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    TBC1D23 TBC1 domain family member 23 [ Homo sapiens (human) ]

    Gene ID: 55773, updated on 5-May-2024

    Summary

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    Official Symbol
    TBC1D23provided by HGNC
    Official Full Name
    TBC1 domain family member 23provided by HGNC
    Primary source
    HGNC:HGNC:25622
    See related
    Ensembl:ENSG00000036054 MIM:617687; AllianceGenome:HGNC:25622
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PCH11; NS4ATP1
    Summary
    Involved in brain development; retrograde transport, endosome to Golgi; and vesicle tethering to Golgi. Located in cytoplasmic vesicle and trans-Golgi network. Colocalizes with WASH complex. Implicated in pontocerebellar hypoplasia. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal (RPKM 11.3), placenta (RPKM 11.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3q12.1-q12.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (100260992..100325238)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (102966332..103030580)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (99979836..100044082)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene dual specificity phosphatase 12 pseudogene 1 Neighboring gene vesicle transport through interaction with t-SNAREs 1B pseudogene 1 Neighboring gene hESC enhancers GRCh37_chr3:99979240-99979908 and GRCh37_chr3:99979909-99980577 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:99981915-99982583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20153 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:100047046-100047276 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:100053369-100053937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20155 Neighboring gene Sharpr-MPRA regulatory region 4023 Neighboring gene nitrilase family member 2 Neighboring gene translocase of outer mitochondrial membrane 70 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:100118351-100119270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14571

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. TBC1 domain family member 23 interacts with Ras-related protein Rab-11A to promote poor prognosis of non-small-cell lung cancer via β1-integrin. Zhang Y, et al. J Cell Mol Med, 2021 Sep. PMID 34363324, Free PMC Article
    2. Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical Development. Ivanova EL, et al. Am J Hum Genet, 2017 Sep 7. PMID 28823707, Free PMC Article
    3. Homozygous Mutations in TBC1D23 Lead to a Non-degenerative Form of Pontocerebellar Hypoplasia. Marin-Valencia I, et al. Am J Hum Genet, 2017 Sep 7. PMID 28823706, Free PMC Article
    4. Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP. De Arras L, et al. J Immunol, 2012 Mar 15. PMID 22312129, Free PMC Article
    5. Structure of TBC1D23 N-terminus reveals a novel role for rhodanese domain. Liu D, et al. PLoS Biol, 2020 May. PMID 32453802, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FAM91A1-TBC1D23 complex structure reveals human genetic variations susceptible for PCH.
      Title: FAM91A1-TBC1D23 complex structure reveals human genetic variations susceptible for PCH.
    2. TBC1 domain family member 23 interacts with Ras-related protein Rab-11A to promote poor prognosis of non-small-cell lung cancer via beta1-integrin.
      Title: TBC1 domain family member 23 interacts with Ras-related protein Rab-11A to promote poor prognosis of non-small-cell lung cancer via β1-integrin.
    3. rhodanese domain packs against the TBC domain and forms part of the platform to interact with golgin-97/245
      Title: Structure of TBC1D23 N-terminus reveals a novel role for rhodanese domain.
    4. Mutation of key residues of TBC1D23 or FAM21 selectively disrupts the endosomal vesicular trafficking toward the Trans-Golgi Network.
      Title: Structural and functional studies of TBC1D23 C-terminal domain provide a link between endosomal trafficking and PCH.
    5. The Rab GAP domain of TBC1D23 binds to a conserved motif at the tip of golgin-245 and golgin-97 at the trans-Golgi, while the C terminus binds to the WASH complex on endosome-derived vesicles. Thus, TBC1D23 is a specificity determinant that links the vesicle to the target membrane during endosome-to-Golgi trafficking.
      Title: TBC1D23 is a bridging factor for endosomal vesicle capture by golgins at the trans-Golgi.
    6. Homozygous Truncating Variants in TBC1D23 gene are associated with Pontocerebellar Hypoplasia and Alter Cortical Development.
      Title: Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical Development.
    7. Homozygous Mutations in TBC1D23 gene are associated with Non-degenerative Form of Pontocerebellar Hypoplasia.
      Title: Homozygous Mutations in TBC1D23 Lead to a Non-degenerative Form of Pontocerebellar Hypoplasia.
    Submit: New GeneRIF Correction

    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
    Pontocerebellar hypoplasia, type 11
    MedGen: C4540164 OMIM: 617695 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11046, DKFZp667G062

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in embryonic brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle tethering to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle tethering to Golgi IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in vesicle-mediated transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    part_of WASH complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    TBC1 domain family member 23
    Names
    HCV non-structural protein 4A-transactivated protein 1
    HCV nonstructural protein 4A-transactivated protein 1

    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.

    mRNA and Protein(s)

    1. NM_001199198.3 → NP_001186127.1  TBC1 domain family member 23 isoform 1

      See identical proteins and their annotated locations for NP_001186127.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC020955, DA801258
      Consensus CDS
      CCDS56265.1
      UniProtKB/Swiss-Prot
      B9A6M5, Q8TCN8, Q8WUB7, Q96D90, Q9NUY8, Q9NV75
      Related
      ENSP00000377700.4, ENST00000394144.9
      Conserved Domains (2) summary
      pfam00566
      Location:48 → 246
      RabGAP-TBC; Rab-GTPase-TBC domain
      cl00125
      Location:328 → 439
      RHOD; Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins ...

    2. NM_018309.5 → NP_060779.2  TBC1 domain family member 23 isoform 2

      See identical proteins and their annotated locations for NP_060779.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK001750, BC020955, BX648032, DA801258
      Consensus CDS
      CCDS2936.1
      UniProtKB/Swiss-Prot
      Q9NUY8
      Related
      ENSP00000340693.5, ENST00000344949.9
      Conserved Domains (2) summary
      pfam00566
      Location:48 → 246
      RabGAP-TBC; Rab-GTPase-TBC domain
      cl00125
      Location:328 → 439
      RHOD; Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      100260992..100325238
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006841.3 → XP_016862330.1  TBC1 domain family member 23 isoform X2

      UniProtKB/TrEMBL
      E9PGE5

    2. XM_047448562.1 → XP_047304518.1  TBC1 domain family member 23 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      102966332..103030580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347242.1 → XP_054203217.1  TBC1 domain family member 23 isoform X2

    2. XM_054347241.1 → XP_054203216.1  TBC1 domain family member 23 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NUY8.3 GenPept UniProtKB/Swiss-Prot:Q9NUY8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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