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

Gene ID: 55773, updated on 3-Apr-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
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Genomic context

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See TBC1D23 in Genome Data Viewer
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
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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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