Aliases for TRAPPC12 Gene

Aliases for TRAPPC12 Gene

  • Trafficking Protein Particle Complex Subunit 12 2 3 4
  • Trafficking Protein Particle Complex 12 2 3 5
  • TTC-15 2 3 4
  • Trafficking Of Membranes And Mitosis 3 4
  • Tetratricopeptide Repeat Protein 15 3 4
  • Tetratricopeptide Repeat Domain 15 2 3
  • TPR Repeat Protein 15 3 4
  • CGI-87 2 3
  • TTC15 3 4
  • TRAPPC12 5
  • PEBAS 3
  • TRAMM 4

External Ids for TRAPPC12 Gene

Previous HGNC Symbols for TRAPPC12 Gene

  • TTC15

Summaries for TRAPPC12 Gene

GeneCards Summary for TRAPPC12 Gene

TRAPPC12 (Trafficking Protein Particle Complex Subunit 12) is a Protein Coding gene. Diseases associated with TRAPPC12 include Encephalopathy, Progressive, Early-Onset, With Brain Atrophy And Spasticity and Ceroid Lipofuscinosis, Neuronal, 8. Among its related pathways are Vesicle-mediated transport and RAB GEFs exchange GTP for GDP on RABs. Gene Ontology (GO) annotations related to this gene include structural molecule activity and endopeptidase activity.

UniProtKB/Swiss-Prot Summary for TRAPPC12 Gene

  • Component of the TRAPP complex, which is involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage (PubMed:21525244, PubMed:28777934). Also plays a role in chromosome congression, kinetochore assembly and stability and controls the recruitment of CENPE to the kinetochores (PubMed:25918224).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAPPC12 Gene

Genomics for TRAPPC12 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRAPPC12 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 TRAPPC12 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRAPPC12

Genomic Locations for TRAPPC12 Gene

Latest Assembly
chr2:3,379,245-3,485,094
(GRCh38/hg38)
Size:
105,850 bases
Orientation:
Plus strand

Previous Assembly
chr2:3,383,465-3,483,336
(GRCh37/hg19 by Entrez Gene)
Size:
99,872 bases
Orientation:
Plus strand

chr2:3,383,446-3,488,865
(GRCh37/hg19 by Ensembl)
Size:
105,420 bases
Orientation:
Plus strand

Alternative Locations (GRCh38/hg38)

  • chr2(ALT_REF_LOCI_1):9,876-89,035 (+)

Genomic View for TRAPPC12 Gene

Genes around TRAPPC12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAPPC12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAPPC12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRAPPC12 Gene

Proteins for TRAPPC12 Gene

  • Protein details for TRAPPC12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WVT3-TPC12_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 12
    Protein Accession:
    Q8WVT3
    Secondary Accessions:
    • B3KV01
    • D6W4Y2
    • Q8WVW1
    • Q9Y395

    Protein attributes for TRAPPC12 Gene

    Size:
    735 amino acids
    Molecular mass:
    79375 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 (PubMed:21525244). Interacts with CENPE (PubMed:25918224).
    SequenceCaution:
    • Sequence=AAD34082.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

neXtProt entry for TRAPPC12 Gene

Post-translational modifications for TRAPPC12 Gene

  • Phosphorylated as the cells enter mitosis but is dephosphorylated at or before the onset of anaphase. The phosphorylated form recruits CENPE to kinetochores more efficiently than the non-phosphorylated form.
  • Ubiquitination at Lys354, Lys364, Lys385, Lys510, and Lys601
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TRAPPC12 Gene

Domains & Families for TRAPPC12 Gene

Gene Families for TRAPPC12 Gene

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

Protein Domains for TRAPPC12 Gene

Suggested Antigen Peptide Sequences for TRAPPC12 Gene

GenScript: Design optimal peptide antigens:
  • Tetratricopeptide repeat protein 15 (TTC15_HUMAN)
genes like me logo Genes that share domains with TRAPPC12: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TRAPPC12 Gene

Function for TRAPPC12 Gene

Molecular function for TRAPPC12 Gene

UniProtKB/Swiss-Prot Function:
Component of the TRAPP complex, which is involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage (PubMed:21525244, PubMed:28777934). Also plays a role in chromosome congression, kinetochore assembly and stability and controls the recruitment of CENPE to the kinetochores (PubMed:25918224).

Phenotypes From GWAS Catalog for TRAPPC12 Gene

Gene Ontology (GO) - Molecular Function for TRAPPC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004175 endopeptidase activity IBA --
GO:0005515 protein binding IEA,IPI 21525244
genes like me logo Genes that share ontologies with TRAPPC12: view
genes like me logo Genes that share phenotypes with TRAPPC12: view

Human Phenotype Ontology for TRAPPC12 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for TRAPPC12 Gene

miRTarBase miRNAs that target TRAPPC12

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAPPC12

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TRAPPC12 Gene

Localization for TRAPPC12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAPPC12 Gene

Endoplasmic reticulum-Golgi intermediate compartment. Nucleus. Note=Mainly localizes to structures resembling the Golgi and a small amount is found in the nucleus. {ECO:0000269 PubMed:25918224}.

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 TRAPPC12 gene
Compartment Confidence
nucleus 5
cytosol 4
golgi apparatus 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRAPPC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000776 kinetochore IDA 25918224
GO:0005634 nucleus IEA,IDA 25918224
GO:0005654 nucleoplasm IDA --
GO:0005793 colocalizes_with endoplasmic reticulum-Golgi intermediate compartment IMP 21525244
GO:0005794 Golgi apparatus IDA --
genes like me logo Genes that share ontologies with TRAPPC12: view

Pathways & Interactions for TRAPPC12 Gene

genes like me logo Genes that share pathways with TRAPPC12: view

Pathways by source for TRAPPC12 Gene

Gene Ontology (GO) - Biological Process for TRAPPC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006888 ER to Golgi vesicle-mediated transport IMP 21525244
GO:0007030 Golgi organization IMP 21525244
GO:0016192 vesicle-mediated transport IEA --
GO:0051310 metaphase plate congression IMP 25918224
genes like me logo Genes that share ontologies with TRAPPC12: view

No data available for SIGNOR curated interactions for TRAPPC12 Gene

Drugs & Compounds for TRAPPC12 Gene

No Compound Related Data Available

Transcripts for TRAPPC12 Gene

mRNA/cDNA for TRAPPC12 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
23 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 TRAPPC12

Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC12 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d ^ 14 ^ 15 ^
SP1: - - - - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - - - - -
SP4: - - - -
SP5: - -
SP6: - -
SP7: - - - - - -
SP8:
SP9: -
SP10: - - - - -
SP11:
SP12: -

ExUns: 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20
SP1: - -
SP2: - -
SP3: - - -
SP4: - -
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10:
SP11:
SP12:

Relevant External Links for TRAPPC12 Gene

GeneLoc Exon Structure for
TRAPPC12

Expression for TRAPPC12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAPPC12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRAPPC12 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (10.7), Liver (9.1), and Lymph node (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRAPPC12 Gene



Protein tissue co-expression partners for TRAPPC12 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRAPPC12

SOURCE GeneReport for Unigene cluster for TRAPPC12 Gene:

Hs.252713

Evidence on tissue expression from TISSUES for TRAPPC12 Gene

  • Lung(4.3)
  • Muscle(4.3)
  • Liver(4.2)
  • Nervous system(3.6)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with TRAPPC12: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRAPPC12 Gene

Orthologs for TRAPPC12 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRAPPC12 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TTC15 29 30
  • 99.14 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TRAPPC12 30
  • 85 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia TTC15 29 30
  • 78.54 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TRAPPC12 29 30
  • 78.37 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Trappc12 29
  • 77.88 (n)
Mouse
(Mus musculus)
Mammalia Trappc12 29 16 30
  • 76.64 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TRAPPC12 30
  • 69 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TRAPPC12 29 30
  • 69.65 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TRAPPC12 30
  • 64 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia trappc12 29
  • 67 (n)
Str.4089 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.25574 29
Zebrafish
(Danio rerio)
Actinopterygii trappc12 29 30
  • 64.27 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG11396 29 30
  • 50.13 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011533 29
  • 24.04 (n)
Worm
(Caenorhabditis elegans)
Secernentea trpp-12 30
  • 25 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT4G39820 29
  • 46.03 (n)
Rice
(Oryza sativa)
Liliopsida Os02g0550400 29
  • 46.01 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.736 30
  • 42 (a)
OneToMany
-- 30
  • 21 (a)
OneToMany
Species where no ortholog for TRAPPC12 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 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 TRAPPC12 Gene

ENSEMBL:
Gene Tree for TRAPPC12 (if available)
TreeFam:
Gene Tree for TRAPPC12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRAPPC12: view image
Alliance of Genome Resources:
Additional Orthologs for TRAPPC12

Paralogs for TRAPPC12 Gene

(2) SIMAP similar genes for TRAPPC12 Gene using alignment to 10 proteins:

  • TPC12_HUMAN
  • F8WCB4_HUMAN
  • H0Y550_HUMAN
  • H7C0K3_HUMAN
  • H7C0T3_HUMAN
  • H7C185_HUMAN
  • H7C1E5_HUMAN
  • H7C1M4_HUMAN
  • H7C2F7_HUMAN
  • H7C373_HUMAN

Pseudogenes.org Pseudogenes for TRAPPC12 Gene

genes like me logo Genes that share paralogs with TRAPPC12: view

No data available for Paralogs for TRAPPC12 Gene

Variants for TRAPPC12 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRAPPC12 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
1027666 Likely Pathogenic: Severe hydrocephalus 3,387,984(+) G/T
NM_016030.6(TRAPPC12):c.361G>T (p.Glu121Ter)
NONSENSE
1029567 Uncertain Significance: Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome 3,424,640(+) C/T
NM_016030.6(TRAPPC12):c.1394C>T (p.Pro465Leu)
MISSENSE
1029568 Uncertain Significance: Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome 3,457,687(+) A/G
NM_016030.6(TRAPPC12):c.1597A>G (p.Arg533Gly)
MISSENSE
1029569 Likely Pathogenic: Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome 3,460,262(+) G/T
NM_016030.6(TRAPPC12):c.1604-1G>T
SPLICE_ACCEPTOR
1029570 Uncertain Significance: Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome 3,388,119(+) C/A
NM_016030.6(TRAPPC12):c.496C>A (p.Arg166Ser)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRAPPC12 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 TRAPPC12 Gene

Variant ID Type Subtype PubMed ID
dgv1848n106 CNV deletion 24896259
dgv3702n100 CNV gain 25217958
dgv6655n54 CNV gain 21841781
dgv6656n54 CNV gain+loss 21841781
dgv6657n54 CNV gain+loss 21841781
dgv6658n54 CNV gain 21841781
dgv6659n54 CNV gain 21841781
dgv6660n54 CNV gain+loss 21841781
dgv6661n54 CNV loss 21841781
dgv6662n54 CNV loss 21841781
esv1396860 CNV deletion 17803354
esv2392388 CNV deletion 18987734
esv25165 CNV gain+loss 19812545
esv2656713 CNV deletion 23128226
esv2660858 CNV deletion 23128226
esv2719515 CNV deletion 23290073
esv3589655 CNV gain 21293372
esv3589656 CNV loss 21293372
esv997718 CNV insertion 20482838
nsv1003355 CNV gain 25217958
nsv1006526 CNV loss 25217958
nsv1011656 CNV gain 25217958
nsv1071566 CNV deletion 25765185
nsv1118847 CNV deletion 24896259
nsv1149598 CNV insertion 26484159
nsv214768 CNV insertion 16902084
nsv2584 CNV insertion 18451855
nsv520390 CNV gain 19592680
nsv580773 CNV loss 21841781
nsv580774 CNV gain 21841781
nsv580776 CNV loss 21841781
nsv580796 CNV loss 21841781
nsv580802 CNV loss 21841781
nsv580803 CNV loss 21841781
nsv580807 CNV loss 21841781
nsv580810 CNV loss 21841781
nsv580817 CNV loss 21841781
nsv580818 CNV loss 21841781
nsv580819 CNV loss 21841781
nsv580820 CNV loss 21841781
nsv580821 CNV loss 21841781
nsv821316 CNV deletion 20802225
nsv953388 CNV deletion 24416366

Variation tolerance for TRAPPC12 Gene

Residual Variation Intolerance Score: 10.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.56; 97.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAPPC12 Gene

Human Gene Mutation Database (HGMD)
TRAPPC12
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAPPC12
Leiden Open Variation Database (LOVD)
TRAPPC12

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAPPC12 Gene

Disorders for TRAPPC12 Gene

MalaCards: The human disease database

(6) MalaCards diseases for TRAPPC12 Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

UniProtKB/Swiss-Prot

TPC12_HUMAN
  • Encephalopathy, progressive, early-onset, with brain atrophy and spasticity (PEBAS) [MIM:617669]: An autosomal recessive, progressive encephalopathy characterized by central nervous system atrophy and dysfunction, spasticity, microcephaly, global developmental delay, and hearing loss. {ECO:0000269 PubMed:28777934}. Note=The disease is caused by variants affecting the gene represented in this entry. Cells display a fragmented Golgi apparatus (PubMed:28777934). {ECO:0000269 PubMed:28777934}.

Additional Disease Information for TRAPPC12

genes like me logo Genes that share disorders with TRAPPC12: view

No data available for Genatlas for TRAPPC12 Gene

Publications for TRAPPC12 Gene

  1. Mutations in TRAPPC12 Manifest in Progressive Childhood Encephalopathy and Golgi Dysfunction. (PMID: 28777934) Milev MP … Edvardson S (American journal of human genetics 2017) 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. 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
  4. TRAMM/TrappC12 plays a role in chromosome congression, kinetochore stability, and CENP-E recruitment. (PMID: 25918224) Milev MP … Sacher M (The Journal of cell biology 2015) 3 4
  5. Network organization of the human autophagy system. (PMID: 20562859) Behrends C … Harper JW (Nature 2010) 2 3

Products for TRAPPC12 Gene

Sources for TRAPPC12 Gene