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TRAPPC4 trafficking protein particle complex subunit 4 [ Homo sapiens (human) ]

Gene ID: 51399, updated on 5-Mar-2024

Summary

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Official Symbol
TRAPPC4provided by HGNC
Official Full Name
trafficking protein particle complex subunit 4provided by HGNC
Primary source
HGNC:HGNC:19943
See related
Ensembl:ENSG00000196655 MIM:610971; AllianceGenome:HGNC:19943
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
SBDN; TRS23; PTD009; CGI-104; HSPC172; NEDESBA; SYNBINDIN
Summary
Involved in autophagy and endoplasmic reticulum to Golgi vesicle-mediated transport. Part of TRAPP complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 25.2), adrenal (RPKM 22.1) and 25 other tissues See more
Orthologs
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Genomic context

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See TRAPPC4 in Genome Data Viewer
Location:
11q23.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119018766..119024134)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119039128..119044496)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118889476..118894844)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene centrosomal AT-AC splicing factor Neighboring gene ribosomal protein L23a pseudogene 64 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5616 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118889349-118890047 Neighboring gene ribosomal protein S25 Neighboring gene solute carrier family 37 member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3962 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:118906707-118906861 Neighboring gene HYOU1 antisense RNA 1 Neighboring gene hypoxia up-regulated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5617 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927013-118927514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927515-118928014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5618 Neighboring gene uncharacterized LOC124902769

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. TRAPPC4 regulates the intracellular trafficking of PD-L1 and antitumor immunity. Ren Y, et al. Nat Commun, 2021 Sep 13. PMID 34518538, Free PMC Article
  2. A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome. Ghosh SG, et al. Eur J Hum Genet, 2021 Feb. PMID 32901138, Free PMC Article
  3. Synbindin deficiency inhibits colon carcinogenesis by attenuating Wnt cascade and balancing gut microbiome. Ai L, et al. Int J Cancer, 2019 Jul 1. PMID 30561033
  4. The role of ERK2 in colorectal carcinogenesis is partly regulated by TRAPPC4. Weng YR, et al. Mol Carcinog, 2014 Feb. PMID 23625650
  5. Crystal structure of human synbindin reveals two conformations of longin domain. Fan S, et al. Biochem Biophys Res Commun, 2009 Jan 16. PMID 18466758

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome.
    Title: A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome.
  2. TRAPPC4 regulates the intracellular trafficking of PD-L1 and antitumor immunity.
    Title: TRAPPC4 regulates the intracellular trafficking of PD-L1 and antitumor immunity.
  3. Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability.
    Title: Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability.
  4. Findings identify a critical role of Synbindin in gut microbiome composition and Wnt signaling activation in colorectal carcinogenesis, and highlight Synbindin as an adaptor protein with multifaceted roles.
    Title: Synbindin deficiency inhibits colon carcinogenesis by attenuating Wnt cascade and balancing gut microbiome.
  5. Overexpression of TRAPPC4 increased colorectal carcinogenesis.
    Title: The role of ERK2 in colorectal carcinogenesis is partly regulated by TRAPPC4.
  6. Synbindin contributes to malignant phenotypes of GC by activating ERK on the Golgi, and synbindin is a potential biomarker and therapeutic target for GC.
    Title: Synbindin in extracellular signal-regulated protein kinase spatial regulation and gastric cancer aggressiveness.
  7. Data demonstrate that TRAPPC4 may regulate cell proliferation and apoptosis in CRC by interaction with ERK2 and phosphorylating ERK1/2 as well as modulating the subcellular location of pERK1/2 to activate the relevant signaling pathway.
    Title: TRAPPC4-ERK2 interaction activates ERK1/2, modulates its nuclear localization and regulates proliferation and apoptosis of colorectal cancer cells.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene.
  9. The three-dimensional structure of human synbindin, which contains a longin domain and an atypical PDZ domain is presented.
    Title: Crystal structure of human synbindin reveals two conformations of longin domain.
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
Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy
MedGen: C5394027 OMIM: 618741 GeneReviews: Not available
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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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 COPII vesicle coating NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in vesicle coating NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in vesicle tethering NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi stack ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
part_of TRAPP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of TRAPP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of TRAPP complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of TRAPPII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of TRAPPIII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
  
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in synaptic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
trafficking protein particle complex subunit 4
Names
TRS23 homolog
hematopoietic stem/progenitor cell protein 172
trafficking protein particle complex 4

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_001318486.2 → NP_001305415.1  trafficking protein particle complex subunit 4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BP246594
    UniProtKB/Swiss-Prot
    Q9Y296
    Conserved Domains (1) summary
    cl21566
    Location:45 → 103
    Sedlin_N; Sedlin, N-terminal conserved region

  2. NM_001318488.2 → NP_001305417.1  trafficking protein particle complex subunit 4 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AK293977, AP003392
    Consensus CDS
    CCDS81634.1
    UniProtKB/TrEMBL
    B4DF86, J3KP27
    Related
    ENSP00000351896.4, ENST00000359005.8
    Conserved Domains (1) summary
    cl38905
    Location:4 → 167
    longin-like; Longin-like domains

  3. NM_001318489.2 → NP_001305418.1  trafficking protein particle complex subunit 4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains two alternate neighboring splice junctions in the coding region compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AK297422, AP003392
    Consensus CDS
    CCDS81633.1
    UniProtKB/Swiss-Prot
    Q9Y296
    Related
    ENSP00000405033.2, ENST00000434101.6
    Conserved Domains (1) summary
    cd14856
    Location:4 → 151
    TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

  4. NM_001318490.2 → NP_001305419.1  trafficking protein particle complex subunit 4 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate in-frame splice junction compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BP332308
    Consensus CDS
    CCDS81632.1
    UniProtKB/TrEMBL
    E9PQE8
    Related
    ENSP00000436827.1, ENST00000528230.5
    Conserved Domains (1) summary
    cd14856
    Location:4 → 162
    TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

  5. NM_001318492.2 → NP_001305421.1  trafficking protein particle complex subunit 4 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an alternate splice junction compared to variant 1. The resulting isoform (6) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BF971819
    UniProtKB/Swiss-Prot
    Q9Y296
    Conserved Domains (1) summary
    cd14856
    Location:13 → 100
    TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

  6. NM_001318494.2 → NP_001305423.1  trafficking protein particle complex subunit 4 isoform 7

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) lacks two consecutive coding exons compared to variant 1. The resulting isoform (7) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF105025, AP003392, BU624012
    Consensus CDS
    CCDS81635.1
    UniProtKB/TrEMBL
    E9PKS9
    Related
    ENSP00000435339.1, ENST00000525303.5
    Conserved Domains (1) summary
    cl38905
    Location:4 → 112
    longin-like; Longin-like domains

  7. NM_016146.6 → NP_057230.1  trafficking protein particle complex subunit 4 isoform 1

    See identical proteins and their annotated locations for NP_057230.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF105025, AP003392
    Consensus CDS
    CCDS8407.1
    UniProtKB/Swiss-Prot
    A8K3A5, B4DME1, Q9Y296
    UniProtKB/TrEMBL
    B4DF86
    Related
    ENSP00000436005.1, ENST00000533632.6
    Conserved Domains (1) summary
    cd14856
    Location:4 → 205
    TRAPPC4_synbindin; Trafficking protein particle complex subunit 4

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    119018766..119024134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427114.1 → XP_047283070.1  trafficking protein particle complex subunit 4 isoform X1

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646203.1 Reference GRCh38.p14 PATCHES

    Range
    40366..45734
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331617.1 → XP_054187592.1  trafficking protein particle complex subunit 4 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119039128..119044496
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369106.1 → XP_054225081.1  trafficking protein particle complex subunit 4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y296.1 GenPept UniProtKB/Swiss-Prot:Q9Y296

Gene LinkOut

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