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    TRAPPC6A trafficking protein particle complex subunit 6A [ Homo sapiens (human) ]

    Gene ID: 79090, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TRAPPC6Aprovided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 6Aprovided by HGNC
    Primary source
    HGNC:HGNC:23069
    See related
    Ensembl:ENSG00000007255 MIM:610396; AllianceGenome:HGNC:23069
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TRS33
    Summary
    This gene encodes a component of the trafficking protein particle complex, which tethers transport vesicles to the cis-Golgi membrane. Loss of expression of the related gene in mouse affects coat and eye pigmentation, suggesting that the encoded protein may be involved in melanosome biogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2012]
    Expression
    Ubiquitous expression in kidney (RPKM 18.2), spleen (RPKM 12.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRAPPC6A in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45162933..45178237, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (47988066..48003370, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (45666191..45681495, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 37 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45632987-45633488 Neighboring gene Sharpr-MPRA regulatory region 10789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45638457-45639261 Neighboring gene MPRA-validated peak3514 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45641146-45641718 Neighboring gene eukaryotic translation initiation factor 5A pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45656063-45656688 Neighboring gene uncharacterized LOC105372420 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:45657908-45658134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45658871-45659588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45663890-45664522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14787 Neighboring gene NTPase KAP family P-loop domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45680873-45681816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14789 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:45682829-45683329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45683755-45684256 Neighboring gene Sharpr-MPRA regulatory region 2997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10758 Neighboring gene biogenesis of lysosomal organelles complex 1 subunit 3 Neighboring gene Sharpr-MPRA regulatory region 12921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45719170-45719704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45720327-45721022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:45721023-45721716 Neighboring gene exocyst complex component 3 like 2 Neighboring gene exocyst complex component 3 like 4 pseudogene

    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 missense mutation in TRAPPC6A leads to build-up of the protein, in patients with a neurodevelopmental syndrome and dysmorphic features. Mohamoud HS, et al. Sci Rep, 2018 Feb 1. PMID 29391579, Free PMC Article
    2. Alzheimer's disease genes are associated with measures of cognitive ageing in the lothian birth cohorts of 1921 and 1936. Hamilton G, et al. Int J Alzheimers Dis, 2011. PMID 21766012, Free PMC Article
    3. Host Cellular Protein TRAPPC6AΔ Interacts with Influenza A Virus M2 Protein and Regulates Viral Propagation by Modulating M2 Trafficking. Zhu P, et al. J Virol, 2017 Jan 1. PMID 27795429, Free PMC Article
    4. Entry and exit mechanisms at the cis-face of the Golgi complex. Lorente-Rodríguez A, et al. Cold Spring Harb Perspect Biol, 2011 Jul 1. PMID 21482742, Free PMC Article
    5. Structure of the Bet3-Tpc6B core of TRAPP: two Tpc6 paralogs form trimeric complexes with Bet3 and Mum2. Kümmel D, et al. J Mol Biol, 2006 Aug 4. PMID 16828797

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Missense mutation in TRAPPC6A identified in patients with a neurodevelopmental syndrome, affects stability of the TRAPP complex.
      Title: A missense mutation in TRAPPC6A leads to build-up of the protein, in patients with a neurodevelopmental syndrome and dysmorphic features.
    2. Host cellular protein TRAPPC6ADelta interacts with influenza A virus M2 protein and regulates viral propagation by modulating M2 trafficking.
      Title: Host Cellular Protein TRAPPC6AΔ Interacts with Influenza A Virus M2 Protein and Regulates Viral Propagation by Modulating M2 Trafficking.
    3. Mapping and characterization of mouse Trappc6a, along with a description of the human homolog.
      Title: A mouse TRAPP-related protein is involved in pigmentation.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • MGC2650

    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 COPII vesicle coating NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 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 TRAPPIII 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 6A
    Names
    TRAPP complex subunit 6A
    trafficking protein particle complex 6A

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_033044.1 RefSeqGene

      Range
      5007..20311
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001270891.2 → NP_001257820.1  trafficking protein particle complex subunit 6A isoform 2

      See identical proteins and their annotated locations for NP_001257820.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as TRAPPC6Adelta29-42) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AF161407, BC001907, CN256687
      Consensus CDS
      CCDS59397.1
      UniProtKB/Swiss-Prot
      K7ERB1, K7ERQ4, O75865, Q9BQ45, Q9P092
      UniProtKB/TrEMBL
      B7TZ90
      Related
      ENSP00000468612.1, ENST00000585934.1
      Conserved Domains (1) summary
      cd14944
      Location:3 → 157
      TRAPPC6A_Trs33; Trs33 subunit of the TRAPP complex

    2. NM_001270892.2 → NP_001257821.1  trafficking protein particle complex subunit 6A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC001907, CN256686, CN256687
      Consensus CDS
      CCDS59395.1
      UniProtKB/Swiss-Prot
      O75865
      Related
      ENSP00000468182.1, ENST00000592647.1

    3. NM_001270893.2 → NP_001257822.1  trafficking protein particle complex subunit 6A isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences in the coding region, one of which results in a frameshift, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC001907, BI462720
      Consensus CDS
      CCDS59396.1
      UniProtKB/Swiss-Prot
      O75865
      Related
      ENSP00000468363.1, ENST00000588062.5

    4. NM_024108.3 → NP_077013.1  trafficking protein particle complex subunit 6A isoform 1

      See identical proteins and their annotated locations for NP_077013.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC001907, CN256687
      Consensus CDS
      CCDS12655.1
      UniProtKB/Swiss-Prot
      O75865
      Related
      ENSP00000006275.3, ENST00000006275.8
      Conserved Domains (1) summary
      cd14944
      Location:3 → 171
      TRAPPC6A_Trs33; Trs33 subunit of the TRAPP complex

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      45162933..45178237 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439420.1 → XP_047295376.1  trafficking protein particle complex subunit 6A isoform X2

    2. XM_047439419.1 → XP_047295375.1  trafficking protein particle complex subunit 6A isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      47988066..48003370 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322116.1 → XP_054178091.1  trafficking protein particle complex subunit 6A isoform X2

    2. XM_054322115.1 → XP_054178090.1  trafficking protein particle complex subunit 6A isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75865.2 GenPept UniProtKB/Swiss-Prot:O75865

    Gene LinkOut

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

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