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    TRAPPC6B trafficking protein particle complex subunit 6B [ Homo sapiens (human) ]

    Gene ID: 122553, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TRAPPC6Bprovided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 6Bprovided by HGNC
    Primary source
    HGNC:HGNC:23066
    See related
    Ensembl:ENSG00000182400 MIM:610397; AllianceGenome:HGNC:23066
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TPC6; NEDMEBA
    Summary
    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]
    Expression
    Ubiquitous expression in brain (RPKM 16.1), thyroid (RPKM 9.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    14q21.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (39147814..39170333, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (33336495..33359014, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (39617018..39639537, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:39579989-39580506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8285 Neighboring gene peptidylprolyl isomerase A pseudogene 4 Neighboring gene gem nuclear organelle associated protein 2 Neighboring gene ribosomal protein L7a pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:39638995-39639584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:39640175-39640764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8287 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:39644148-39645347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:39646527-39647027 Neighboring gene PNN antisense RNA 1 Neighboring gene pinin, desmosome associated protein Neighboring gene transmembrane protein 92 pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:39672946-39674145

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A TRAPPC6B splicing variant associates to restless legs syndrome. Aridon P, et al. Parkinsonism Relat Disord, 2016 Oct. PMID 27569842
    2. The structure of the TRAPP subunit TPC6 suggests a model for a TRAPP subcomplex. Kümmel D, et al. EMBO Rep, 2005 Aug. PMID 16025134, Free PMC Article
    3. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features. Marin-Valencia I, et al. J Med Genet, 2018 Jan. PMID 28626029, Free PMC Article
    4. Unique self-palmitoylation activity of the transport protein particle component Bet3: a mechanism required for protein stability. Kümmel D, et al. Proc Natl Acad Sci U S A, 2006 Aug 22. PMID 16908848, Free PMC Article
    5. Distinct isocomplexes of the TRAPP trafficking factor coexist inside human cells. Kümmel D, et al. FEBS Lett, 2008 Nov 12. PMID 18930054

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRAPPC6B biallelic variants cause a neurodevelopmental disorder with TRAPP II and trafficking disruptions.
      Title: TRAPPC6B biallelic variants cause a neurodevelopmental disorder with TRAPP II and trafficking disruptions.
    2. This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function.
      Title: A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features.
    3. This study identified a TRAPPC6B gene mutation associated to the RLS locus on chromosome 14.
      Title: A TRAPPC6B splicing variant associates to restless legs syndrome.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy
    MedGen: C4693390 OMIM: 617862 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ17772, FLJ79549

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle coating NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vesicle tethering NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of TRAPP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of TRAPPII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in cis-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    trafficking protein particle complex subunit 6B
    Names
    TRAPP complex subunit 6B
    trafficking protein particle complex 6B

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001079537.2 → NP_001073005.1  trafficking protein particle complex subunit 6B isoform 1

      See identical proteins and their annotated locations for NP_001073005.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK025437, AL132639, BX161510
      Consensus CDS
      CCDS41947.1
      UniProtKB/Swiss-Prot
      B3KPS2, Q5JPD6, Q86SZ2, Q86U35, Q86X35
      Related
      ENSP00000330289.5, ENST00000330149.10
      Conserved Domains (1) summary
      cd14944
      Location:3 → 156
      TRAPPC6A_Trs33; Trs33 subunit of the TRAPP complex

    2. NM_177452.4 → NP_803235.1  trafficking protein particle complex subunit 6B isoform 2

      See identical proteins and their annotated locations for NP_803235.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the mid-coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AL132639, BC047328
      Consensus CDS
      CCDS9670.1
      UniProtKB/Swiss-Prot
      Q86SZ2
      Related
      ENSP00000335171.6, ENST00000347691.9
      Conserved Domains (1) summary
      cd14944
      Location:3 → 128
      TRAPPC6A_Trs33; Trs33 subunit of the TRAPP complex

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      39147814..39170333 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      33336495..33359014 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86SZ2.1 GenPept UniProtKB/Swiss-Prot:Q86SZ2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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