me logo Genes that share ontologies with TBC1D23: view

Pathways & Interactions for TBC1D23 Gene

PathCards logo

SuperPathways for TBC1D23 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TBC1D23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007420 brain development IMP 28823706
GO:0016192 vesicle-mediated transport IEA,ISS --
GO:0031175 neuron projection development IEA,ISS --
GO:0032680 regulation of tumor necrosis factor production IEA --
genes like me logo Genes that share ontologies with TBC1D23: view

No data available for Pathways by source and SIGNOR curated interactions for TBC1D23 Gene

Drugs & Compounds for TBC1D23 Gene

No Compound Related Data Available

Transcripts for TBC1D23 Gene

mRNA/cDNA for TBC1D23 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBC1D23

Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D23 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^
SP1: - - - - -
SP2: - - - - -
SP3: -
SP4: - - - -
SP5: - - - - - -
SP6: - - - -
SP7: - - -
SP8: - - - -
SP9: - - -
SP10:

ExUns: 16a · 16b ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b
SP1: -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for TBC1D23 Gene

GeneLoc Exon Structure for
TBC1D23

Expression for TBC1D23 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TBC1D23 Gene

Protein differential expression in normal tissues from HIPED for TBC1D23 Gene

This gene is overexpressed in Salivary gland (10.3) and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TBC1D23 Gene



Protein tissue co-expression partners for TBC1D23 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBC1D23

SOURCE GeneReport for Unigene cluster for TBC1D23 Gene:

Hs.477003

mRNA Expression by UniProt/SwissProt for TBC1D23 Gene:

Q9NUY8-TBC23_HUMAN
Tissue specificity: Isoform 1: Widely expressed, including in fetal adult brain (corpus callosum, pons, cerebellum), spinal cord, heart, skeletal muscle, thymus and bone marrow, and at lower levels in spleen. Hardly detected in liver, kidney, colon and testis. Isoform 2: Expressed at high levels in liver, kidney, colon and testis. Hardly detected in tissues expressing high levels of isoform 1. Expressed at low levels in spleen.

Evidence on tissue expression from TISSUES for TBC1D23 Gene

  • Nervous system(4.9)
  • Intestine(4.2)
  • Lymph node(4.2)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with TBC1D23: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TBC1D23 Gene

Orthologs for TBC1D23 Gene

This gene was present in the common ancestor of animals.

Orthologs for TBC1D23 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TBC1D23 30 31
  • 99.48 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TBC1D23 30 31
  • 94.71 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TBC1D23 30 31
  • 93.13 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TBC1D23 31
  • 92 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tbc1d23 30
  • 89.94 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D23 31
  • 89 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Tbc1d23 30 17 31
  • 88.6 (n)
OneToOne
Chicken
(Gallus gallus)
Aves TBC1D23 30 31
  • 82.03 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TBC1D23 31
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tbc1d23 30
  • 74.92 (n)
Str.10381 30
Zebrafish
(Danio rerio)
Actinopterygii tbc1d23 30 31
  • 72.12 (n)
OneToOne
zgc63756 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007749 30
  • 51.23 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG4552 30 31
  • 50.25 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea tbc-1 30 31
  • 47.29 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 42 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4706 30
Species where no ortholog for TBC1D23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • 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 TBC1D23 Gene

ENSEMBL:
Gene Tree for TBC1D23 (if available)
TreeFam:
Gene Tree for TBC1D23 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TBC1D23: view image

Paralogs for TBC1D23 Gene

No data available for Paralogs for TBC1D23 Gene

Variants for TBC1D23 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBC1D23 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
709751 Benign: not provided 100,283,761(+) C/G SYNONYMOUS_VARIANT
709752 Benign: not provided 100,295,302(+) A/G SYNONYMOUS_VARIANT
780384 Benign: not provided 100,279,642(+) T/G INTRON_VARIANT
791940 Benign: not provided 100,323,623(+) C/G SYNONYMOUS_VARIANT
801991 Likely Benign: PONTOCEREBELLAR HYPOPLASIA, TYPE 11 100,279,687(+) G/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for TBC1D23 Gene

Structural Variations from Database of Genomic Variants (DGV) for TBC1D23 Gene

Variant ID Type Subtype PubMed ID
esv3597171 CNV loss 21293372
nsv1114410 CNV deletion 24896259
nsv473129 CNV novel sequence insertion 20440878

Variation tolerance for TBC1D23 Gene

Residual Variation Intolerance Score: 10.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.44; 28.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBC1D23 Gene

Human Gene Mutation Database (HGMD)
TBC1D23
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBC1D23

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBC1D23 Gene

Disorders for TBC1D23 Gene

MalaCards: The human disease database

(7) MalaCards diseases for TBC1D23 Gene - From: OMIM, ClinVar, GTR, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TBC23_HUMAN
  • Pontocerebellar hypoplasia 11 (PCH11) [MIM:617695]: A non-degenerative form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum, evident upon brain imaging. PCH11 features include severely delayed psychomotor development with intellectual disability and poor speech, microcephaly, dysmorphic features, and pontocerebellar hypoplasia. PCH11 inheritance is autosomal recessive. {ECO:0000269 PubMed:28823706, ECO:0000269 PubMed:28823707}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with TBC1D23: view

No data available for Genatlas for TBC1D23 Gene

Publications for TBC1D23 Gene

  1. TBC1D23 is a bridging factor for endosomal vesicle capture by golgins at the trans-Golgi. (PMID: 29084197) Shin JJH … Munro S (Nature cell biology 2017) 2 3 4
  2. The WDR11 complex facilitates the tethering of AP-1-derived vesicles. (PMID: 29426865) Navarro Negredo P … Robinson MS (Nature communications 2018) 3 4
  3. Homozygous Mutations in TBC1D23 Lead to a Non-degenerative Form of Pontocerebellar Hypoplasia. (PMID: 28823706) Marin-Valencia I … Gleeson JG (American journal of human genetics 2017) 3 4
  4. Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical Development. (PMID: 28823707) Ivanova EL … Chelly J (American journal of human genetics 2017) 3 4
  5. Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP. (PMID: 22312129) De Arras L … Alper S (Journal of immunology (Baltimore, Md. : 1950) 2012) 2 3

Products for TBC1D23 Gene

Sources for TBC1D23 Gene