TRAPPC11 Gene (Protein Coding)

Trafficking Protein Particle Complex Subunit 11

GC04P183659
GIFtS:
36
The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2013] See more...

Aliases for TRAPPC11 Gene

Aliases for TRAPPC11 Gene

  • Trafficking Protein Particle Complex Subunit 11 2 3 4
  • Trafficking Protein Particle Complex 11 2 3 5
  • C4orf41 3 4
  • Chromosome 4 Open Reading Frame 41 2
  • Foie Gras Homolog (Zebrafish) 2
  • Gryzun Homolog (Drosophila) 2
  • Foie Gras Homolog 3
  • Gryzun Homolog 3
  • TRAPPC11 5
  • FLJ12716 2
  • LGMDR18 3
  • LGMD2S 3
  • FOIGR 3
  • Foigr 2
  • GRY 3
  • Gry 2

External Ids for TRAPPC11 Gene

Previous HGNC Symbols for TRAPPC11 Gene

  • C4orf41

Previous GeneCards Identifiers for TRAPPC11 Gene

  • GC04P184581

Summaries for TRAPPC11 Gene

Entrez Gene Summary for TRAPPC11 Gene

  • The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2013]

GeneCards Summary for TRAPPC11 Gene

TRAPPC11 (Trafficking Protein Particle Complex Subunit 11) is a Protein Coding gene. Diseases associated with TRAPPC11 include Muscular Dystrophy, Limb-Girdle, Autosomal Recessive 18 and Muscular Dystrophy, Limb-Girdle, Autosomal Recessive 1. Among its related pathways are Vesicle-mediated transport and RAB GEFs exchange GTP for GDP on RABs.

UniProtKB/Swiss-Prot Summary for TRAPPC11 Gene

  • Involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage.

Additional gene information for TRAPPC11 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAPPC11 Gene

Genomics for TRAPPC11 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TRAPPC11 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 TRAPPC11 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRAPPC11

Genomic Locations for TRAPPC11 Gene

Latest Assembly
chr4:183,659,267-183,713,594
(GRCh38/hg38)
Size:
54,328 bases
Orientation:
Plus strand

Previous Assembly
chr4:184,580,446-184,634,742
(GRCh37/hg19 by Entrez Gene)
Size:
54,297 bases
Orientation:
Plus strand

chr4:184,580,420-184,634,745
(GRCh37/hg19 by Ensembl)
Size:
54,326 bases
Orientation:
Plus strand

Genomic View for TRAPPC11 Gene

Genes around TRAPPC11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAPPC11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAPPC11 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TRAPPC11 Gene

Proteins for TRAPPC11 Gene

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  • Protein details for TRAPPC11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z392-TPC11_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 11
    Protein Accession:
    Q7Z392
    Secondary Accessions:
    • A4QPB8
    • B2RCD6
    • Q5U5I7
    • Q6FI73
    • Q86T25
    • Q9H0L1
    • Q9H5K9
    • Q9H8Q1
    • Q9H9I7

    Protein attributes for TRAPPC11 Gene

    Size:
    1133 amino acids
    Molecular mass:
    128881 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.
    SequenceCaution:
    • Sequence=BAB14240.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB14556.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB15617.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305}; Sequence=BAG37533.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAB66686.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAD91169.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=CAD97983.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for TRAPPC11 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRAPPC11 Gene

Protein Expression for TRAPPC11 Gene

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

Post-translational modifications for TRAPPC11 Gene

  • Ubiquitination at Lys898 and Lys1119
  • Modification sites at PhosphoSitePlus

Other Protein References for TRAPPC11 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TRAPPC11 Gene

Domains & Families for TRAPPC11 Gene

Gene Families for TRAPPC11 Gene

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

Protein Domains for TRAPPC11 Gene

InterPro:
Blocks:
  • Protein of unknown function DUF1683, C-terminal

Suggested Antigen Peptide Sequences for TRAPPC11 Gene

GenScript: Design optimal peptide antigens:
  • UPF0636 protein C4orf41 (CD041_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q7Z392

UniProtKB/Swiss-Prot:

TPC11_HUMAN :
  • Belongs to the TRAPPC11 family.
Family:
  • Belongs to the TRAPPC11 family.
genes like me logo Genes that share domains with TRAPPC11: view

Function for TRAPPC11 Gene

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Molecular function for TRAPPC11 Gene

UniProtKB/Swiss-Prot Function:
Involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage.

Phenotypes From GWAS Catalog for TRAPPC11 Gene

Gene Ontology (GO) - Molecular Function for TRAPPC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21525244
genes like me logo Genes that share ontologies with TRAPPC11: view

Phenotypes for TRAPPC11 Gene

MGI mutant phenotypes for TRAPPC11:
inferred from 1 alleles
GenomeRNAi human phenotypes for TRAPPC11:
genes like me logo Genes that share phenotypes with TRAPPC11: view

Human Phenotype Ontology for TRAPPC11 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for research

miRNA for TRAPPC11 Gene

miRTarBase miRNAs that target TRAPPC11

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAPPC11

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TRAPPC11 Gene

Localization for TRAPPC11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAPPC11 Gene

Golgi apparatus. Golgi apparatus, cis-Golgi network.

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 TRAPPC11 gene
Compartment Confidence
golgi apparatus 5
cytosol 4
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
peroxisome 0

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for TRAPPC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IEA,IDA 27862579
GO:0005829 cytosol TAS --
GO:0030008 TRAPP complex IMP 21525244
genes like me logo Genes that share ontologies with TRAPPC11: view

Pathways & Interactions for TRAPPC11 Gene

genes like me logo Genes that share pathways with TRAPPC11: view

Pathways by source for TRAPPC11 Gene

Gene Ontology (GO) - Biological Process for TRAPPC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006888 ER to Golgi vesicle-mediated transport IMP 21525244
GO:0007030 Golgi organization IMP 21525244
GO:0016192 vesicle-mediated transport IEA --
GO:0045054 constitutive secretory pathway IMP 19942856
GO:0061635 regulation of protein complex stability IMP 21525244
genes like me logo Genes that share ontologies with TRAPPC11: view

No data available for SIGNOR curated interactions for TRAPPC11 Gene

Drugs & Compounds for TRAPPC11 Gene

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No Compound Related Data Available

Transcripts for TRAPPC11 Gene

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mRNA/cDNA for TRAPPC11 Gene

2 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
10 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 TRAPPC11

Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC11 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: - - -
SP2:
SP3:
SP4:
SP5:
SP6:

ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32a · 32b · 32c
SP1: - - -
SP2: - - -
SP3: - -
SP4:
SP5:
SP6:

Relevant External Links for TRAPPC11 Gene

GeneLoc Exon Structure for
TRAPPC11

Expression for TRAPPC11 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAPPC11 Gene

mRNA expression in normal human tissues for TRAPPC11 Gene
mRNA expression by GTEx for TRAPPC11 GenemRNA expression by BioGPS for TRAPPC11 Gene

Protein differential expression in normal tissues from HIPED for TRAPPC11 Gene

This gene is overexpressed in Stomach (7.0) and Lymph node (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRAPPC11 Gene



Protein tissue co-expression partners for TRAPPC11 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRAPPC11

SOURCE GeneReport for Unigene cluster for TRAPPC11 Gene:

Hs.443240

Evidence on tissue expression from TISSUES for TRAPPC11 Gene

  • Intestine(4.2)
  • Nervous system(3.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TRAPPC11 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • mouth
  • skull
  • tongue
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
Limb:
  • arm
  • digit
  • femur
  • finger
  • foot
  • hand
  • hip
  • lower limb
  • thigh
  • toe
  • upper limb
General:
  • peripheral nervous system
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with TRAPPC11: 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 and mRNA Expression by UniProt/SwissProt for TRAPPC11 Gene

Orthologs for TRAPPC11 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRAPPC11 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TRAPPC11 29 30
  • 99.59 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TRAPPC11 29 30
  • 92.47 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 90 (a)
 OneToMany
-- 30
  • 85 (a)
 OneToMany
-- 30
  • 68 (a)
 OneToMany
Cow
(Bos Taurus)
 Mammalia TRAPPC11 29 30
  • 89.56 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TRAPPC11 30
  • 89 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Trappc11 29
  • 88.17 (n)
Mouse
(Mus musculus)
 Mammalia Trappc11 29 16 30
  • 87.2 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves C4H4ORF41 29 30
  • 79 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TRAPPC11 30
  • 88 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia trappc11 29
  • 76.29 (n)
Str.7134 29
African clawed frog
(Xenopus laevis)
 Amphibia Xl.16501 29
Zebrafish
(Danio rerio)
 Actinopterygii trappc11 29 30
  • 71 (n)
 OneToOne
wufb78g05 29
Fruit Fly
(Drosophila melanogaster)
 Insecta gry 29 30
  • 47.41 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006517 29
  • 44.55 (n)
Worm
(Caenorhabditis elegans)
 Secernentea B0412.3 29
  • 46.2 (n)
trpp-11 30
  • 26 (a)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT5G65950 29
  • 42.21 (n)
Rice
(Oryza sativa)
 Liliopsida Os02g0714500 29
  • 43.94 (n)
Species where no ortholog for TRAPPC11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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 TRAPPC11 Gene

ENSEMBL:
Gene Tree for TRAPPC11 (if available)
TreeFam:
Gene Tree for TRAPPC11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRAPPC11: view image
Alliance of Genome Resources:
Additional Orthologs for TRAPPC11

Paralogs for TRAPPC11 Gene

No data available for Paralogs for TRAPPC11 Gene

Variants for TRAPPC11 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRAPPC11 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
1002777 Uncertain Significance: Limb-girdle muscular dystrophy, type 2S 183,692,957(+) T/C
NM_021942.6(TRAPPC11):c.2050-3T>C 		INTRON
1002837 Uncertain Significance: Limb-girdle muscular dystrophy, type 2S 183,697,827(+) T/G
NM_021942.6(TRAPPC11):c.2843T>G (p.Val948Gly) 		MISSENSE
1004942 Uncertain Significance: Limb-girdle muscular dystrophy, type 2S 183,679,469(+) T/G
NM_021942.6(TRAPPC11):c.948T>G (p.Asp316Glu) 		MISSENSE
1006292 Uncertain Significance: Limb-girdle muscular dystrophy, type 2S 183,693,989(+) C/T
NM_021942.6(TRAPPC11):c.2459C>T (p.Pro820Leu) 		MISSENSE
1007772 Uncertain Significance: Limb-girdle muscular dystrophy, type 2S 183,697,833(+) A/G
NM_021942.6(TRAPPC11):c.2849A>G (p.Asn950Ser) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRAPPC11 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 TRAPPC11 Gene

Variant ID Type Subtype PubMed ID
dgv2964n106 CNV deletion 24896259
esv1002560 CNV deletion 20482838
esv1205233 CNV deletion 17803354
esv2659078 CNV deletion 23128226
esv2728876 CNV deletion 23290073
esv3063065 CNV deletion 24192839
esv3384 CNV loss 18987735
esv3397171 CNV insertion 20981092
esv3603444 CNV loss 21293372
esv3603445 CNV gain 21293372
esv3603446 CNV loss 21293372
nsv1025333 CNV gain 25217958
nsv1030766 CNV gain 25217958
nsv292013 CNV deletion 16902084
nsv508338 CNV deletion 20534489

Variation tolerance for TRAPPC11 Gene

Residual Variation Intolerance Score: 5.56% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.72; 86.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAPPC11 Gene

Human Gene Mutation Database (HGMD)
TRAPPC11
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAPPC11
Leiden Open Variation Database (LOVD)
TRAPPC11

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAPPC11 Gene

Disorders for TRAPPC11 Gene

MalaCards: The human disease database

(28) MalaCards diseases for TRAPPC11 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TPC11_HUMAN
  • Muscular dystrophy, limb-girdle, autosomal recessive 18 (LGMDR18) [MIM:615356]: A form of limb-girdle muscular dystrophy characterized by proximal muscle weakness with childhood onset, resulting in gait abnormalities and scapular winging. Serum creatine kinase is increased. A subset of patients may show a hyperkinetic movement disorder with chorea, ataxia, or dystonia and global developmental delay. {ECO:0000269 PubMed:23830518}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for TRAPPC11

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 TRAPPC11: view

No data available for Genatlas for TRAPPC11 Gene

Publications for TRAPPC11 Gene

  1. Recessive TRAPPC11 mutations cause a disease spectrum of limb girdle muscular dystrophy and myopathy with movement disorder and intellectual disability. (PMID: 23830518) Bögershausen N … Lamont RE (American journal of human genetics 2013) 3 4 72
  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. Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation. (PMID: 27862579) Matalonga L … Girós M (Human mutation 2017) 3 4
  4. A novel TRAPPC11 mutation in two Turkish families associated with cerebral atrophy, global retardation, scoliosis, achalasia and alacrima. (PMID: 27707803) Koehler K … Sacher M (Journal of medical genetics 2017) 3 72
  5. trappc11 is required for protein glycosylation in zebrafish and humans. (PMID: 26912795) DeRossi C … Sadler KC (Molecular biology of the cell 2016) 3 72

ExternalLinks

View latest publications for TRAPPC11 gene in Mastermind

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