Aliases for TRAPPC4 Gene

Aliases for TRAPPC4 Gene

  • Trafficking Protein Particle Complex Subunit 4 2 3 4
  • Trafficking Protein Particle Complex 4 2 3 5
  • SBDN 2 3 4
  • Hematopoietic Stem/Progenitor Cell Protein 172 3 4
  • TRS23 Homolog 3 4
  • PTD009 2 3
  • TRS23 2 3
  • SYNBINDIN 3
  • Synbindin 4
  • CGI-104 3
  • HSPC172 3
  • NEDESBA 3
  • TRAPPC4 5

External Ids for TRAPPC4 Gene

Previous GeneCards Identifiers for TRAPPC4 Gene

  • GC11P118923
  • GC11P118426
  • GC11P118394
  • GC11P114828
  • GC11P118889

Summaries for TRAPPC4 Gene

GeneCards Summary for TRAPPC4 Gene

TRAPPC4 (Trafficking Protein Particle Complex Subunit 4) is a Protein Coding gene. Diseases associated with TRAPPC4 include Neurodevelopmental Disorder With Epilepsy, Spasticity, And Brain Atrophy and Neurodevelopmental Disorder With Progressive Microcephaly, Spasticity, And Brain Anomalies. Among its related pathways are MET promotes cell motility and Degradation of the extracellular matrix. Gene Ontology (GO) annotations related to this gene include Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is TRAPPC1.

UniProtKB/Swiss-Prot Summary for TRAPPC4 Gene

  • Core component of the TRAPP complexes which has a function of guanine nucleotide exchange factor activity for Rab1 GTPase (Probable). Plays a role in vesicular transport from endoplasmic reticulum to Golgi and autophagy (PubMed:31794024). May play a role in dendrite postsynaptic membrane trafficking (By similarity).

Gene Wiki entry for TRAPPC4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAPPC4 Gene

Genomics for TRAPPC4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRAPPC4 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
GH11J119015 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 348 +0.4 408 6.9 BCLAF1 SP1 ZNF207 MYC SIX5 ZNF580 ZNF592 POLR2A CEBPA ATF3 TRAPPC4 RPS25 ENSG00000283704 HSALNG0087601 lnc-RPS25-2 piR-31150 BCL9L HINFP CENATAC ENSG00000254909
GH11J119024 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 97.8 +9.4 9379 7.7 BCLAF1 SP1 ZNF654 IKZF1 MYC SSRP1 ZNF592 KLF9 CEBPA ZNF223 SLC37A4 TRAPPC4 VPS11 lnc-SLC37A4-1 piR-37181
GH11J118996 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 63.5 -20.7 -20705 3.2 MYC SSRP1 JUND ZNF592 KLF9 POLR2A ZBTB10 YY1 MXD4 CTCF CENATAC CENATAC-DT TRAPPC4 FOXR1 HSALNG0087578
GH11J119025 Enhancer 0.6 Ensembl ENCODE 100.9 +4.9 4858 0.8 FEZF1 ZNF513 GLIS1 OSR2 GATAD2B HIC1 piR-37181 TRAPPC4 RPS25 HSALNG0087601 SLC37A4 lnc-SLC37A4-1
GH11J119016 Enhancer 0.6 ENCODE 73.3 -3.3 -3297 0.2 POLR2A YY1 CTCF TEAD3 RAD21 THRAP3 ZBTB40 SUPT5H ZNF652 ZBTB33 TRAPPC4 MN309414 RPS25 lnc-RPS25-2 CENATAC
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRAPPC4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRAPPC4

Top Transcription factor binding sites by QIAGEN in the TRAPPC4 gene promoter:
  • AML1a
  • Gfi-1
  • HNF-4alpha1
  • Ik-2
  • ITF-2
  • NF-1
  • NF-1/L
  • Nkx6-1
  • Tal-1beta

Genomic Locations for TRAPPC4 Gene

Latest Assembly
chr11:119,018,763-119,025,454
(GRCh38/hg38)
Size:
6,692 bases
Orientation:
Plus strand

Previous Assembly
chr11:118,889,476-118,894,844
(GRCh37/hg19 by Entrez Gene)
Size:
5,369 bases
Orientation:
Plus strand

chr11:118,889,142-118,896,164
(GRCh37/hg19 by Ensembl)
Size:
7,023 bases
Orientation:
Plus strand

Alternative Locations (GRCh38/hg38)

  • chr11(PATCHES):40,366-45,734 (+)

Genomic View for TRAPPC4 Gene

Genes around TRAPPC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAPPC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAPPC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRAPPC4 Gene

Proteins for TRAPPC4 Gene

  • Protein details for TRAPPC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y296-TPPC4_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 4
    Protein Accession:
    Q9Y296
    Secondary Accessions:
    • A8K3A5
    • B4DME1

    Protein attributes for TRAPPC4 Gene

    Size:
    219 amino acids
    Molecular mass:
    24340 Da
    Quaternary structure:
    • Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12 (Probable). Interacts with SDC2 (By similarity).

    Three dimensional structures from OCA and Proteopedia for TRAPPC4 Gene

    Alternative splice isoforms for TRAPPC4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRAPPC4 Gene

Post-translational modifications for TRAPPC4 Gene

  • Ubiquitination at Lys41
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TRAPPC4 Gene

Domains & Families for TRAPPC4 Gene

Gene Families for TRAPPC4 Gene

Protein Domains for TRAPPC4 Gene

InterPro:
Blocks:
  • Sybindin-like protein

Suggested Antigen Peptide Sequences for TRAPPC4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55104, moderately similar to Trafficking protein particle complex subunit4 (B4DME1_HUMAN)
  • TRS23 homolog (TPPC4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y296

UniProtKB/Swiss-Prot:

TPPC4_HUMAN :
  • Belongs to the TRAPP small subunits family. TRAPPC4 subfamily.
Family:
  • Belongs to the TRAPP small subunits family. TRAPPC4 subfamily.
genes like me logo Genes that share domains with TRAPPC4: view

Function for TRAPPC4 Gene

Molecular function for TRAPPC4 Gene

UniProtKB/Swiss-Prot Function:
Core component of the TRAPP complexes which has a function of guanine nucleotide exchange factor activity for Rab1 GTPase (Probable). Plays a role in vesicular transport from endoplasmic reticulum to Golgi and autophagy (PubMed:31794024). May play a role in dendrite postsynaptic membrane trafficking (By similarity).

Phenotypes From GWAS Catalog for TRAPPC4 Gene

Gene Ontology (GO) - Molecular Function for TRAPPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17110339
genes like me logo Genes that share ontologies with TRAPPC4: view
genes like me logo Genes that share phenotypes with TRAPPC4: view

Human Phenotype Ontology for TRAPPC4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAPPC4

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TRAPPC4 Gene

Localization for TRAPPC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAPPC4 Gene

Cell junction, synapse, postsynaptic cell membrane. Golgi apparatus membrane. Endoplasmic reticulum. Vesicle. Note=Associated with postsynaptic membranes and in intracellular cisterns and vesicles (Golgi). {ECO:0000250 UniProtKB:Q9ES56}.

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 TRAPPC4 gene
Compartment Confidence
cytosol 5
plasma membrane 4
endoplasmic reticulum 4
golgi apparatus 4
mitochondrion 2
nucleus 2
endosome 2
extracellular 1
cytoskeleton 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TRAPPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005795 Golgi stack IEA,ISS 11018053
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with TRAPPC4: view

Pathways & Interactions for TRAPPC4 Gene

genes like me logo Genes that share pathways with TRAPPC4: view

Gene Ontology (GO) - Biological Process for TRAPPC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006888 ER to Golgi vesicle-mediated transport IEA,IMP 31794024
GO:0006914 autophagy IMP 31794024
GO:0016192 vesicle-mediated transport IEA --
GO:0016358 dendrite development IEA,ISS 11018053
GO:0048208 COPII vesicle coating TAS --
genes like me logo Genes that share ontologies with TRAPPC4: view

No data available for SIGNOR curated interactions for TRAPPC4 Gene

Drugs & Compounds for TRAPPC4 Gene

(1) Drugs for TRAPPC4 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-palmitoyl-L-cysteine Experimental Pharma Target 0
genes like me logo Genes that share compounds with TRAPPC4: view

Transcripts for TRAPPC4 Gene

mRNA/cDNA for TRAPPC4 Gene

7 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAPPC4

Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC4 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b · 7c
SP1: - - -
SP2: - - - -
SP3: - - - - -
SP4: - - - -
SP5: -
SP6:
SP7:

Relevant External Links for TRAPPC4 Gene

GeneLoc Exon Structure for
TRAPPC4

Expression for TRAPPC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAPPC4 Gene

Protein differential expression in normal tissues from HIPED for TRAPPC4 Gene

This gene is overexpressed in Bone (14.8) and Serum (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRAPPC4 Gene



Protein tissue co-expression partners for TRAPPC4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRAPPC4

SOURCE GeneReport for Unigene cluster for TRAPPC4 Gene:

Hs.132760

Evidence on tissue expression from TISSUES for TRAPPC4 Gene

  • Nervous system(4.8)
  • Lung(4.4)
  • Blood(4.3)
  • Kidney(2.3)
  • Skin(2.3)
  • Intestine(2)
genes like me logo Genes that share expression patterns with TRAPPC4: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRAPPC4 Gene

Orthologs for TRAPPC4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRAPPC4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TRAPPC4 29 30
  • 100 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TRAPPC4 30
  • 96 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TRAPPC4 30
  • 92 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Trappc4 29 16 30
  • 91.17 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Trappc4 29
  • 90.72 (n)
Dog
(Canis familiaris)
Mammalia TRAPPC4 29 30
  • 90.56 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TRAPPC4 29 30
  • 90.41 (n)
OneToOne
Chicken
(Gallus gallus)
Aves TRAPPC4 29 30
  • 78.54 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TRAPPC4 30
  • 88 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia trappc4 29
  • 76.56 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.11434 29
Zebrafish
(Danio rerio)
Actinopterygii trappc4 29 30
  • 75.95 (n)
OneToOne
zgc73260 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008106 29
  • 61.37 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Trs23 29 30
  • 61.03 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea F36D4.2 29
  • 53.24 (n)
trpp-4 30
  • 47 (a)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12144g 29
  • 50.15 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AFR459W 29
  • 45.57 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRS23 29 30 32
  • 43.55 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G02280 29
  • 58.81 (n)
Rice
(Oryza sativa)
Liliopsida Os07g0454700 29
  • 56.92 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU11085 29
  • 57.2 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trs23 29
  • 56.77 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.7090 29
Species where no ortholog for TRAPPC4 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TRAPPC4 Gene

ENSEMBL:
Gene Tree for TRAPPC4 (if available)
TreeFam:
Gene Tree for TRAPPC4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRAPPC4: view image
Alliance of Genome Resources:
Additional Orthologs for TRAPPC4

Paralogs for TRAPPC4 Gene

Paralogs for TRAPPC4 Gene

genes like me logo Genes that share paralogs with TRAPPC4: view

Variants for TRAPPC4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRAPPC4 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
916549 Likely Pathogenic: Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy 119,023,370(+) AAGGCTGGAACTTTTG
NM_016146.6(TRAPPC4):c.638_*4del (p.Gly213_Ter220delinsXaa)
STOP_LOST
996553 Uncertain Significance: Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy 119,019,158(+) T/C
NM_016146.6(TRAPPC4):c.191T>C (p.Leu64Pro)
MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON
rs375776811 Pathogenic: Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy; Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies; not provided 119,020,256(+) A/G
NM_016146.6(TRAPPC4):c.454+3A>G
INTRON
rs11640 -- p.Asp78Ala

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRAPPC4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TRAPPC4 Gene

Variant ID Type Subtype PubMed ID
nsv826101 CNV gain 20364138
nsv983067 CNV duplication 23825009

Variation tolerance for TRAPPC4 Gene

Residual Variation Intolerance Score: 25.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.37; 85.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAPPC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAPPC4
Leiden Open Variation Database (LOVD)
TRAPPC4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAPPC4 Gene

Disorders for TRAPPC4 Gene

MalaCards: The human disease database

(8) MalaCards diseases for TRAPPC4 Gene - From: OMI, CVR, ORP, COP, and GCD

UniProtKB/Swiss-Prot

TPPC4_HUMAN
  • Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy (NEDESBA) [MIM:618741]: An autosomal recessive disorder characterized by severely impaired global development apparent soon after birth, early-onset seizures, lack of psychomotor development, spastic quadriparesis, progressive cortical and cerebellar atrophy, and dysmorphic features, including microcephaly. Death in childhood may occur. {ECO:0000269 PubMed:31794024}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for TRAPPC4

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TRAPPC4: view

No data available for Genatlas for TRAPPC4 Gene

Publications for TRAPPC4 Gene

  1. Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability. (PMID: 31794024) Van Bergen NJ … Christodoulou J (Brain : a journal of neurology 2020) 3 4 72
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4
  3. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. (PMID: 21525244) Scrivens PJ … Sacher M (Molecular biology of the cell 2011) 3 4
  4. Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene. (PMID: 20035503) Elstner M … Turnbull DM (Annals of neurology 2009) 3 40
  5. Crystal structure of human synbindin reveals two conformations of longin domain. (PMID: 18466758) Fan S … Gong W (Biochemical and biophysical research communications 2009) 3 22

Products for TRAPPC4 Gene

  • Biorbyt antibodies for TRAPPC4

Sources for TRAPPC4 Gene