TRAPPC2L Gene (Protein Coding)

Trafficking Protein Particle Complex Subunit 2L

GC16P088856
GIFtS:
38
This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is ... See more...

Aliases for TRAPPC2L Gene

Aliases for TRAPPC2L Gene

  • Trafficking Protein Particle Complex Subunit 2L 2 3
  • Trafficking Protein Particle Complex 2 Like 2 3 5
  • Trafficking Protein Particle Complex Subunit 2-Like Protein 3 4
  • HSPC176 2 3
  • Trafficking Protein Particle Complex 2-Like 2
  • Hematopoietic Stem/Progenitor Cells 176 3
  • TRAPPC2L 5
  • PERRB 3

External Ids for TRAPPC2L Gene

Previous GeneCards Identifiers for TRAPPC2L Gene

  • GC16P087452
  • GC16P088923
  • GC16P074620

Summaries for TRAPPC2L Gene

Entrez Gene Summary for TRAPPC2L Gene

  • This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is located on the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

GeneCards Summary for TRAPPC2L Gene

TRAPPC2L (Trafficking Protein Particle Complex Subunit 2L) is a Protein Coding gene. Diseases associated with TRAPPC2L include Encephalopathy, Progressive, Early-Onset, With Episodic Rhabdomyolysis and Mucopolysaccharidosis, Type Iva. Among its related pathways are Vesicle-mediated transport and Metabolism of proteins. An important paralog of this gene is TRAPPC2B.

UniProtKB/Swiss-Prot Summary for TRAPPC2L Gene

  • Plays a role in vesicular transport from endoplasmic reticulum to Golgi.

Additional gene information for TRAPPC2L Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAPPC2L Gene

Genomics for TRAPPC2L Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TRAPPC2L Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRAPPC2L on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRAPPC2L

Top Transcription factor binding sites by QIAGEN in the TRAPPC2L gene promoter:
  • AML1a
  • GATA-1
  • HOXA5
  • IRF-2
  • Max1
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • Pax-4a
  • Pax-5

Genomic Locations for TRAPPC2L Gene

Latest Assembly
chr16:88,856,220-88,862,686
(GRCh38/hg38)
Size:
6,467 bases
Orientation:
Plus strand

Previous Assembly
chr16:88,922,628-88,929,086
(GRCh37/hg19 by Entrez Gene)
Size:
6,459 bases
Orientation:
Plus strand

chr16:88,922,628-88,929,094
(GRCh37/hg19 by Ensembl)
Size:
6,467 bases
Orientation:
Plus strand

Genomic View for TRAPPC2L Gene

Genes around TRAPPC2L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAPPC2L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAPPC2L Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TRAPPC2L Gene

Proteins for TRAPPC2L Gene

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  • Protein details for TRAPPC2L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UL33-TPC2L_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 2-like protein
    Protein Accession:
    Q9UL33
    Secondary Accessions:
    • B2R4M9
    • Q6ZTA7
    • Q9NZZ4

    Protein attributes for TRAPPC2L Gene

    Size:
    140 amino acids
    Molecular mass:
    16146 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. Interacts with the heterodimer TRAPPC3-TRAPPC6A. Interacts with TRAPPC6A.
    SequenceCaution:
    • Sequence=BAC86686.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

    Alternative splice isoforms for TRAPPC2L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRAPPC2L Gene

Protein Expression for TRAPPC2L Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TRAPPC2L Gene

  • Ubiquitination at Lys48
  • Modification sites at PhosphoSitePlus

Other Protein References for TRAPPC2L Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Boster Bio Antibodies for TRAPPC2L
  • Santa Cruz Biotechnology (SCBT) Antibodies for TRAPPC2L

No data available for DME Specific Peptides for TRAPPC2L Gene

Domains & Families for TRAPPC2L Gene

Gene Families for TRAPPC2L Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TRAPPC2L Gene

InterPro:
Blocks:
  • Sedlin, N-terminal conserved region
ProtoNet:

Suggested Antigen Peptide Sequences for TRAPPC2L Gene

GenScript: Design optimal peptide antigens:
  • Trafficking protein particle complex subunit 2-like protein (TPC2L_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UL33

UniProtKB/Swiss-Prot:

TPC2L_HUMAN :
  • Belongs to the TRAPP small subunits family. Sedlin subfamily.
Family:
  • Belongs to the TRAPP small subunits family. Sedlin subfamily.
genes like me logo Genes that share domains with TRAPPC2L: view

Function for TRAPPC2L Gene

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  6. Cell Lines for research

Molecular function for TRAPPC2L Gene

UniProtKB/Swiss-Prot Function:
Plays a role in vesicular transport from endoplasmic reticulum to Golgi.

Phenotypes From GWAS Catalog for TRAPPC2L Gene

Gene Ontology (GO) - Molecular Function for TRAPPC2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with TRAPPC2L: view
genes like me logo Genes that share phenotypes with TRAPPC2L: view

Human Phenotype Ontology for TRAPPC2L Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAPPC2L

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TRAPPC2L Gene

Localization for TRAPPC2L Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAPPC2L Gene

Cytoplasm, perinuclear region. Endoplasmic reticulum. Golgi apparatus.

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 TRAPPC2L gene
Compartment Confidence
cytosol 5
nucleus 3
endoplasmic reticulum 3
golgi apparatus 3
cytoskeleton 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRAPPC2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IBA 21873635
GO:0005783 endoplasmic reticulum IEA --
GO:0005794 Golgi apparatus IEA --
genes like me logo Genes that share ontologies with TRAPPC2L: view

Pathways & Interactions for TRAPPC2L Gene

genes like me logo Genes that share pathways with TRAPPC2L: view

Gene Ontology (GO) - Biological Process for TRAPPC2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006888 ER to Golgi vesicle-mediated transport IEA,IBA 21873635
GO:0016192 vesicle-mediated transport IEA --
GO:0048208 COPII vesicle coating TAS --
genes like me logo Genes that share ontologies with TRAPPC2L: view

No data available for SIGNOR curated interactions for TRAPPC2L Gene

Drugs & Compounds for TRAPPC2L Gene

Products:

  1. Drug products for research
No Compound Related Data Available

Transcripts for TRAPPC2L Gene

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mRNA/cDNA for TRAPPC2L Gene

9 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
15 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 TRAPPC2L

Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC2L Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g
SP1: - - - - - -
SP2: - - - - - -
SP3: - - - - - - -
SP4: - - - - - - -
SP5: - - - - -
SP6: - - -
SP7: - - - - - - - -
SP8: - -
SP9: - - - - -
SP10: -
SP11: -

Relevant External Links for TRAPPC2L Gene

GeneLoc Exon Structure for
TRAPPC2L

Expression for TRAPPC2L Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAPPC2L Gene

mRNA expression in normal human tissues for TRAPPC2L Gene
mRNA expression by GTEx for TRAPPC2L GenemRNA expression by BioGPS for TRAPPC2L Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRAPPC2L Gene

This gene is overexpressed in Peripheral blood mononuclear cells (32.0) and Placenta (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TRAPPC2L Gene



Protein tissue co-expression partners for TRAPPC2L Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRAPPC2L

SOURCE GeneReport for Unigene cluster for TRAPPC2L Gene:

Hs.461722

mRNA Expression by UniProt/SwissProt for TRAPPC2L Gene:

Q9UL33-TPC2L_HUMAN
Tissue specificity: Expressed in testis, liver, bladder, lung, spleen and brain, several cell lines and primary chondrocytes cell line.

Evidence on tissue expression from TISSUES for TRAPPC2L Gene

  • Nervous system(4.7)
  • Eye(4.2)
  • Blood(4.1)
  • Stomach(2.2)
genes like me logo Genes that share expression patterns with TRAPPC2L: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRAPPC2L Gene

Orthologs for TRAPPC2L Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRAPPC2L Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TRAPPC2L 30 31
  • 99.52 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TRAPPC2L 31
  • 94 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Trappc2l 30
  • 89.21 (n)
Cow
(Bos Taurus)
 Mammalia TRAPPC2L 30 31
  • 89.21 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Trappc2l 30 17 31
  • 88.97 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TRAPPC2L 30 31
  • 88.97 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia TRAPPC2L 31
  • 71 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves TRAPPC2L 30 31
  • 84.41 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TRAPPC2L 31
  • 78 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia trappc2l 30
  • 78.18 (n)
Zebrafish
(Danio rerio)
 Actinopterygii trappc2l 30
  • 78.1 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CG9067 30 31
  • 63.68 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP013488 30
  • 61.98 (n)
Worm
(Caenorhabditis elegans)
 Secernentea T10F2.5 31
  • 31 (a)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT2G20930 30
  • 55.39 (n)
Rice
(Oryza sativa)
 Liliopsida Os09g0541500 30
  • 54.39 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.6514 31
  • 59 (a)
 OneToOne
Species where no ortholog for TRAPPC2L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 TRAPPC2L Gene

ENSEMBL:
Gene Tree for TRAPPC2L (if available)
TreeFam:
Gene Tree for TRAPPC2L (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRAPPC2L: view image

Paralogs for TRAPPC2L Gene

Paralogs for TRAPPC2L Gene

Pseudogenes.org Pseudogenes for TRAPPC2L Gene

genes like me logo Genes that share paralogs with TRAPPC2L: view

Variants for TRAPPC2L Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRAPPC2L Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
837574 Uncertain Significance: Mucopolysaccharidosis, MPS-IV-A 88,856,754(+) T/C
NM_000512.5(GALNS):c.120+4A>G 		INTRON
843497 Uncertain Significance: Mucopolysaccharidosis, MPS-IV-A 88,856,812(+) C/A
NM_000512.5(GALNS):c.66G>T (p.Met22Ile) 		MISSENSE_VARIANT,FIVE_PRIME_UTR
847815 Pathogenic: Mucopolysaccharidosis, MPS-IV-A 88,856,760(+) C/G
NM_000512.5(GALNS):c.118G>C (p.Asp40His) 		MISSENSE_VARIANT,FIVE_PRIME_UTR
847816 Pathogenic: Mucopolysaccharidosis, MPS-IV-A 88,856,757(+) C/G
NM_000512.5(GALNS):c.120+1G>C 		SPLICE_DONOR
870481 Likely Pathogenic: Mucopolysaccharidosis, MPS-IV-A 88,856,762(+) T/C
NM_000512.5(GALNS):c.116A>G (p.Asp39Gly) 		MISSENSE_VARIANT,FIVE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRAPPC2L 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 TRAPPC2L Gene

Variant ID Type Subtype PubMed ID
dgv3065n100 CNV gain 25217958
dgv37n68 CNV loss 17160897
esv3639555 CNV gain 21293372
esv3639561 CNV gain 21293372
nsv1061256 CNV gain 25217958
nsv1063024 CNV gain 25217958
nsv1063441 CNV loss 25217958
nsv471115 CNV loss 18288195
nsv482951 CNV loss 15286789
nsv521217 CNV loss 19592680
nsv573674 CNV gain 21841781
nsv819907 CNV gain 19587683
nsv952071 CNV deletion 24416366

Variation tolerance for TRAPPC2L Gene

Residual Variation Intolerance Score: 59.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.19; 69.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAPPC2L Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAPPC2L

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAPPC2L Gene

Disorders for TRAPPC2L Gene

MalaCards: The human disease database

(5) MalaCards diseases for TRAPPC2L Gene - From: OMI, CVR, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TPC2L_HUMAN
  • Encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (PEERB) [MIM:618331]: An autosomal recessive disease characterized by progressive encephalopathy exacerbated by febrile illness and associated with severe neurodevelopmental delay, episodes of rhabdomyolysis, developmental regression, epilepsy and tetraplegia. {ECO:0000269 PubMed:30120216}. Note=The disease may be caused by variants affecting the gene represented in this entry.

Additional Disease Information for TRAPPC2L

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 TRAPPC2L: view

No data available for Genatlas for TRAPPC2L Gene

Publications for TRAPPC2L Gene

  1. Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts. (PMID: 30120216) Milev MP … van Hasselt PM (Journal of medical genetics 2018) 3 4 74
  2. 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) 2 3 4
  3. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PMID: 11042152) Zhang QH … Chen Z (Genome research 2000) 2 3 4
  4. TRAPPC2L is a novel, highly conserved TRAPP-interacting protein. (PMID: 19416478) Scrivens PJ … Sacher M (Traffic (Copenhagen, Denmark) 2009) 3 4
  5. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. (PMID: 32694731) Aregger M … Moffat J (Nature metabolism 2020) 3

ExternalLinks

View latest publications for TRAPPC2L gene in Mastermind

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