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Aliases for TBC1D23 Gene

Aliases for TBC1D23 Gene

  • TBC1 Domain Family Member 23 2 3 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
  • 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 Pontoneocerebellar Hypoplasia.

UniProtKB/Swiss-Prot for TBC1D23 Gene

  • Putative Rab GTPase-activating protein which plays a role in vesicular trafficking (PubMed:28823707). 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 , fRNAdb sequence ontologies and piRNA Summary for TBC1D23 Gene

Genomics for TBC1D23 Gene

GeneHancer (GH) Regulatory Elements for TBC1D23 Gene

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
GH03I100259 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 587.9 +0.0 28 3.4 HDGF PKNOX1 SMAD1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 TBC1D23 GC03P100236 NIT2
GH03I100039 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 21.3 -216.2 -216227 9.8 PKNOX1 FOXA2 SIN3A FEZF1 IRF4 YY1 FOS ATF7 RUNX3 JUNB GC03M100040 PIR33357 FILIP1L TBC1D23 CMSS1 TMEM45A
GH03I100333 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 16.7 +74.6 74578 3.4 HDGF PKNOX1 ATF1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF48 NIT2 LNP1 TOMM70 TBC1D23
GH03I100262 Enhancer 0.7 Ensembl 37.9 +2.1 2084 0.2 KLF1 TAL1 MZF1 ZBTB40 TCF12 CC2D1A CTBP1 EGR1 NCOR1 ZSCAN5C TBC1D23 GC03P100236 NIT2
GH03I100263 Enhancer 0.7 Ensembl 37.9 +3.2 3184 1.2 MZF1 EBF1 ZNF335 CTBP1 EGR1 ZNF366 PRDM10 ZNF600 SMARCE1 SCRT1 TBC1D23 GC03P100236 NIT2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TBC1D23 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TBC1D23 gene promoter:

Genomic Locations for TBC1D23 Gene

Genomic Locations for TBC1D23 Gene
chr3:100,260,817-100,325,252
(GRCh38/hg38)
Size:
64,436 bases
Orientation:
Plus strand
chr3:99,979,686-100,044,095
(GRCh37/hg19)

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:
    No Data Available
    SequenceCaution:
    • Sequence=AAH10221.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH20955.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA91881.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for TBC1D23 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D23 Gene

Post-translational modifications 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):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for TBC1D23 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TBC1D23: view

No data available for 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). 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

Animal Model Products

miRNA for TBC1D23 Gene

miRTarBase miRNAs that target TBC1D23

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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. Note=Localization to the trans-Golgi is regulated by ARL1 and ARL5B/ARL8. ARL1 increases Golgi localization, while ARL5B decreases it. {ECO:0000269 PubMed:28823706}.

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 4
endosome 2
plasma membrane 1
extracellular 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1

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:0005794 Golgi apparatus IDA --
GO:0005802 trans-Golgi network IDA 28823706
GO:0005829 cytosol IEA --
GO:0071203 colocalizes_with WASH complex IDA 29084197
genes like me logo Genes that share ontologies with TBC1D23: view

Pathways & Interactions for TBC1D23 Gene

SuperPathways for TBC1D23 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TBC1D23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007420 brain development IMP 28823706
GO:0016192 vesicle-mediated transport ISS,IEA --
GO:0031175 neuron projection development ISS,IEA --
GO:0032680 regulation of tumor necrosis factor production IEA --
GO:0032755 positive regulation of interleukin-6 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

Unigene Clusters for TBC1D23 Gene

TBC1 domain family, member 23:
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
TBC1D23

Expression for TBC1D23 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for TBC1D23 Gene



Protein tissue co-expression partners for TBC1D23 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TBC1D23 Gene:

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)
  • Liver(4.2)
  • Lymph node(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 33 34
  • 99.48 (n)
dog
(Canis familiaris)
Mammalia TBC1D23 33 34
  • 94.71 (n)
cow
(Bos Taurus)
Mammalia TBC1D23 33 34
  • 93.13 (n)
oppossum
(Monodelphis domestica)
Mammalia TBC1D23 34
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tbc1d23 33
  • 89.94 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D23 34
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tbc1d23 33 16 34
  • 88.6 (n)
chicken
(Gallus gallus)
Aves TBC1D23 33 34
  • 82.03 (n)
lizard
(Anolis carolinensis)
Reptilia TBC1D23 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tbc1d23 33
  • 74.92 (n)
Str.10381 33
zebrafish
(Danio rerio)
Actinopterygii tbc1d23 33 34
  • 72.12 (n)
zgc63756 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007749 33
  • 51.23 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4552 33 34
  • 50.25 (n)
worm
(Caenorhabditis elegans)
Secernentea tbc-1 33 34
  • 47.29 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 42 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4706 33
Species where no ortholog for TBC1D23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for TBC1D23 Gene

No data available for Paralogs for TBC1D23 Gene

Variants for TBC1D23 Gene

Sequence variations from dbSNP and Humsavar for TBC1D23 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
VAR_080040 Pontocerebellar hypoplasia 11 (PCH11) [MIM:617695] p.Arg518Gln
rs1000019694 -- 100,306,423(+) T/A intron_variant
rs1000020430 -- 100,262,506(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000033394 -- 100,299,850(+) A/G intron_variant
rs1000085353 -- 100,300,200(+) C/T intron_variant

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

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

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

(3) MalaCards diseases for TBC1D23 Gene - From: HGMD, OMIM, ClinVar, 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.

Additional Disease Information for TBC1D23

genes like me logo Genes that share disorders with TBC1D23: view

No data available for Genatlas for TBC1D23 Gene

Publications for TBC1D23 Gene

  1. 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 58
  2. 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 58
  3. 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 58
  4. 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 58
  5. 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

Products for TBC1D23 Gene

Sources for TBC1D23 Gene

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