TRAPPC6B is a component of TRAPP complexes, which are tethering complexes involved in vesicle transport (Kummel et al., 2005 [PubMed 16025134]).[supplied by OMIM, Mar 2008] See more...

Aliases for TRAPPC6B Gene

Aliases for TRAPPC6B Gene

  • Trafficking Protein Particle Complex Subunit 6B 2 3 4
  • Trafficking Protein Particle Complex 6B 2 3 5
  • TRAPP Complex Subunit 6B 3 4
  • TRAPPC6B 5
  • NEDMEBA 3
  • TPC6 3

External Ids for TRAPPC6B Gene

Previous GeneCards Identifiers for TRAPPC6B Gene

  • GC14M037607
  • GC14M038686
  • GC14M039617
  • GC14M019731

Summaries for TRAPPC6B Gene

Entrez Gene Summary for TRAPPC6B Gene

  • TRAPPC6B is a component of TRAPP complexes, which are tethering complexes involved in vesicle transport (Kummel et al., 2005 [PubMed 16025134]).[supplied by OMIM, Mar 2008]

GeneCards Summary for TRAPPC6B Gene

TRAPPC6B (Trafficking Protein Particle Complex Subunit 6B) is a Protein Coding gene. Diseases associated with TRAPPC6B include Neurodevelopmental Disorder With Microcephaly, Epilepsy, And Brain Atrophy and Epilepsy. Among its related pathways are Vesicle-mediated transport and RAB GEFs exchange GTP for GDP on RABs. An important paralog of this gene is TRAPPC6A.

UniProtKB/Swiss-Prot Summary for TRAPPC6B Gene

  • Component of a transport protein particle (TRAPP) complex that may function in specific stages of inter-organelle traffic (PubMed:16025134, PubMed:16828797). Specifically involved in the early development of neural circuitry, likely by controlling the frequency and amplitude of intracellular calcium transients implicated in the regulation of neuron differentiation and survival (Probable).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAPPC6B Gene

Genomics for TRAPPC6B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRAPPC6B 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 TRAPPC6B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRAPPC6B

Top Transcription factor binding sites by QIAGEN in the TRAPPC6B gene promoter:
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU2F2C

Genomic Locations for TRAPPC6B Gene

Latest Assembly
chr14:39,147,811-39,170,532
(GRCh38/hg38)
Size:
22,722 bases
Orientation:
Minus strand

Previous Assembly
chr14:39,617,018-39,639,537
(GRCh37/hg19 by Entrez Gene)
Size:
22,520 bases
Orientation:
Minus strand

chr14:39,617,015-39,639,736
(GRCh37/hg19 by Ensembl)
Size:
22,722 bases
Orientation:
Minus strand

Genomic View for TRAPPC6B Gene

Genes around TRAPPC6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAPPC6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAPPC6B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRAPPC6B Gene

Proteins for TRAPPC6B Gene

  • Protein details for TRAPPC6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86SZ2-TPC6B_HUMAN
    Recommended name:
    Trafficking protein particle complex subunit 6B
    Protein Accession:
    Q86SZ2
    Secondary Accessions:
    • B3KPS2
    • Q5JPD6
    • Q86U35
    • Q86X35

    Protein attributes for TRAPPC6B Gene

    Size:
    158 amino acids
    Molecular mass:
    17983 Da
    Quaternary structure:
    • Homodimer (PubMed:16025134, PubMed:16828797). Part of a TRAPP complex. Heterodimer with TRAPPC3 (PubMed:16025134, PubMed:16828797). The heterodimer TRAPPC6B-TRAPPC3 interacts with TRAPPC1 likely providing a core for TRAPP complex formation (PubMed:16828797).
    SequenceCaution:
    • Sequence=CAD62341.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TRAPPC6B Gene

    Alternative splice isoforms for TRAPPC6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRAPPC6B Gene

Post-translational modifications for TRAPPC6B Gene

  • Ubiquitination at Lys109
  • Modification sites at PhosphoSitePlus

Antibodies for research

  • Biorbyt antibodies for TRAPPC6B
  • Boster Bio Antibodies for TRAPPC6B

No data available for DME Specific Peptides for TRAPPC6B Gene

Domains & Families for TRAPPC6B Gene

Gene Families for TRAPPC6B Gene

Protein Domains for TRAPPC6B Gene

InterPro:
Blocks:
  • Transport protein particle (TRAPP) component, Bet3

Suggested Antigen Peptide Sequences for TRAPPC6B Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ79549, highly similar to Trafficking protein particle complex subunit6B (B0AZV9_HUMAN)
  • Trafficking protein particle complex subunit 6B (TPC6B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86SZ2

UniProtKB/Swiss-Prot:

TPC6B_HUMAN :
  • Belongs to the TRAPP small subunits family. BET3 subfamily.
Family:
  • Belongs to the TRAPP small subunits family. BET3 subfamily.
genes like me logo Genes that share domains with TRAPPC6B: view

Function for TRAPPC6B Gene

Molecular function for TRAPPC6B Gene

UniProtKB/Swiss-Prot Function:
Component of a transport protein particle (TRAPP) complex that may function in specific stages of inter-organelle traffic (PubMed:16025134, PubMed:16828797). Specifically involved in the early development of neural circuitry, likely by controlling the frequency and amplitude of intracellular calcium transients implicated in the regulation of neuron differentiation and survival (Probable).

Phenotypes From GWAS Catalog for TRAPPC6B Gene

Gene Ontology (GO) - Molecular Function for TRAPPC6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16908848
genes like me logo Genes that share ontologies with TRAPPC6B: view
genes like me logo Genes that share phenotypes with TRAPPC6B: view

Human Phenotype Ontology for TRAPPC6B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAPPC6B

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TRAPPC6B Gene

Localization for TRAPPC6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAPPC6B Gene

Golgi apparatus, cis-Golgi network. Endoplasmic reticulum.

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 TRAPPC6B gene
Compartment Confidence
cytosol 4
golgi apparatus 4
endoplasmic reticulum 3
plasma membrane 1
extracellular 1
mitochondrion 1
nucleus 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRAPPC6B 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:0005801 cis-Golgi network IBA 21873635
GO:0005802 trans-Golgi network IBA 21873635
genes like me logo Genes that share ontologies with TRAPPC6B: view

Pathways & Interactions for TRAPPC6B Gene

genes like me logo Genes that share pathways with TRAPPC6B: view

Gene Ontology (GO) - Biological Process for TRAPPC6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006888 ER to Golgi vesicle-mediated transport IBA 21873635
GO:0007399 nervous system development IEA --
GO:0043087 regulation of GTPase activity IEA --
GO:0048193 Golgi vesicle transport IEA --
GO:0048208 COPII vesicle coating TAS --
genes like me logo Genes that share ontologies with TRAPPC6B: view

No data available for SIGNOR curated interactions for TRAPPC6B Gene

Drugs & Compounds for TRAPPC6B Gene

(1) Drugs for TRAPPC6B 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 TRAPPC6B: view

Transcripts for TRAPPC6B Gene

mRNA/cDNA for TRAPPC6B Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
7 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 TRAPPC6B

Alternative Splicing Database (ASD) splice patterns (SP) for TRAPPC6B Gene

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

Relevant External Links for TRAPPC6B Gene

GeneLoc Exon Structure for
TRAPPC6B

Expression for TRAPPC6B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAPPC6B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRAPPC6B Gene

This gene is overexpressed in Cardia (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRAPPC6B Gene



Protein tissue co-expression partners for TRAPPC6B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRAPPC6B

SOURCE GeneReport for Unigene cluster for TRAPPC6B Gene:

Hs.13303

mRNA Expression by UniProt/SwissProt for TRAPPC6B Gene:

Q86SZ2-TPC6B_HUMAN
Tissue specificity: Both isoforms are expressed ubiquitously (at transcript level), isoform 1 being the most predominant (PubMed:28626029). Expressed in the fetal brain and different regions of the adult brain and spinal cord (PubMed:28626029).

Evidence on tissue expression from TISSUES for TRAPPC6B Gene

  • Lymph node(4.2)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with TRAPPC6B: 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 TRAPPC6B Gene

Orthologs for TRAPPC6B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRAPPC6B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TRAPPC6B 29 30
  • 99.37 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TRAPPC6B 30
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia TRAPPC6B 29 30
  • 97.26 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TRAPPC6B 29 30
  • 96.41 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Trappc6b 29
  • 94.09 (n)
Mouse
(Mus musculus)
Mammalia Trappc6b 29 16 30
  • 92.19 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 91 (a)
OneToMany
-- 30
  • 88 (a)
OneToMany
Chicken
(Gallus gallus)
Aves TRAPPC6B 29 30
  • 83.97 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TRAPPC6B 30
  • 94 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia trappc6b 29
  • 79.96 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC52668 29
Zebrafish
(Danio rerio)
Actinopterygii trappc6b 29 30
  • 72.61 (n)
OneToOne
zgc66304 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13840 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002385 29
  • 60.35 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG6196 29 30
  • 55.19 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea CELE_K08H10.9 29
  • 52.28 (n)
trpp-6 30
  • 39 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRS33 30 32
  • 20 (a)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G05000 29
  • 59.02 (n)
Rice
(Oryza sativa)
Liliopsida Os07g0291100 29
  • 57.92 (n)
Barley
(Hordeum vulgare)
Liliopsida Hv.2066 29
Wheat
(Triticum aestivum)
Liliopsida Ta.7375 29
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 74 (a)
OneToMany
Bread mold
(Neurospora crassa)
Ascomycetes NCU06212 29
  • 53.85 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trs33 29
  • 48.48 (n)
Species where no ortholog for TRAPPC6B 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)
  • 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)
  • 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)
  • 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)

Evolution for TRAPPC6B Gene

ENSEMBL:
Gene Tree for TRAPPC6B (if available)
TreeFam:
Gene Tree for TRAPPC6B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRAPPC6B: view image
Alliance of Genome Resources:
Additional Orthologs for TRAPPC6B

Paralogs for TRAPPC6B Gene

Paralogs for TRAPPC6B Gene

(1) SIMAP similar genes for TRAPPC6B Gene using alignment to 5 proteins:

  • TPC6B_HUMAN
  • B0AZV9_HUMAN
  • G3V2H7_HUMAN
  • G3V4C3_HUMAN
  • L8E9R9_HUMAN
genes like me logo Genes that share paralogs with TRAPPC6B: view

Variants for TRAPPC6B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRAPPC6B Gene

SNP ID Clinical significance and condition Chr 14 pos Variation AA Info Type
974890 Likely Pathogenic: Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy 39,159,481(-) A/T
NM_001079537.2(TRAPPC6B):c.149+2T>A
SPLICE_DONOR
989321 Likely Pathogenic: TRAPPC6B-related neurodevelopmental disorder 39,159,541(-) G/A
NM_001079537.2(TRAPPC6B):c.91C>T (p.Arg31Ter)
NONSENSE
rs1347223331 Pathogenic: Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy 39,158,404(-) T/C
NM_001079537.2(TRAPPC6B):c.150-2A>G
SPLICE_ACCEPTOR
rs144205574 Benign: not provided 39,151,847(-) G/GA
NM_001079537.2(TRAPPC6B):c.352-16dup
INTRON
rs377626365 Pathogenic: Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy 39,159,508(-) G/A
NM_001079537.2(TRAPPC6B):c.124C>T (p.Arg42Ter)
NONSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRAPPC6B 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 TRAPPC6B Gene

Variant ID Type Subtype PubMed ID
esv2670683 CNV deletion 23128226
esv27326 CNV loss 19812545
esv3634140 CNV loss 21293372
nsv1051247 CNV gain 25217958
nsv85488 CNV deletion 16902084
nsv977459 CNV duplication 23825009

Variation tolerance for TRAPPC6B Gene

Residual Variation Intolerance Score: 34% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.44; 9.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAPPC6B Gene

Human Gene Mutation Database (HGMD)
TRAPPC6B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAPPC6B
Leiden Open Variation Database (LOVD)
TRAPPC6B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAPPC6B Gene

Disorders for TRAPPC6B Gene

MalaCards: The human disease database

(4) MalaCards diseases for TRAPPC6B Gene - From: OMI, CVR, GTR, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TPC6B_HUMAN
  • Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy (NEDMEBA) [MIM:617862]: An autosomal recessive neurodevelopmental disorder characterized by microcephaly, global developmental delay, hypotonia, intellectual disability, autistic features such as poor social interaction, language impairment and repetitive automatism behaviors, and generalized tonic-clonic seizures. Brain imaging shows cortical atrophy, thin corpus callosum, and cerebellar and brainstem atrophy. {ECO:0000269 PubMed:28397838, ECO:0000269 PubMed:28626029}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for TRAPPC6B

genes like me logo Genes that share disorders with TRAPPC6B: view

No data available for Genatlas for TRAPPC6B Gene

Publications for TRAPPC6B Gene

  1. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features. (PMID: 28626029) Marin-Valencia I … Gleeson JG (Journal of medical genetics 2018) 3 4 72
  2. The structure of the TRAPP subunit TPC6 suggests a model for a TRAPP subcomplex. (PMID: 16025134) Kümmel D … Heinemann U (EMBO reports 2005) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Wnt regulation: exploring Axin-Disheveled interactions and defining mechanisms by which the SCF E3 ubiquitin ligase is recruited to the destruction complex. (PMID: 32129710) Schaefer KN … Peifer M (Molecular biology of the cell 2020) 3

Products for TRAPPC6B Gene

  • Biorbyt antibodies for TRAPPC6B

Sources for TRAPPC6B Gene