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    TRAPPC2 trafficking protein particle complex subunit 2 [ Homo sapiens (human) ]

    Gene ID: 6399, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TRAPPC2provided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:23068
    See related
    Ensembl:ENSG00000196459 MIM:300202; AllianceGenome:HGNC:23068
    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
    SEDL; SEDT; MIP2A; TRS20; ZNF547L; hYP38334; TRAPPC2P1
    Summary
    The protein encoded by this gene is thought to be part of a large multi-subunit complex involved in the targeting and fusion of endoplasmic reticulum-to-Golgi transport vesicles with their acceptor compartment. In addition, the encoded protein can bind c-myc promoter-binding protein 1 and block its transcriptional repression capability. Mutations in this gene are a cause of spondyloepiphyseal dysplasia tarda (SEDT). A processed pseudogene of this gene is located on chromosome 19, and other pseudogenes are found on chromosomes 8 and Y. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2010]
    Expression
    Ubiquitous expression in lymph node (RPKM 4.2), brain (RPKM 3.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRAPPC2 in Genome Data Viewer
    Location:
    Xp22.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (13712245..13734620, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (13293643..13316052, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (13730364..13752739, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985656 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:13687079-13688278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20668 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:13710181-13710377 Neighboring gene RAB9A, member RAS oncogene family Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:13752241-13753440 Neighboring gene OFD1 centriole and centriolar satellite protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:13778869-13779368 Neighboring gene NANOG hESC enhancer GRCh37_chrX:13820205-13820738 Neighboring gene glycoprotein M6B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:13845691-13846890 Neighboring gene gem nuclear organelle associated protein 8 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:14047600-14048100 and GRCh37_chrX:14048101-14048601

    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 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. Whole exome sequencing and functional studies identify an intronic mutation in TRAPPC2 that causes SEDT. Davis EE, et al. Clin Genet, 2014 Apr. PMID 23656395
    2. [Identification of a novel mutation of the SEDL gene in X-linked spondyloepiphyseal dysplasia tarda]. Lu JF, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2004 Aug. PMID 15300622
    3. Mutation of acceptor splice site of the SEDL gene in X-linked spondyloepiphyseal dysplasia tarda causes the activation of cryptic splice site. Ma HW, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2005 Jun. PMID 15952107
    4. The sedlin gene for spondyloepiphyseal dysplasia tarda escapes X-inactivation and contains a non-canonical splice site. Mumm S, et al. Gene, 2001 Aug 8. PMID 11595175
    5. [Identification of a missense mutation in SEDL gene from a Chinese family with X-linked spondyloepiphyseal dysplasia tarda]. Zhou WJ, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2008 Feb. PMID 18247296

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel loss-of-function variants of TRAPPC2 manifesting X-linked spondyloepiphyseal dysplasia tarda: report of two cases
      Title: Novel loss-of-function variants of TRAPPC2 manifesting X-linked spondyloepiphyseal dysplasia tarda: report of two cases.
    2. c.93+5G>A mutation in the TRAPPC2 gene is associated with X-linked spondyloepiphyseal dysplasia in a Chinese family.
      Title: [Mutation analysis of the TRAPPC2 gene in a Chinese family with X-linked spondyloepiphyseal dysplasia tarda].
    3. a novel hemizygous mutation, c.341-(11_9)delAAT, in an intron of TRAPPC caused spondyloepiphyseal dysplasia tarda
      Title: Whole exome sequencing and functional studies identify an intronic mutation in TRAPPC2 that causes SEDT.
    4. Data suggest that c.267_271delAAGAC frameshift mutation of the exon 5 of the spondyloepiphyseal dysplasia, late protein (SEDL) gene probably underlies the disease in the family.
      Title: [Analysis of SEDL gene mutation in a Chinese pedigree with X-linked spondyloepiphyseal dysplasia tarda].
    5. identification of the novel nonsense mutation (c.61G>T) in the SEDT family enables carrier detection, genetic counseling, and prenatal diagnosis.
      Title: A novel nonsense mutation in the sedlin gene (SEDL) causes severe spondyloepiphyseal dysplasia tarda in a five-generation Chinese pedigree.
    6. A novel splicing mutation in the SEDL gene causes spondyloepiphyseal dysplasia tarda in a large Chinese pedigree.
      Title: A novel splicing mutation in the SEDL gene causes spondyloepiphyseal dysplasia tarda in a large Chinese pedigree.
    7. Studies indicate that splice site mutation that leads to aberrant splicing often causes genetic skeletal system disease, like COL1A1, SEDL and LRP.
      Title: Aberrant and alternative splicing in skeletal system disease.
    8. Sedlin bound and promoted efficient cycling of Sar1, a guanosine triphosphatase that can constrict membranes, and thus allowed nascent carriers to grow and incorporate procollagen prefibrils.
      Title: Sedlin controls the ER export of procollagen by regulating the Sar1 cycle.
    9. Data show that a disease-causing mutation of TRAPPC2, D47Y, failed to interact with either TRAPPC9 or TRAPPC8, suggesting that aspartate 47 in TRAPPC2 is at or near the site of interaction with TRAPPC9 or TRAPPC8.
      Title: The adaptor function of TRAPPC2 in mammalian TRAPPs explains TRAPPC2-associated SEDT and TRAPPC9-associated congenital intellectual disability.
    10. Data indicate SPATA4 interacts with the C2 portion of the TRAPP complex.
      Title: A yeast two hybrid screen identifies SPATA4 as a TRAPP interactor.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2014-01-16)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2014-01-16)

    ClinGen Genome Curation PagePubMed

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transmembrane transporter 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 skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 TRAPP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of TRAPPII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of TRAPPIII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in cytoplasm 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 IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    trafficking protein particle complex subunit 2
    Names
    sedlin
    trafficking protein particle complex 2

    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.

    Genomic

    1. NG_011555.1 RefSeqGene

      Range
      5004..27379
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001011658.4 → NP_001011658.1  trafficking protein particle complex subunit 2 isoform 1

      See identical proteins and their annotated locations for NP_001011658.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the shorter isoform (1). Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AA770629, AC003037, AK313736, DA344866
      Consensus CDS
      CCDS48082.1
      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
      Related
      ENSP00000369953.1, ENST00000380579.6
      Conserved Domains (1) summary
      cd14825
      Location:4 → 138
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2

    2. NM_001128835.3 → NP_001122307.2  trafficking protein particle complex subunit 2 isoform 2

      See identical proteins and their annotated locations for NP_001122307.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate start codon and includes an alternate splice site in its 5' coding region, compared to variant 1. The encoded isoform (2) has a distinct and longer N-terminus, compared to isoform 1.
      Source sequence(s)
      AA770629, AC003037, DA344866, DA542477
      Consensus CDS
      CCDS48083.2
      UniProtKB/Swiss-Prot
      P0DI81
      Related
      ENSP00000507474.1, ENST00000683983.1
      Conserved Domains (1) summary
      cd14825
      Location:38 → 172
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2

    3. NM_014563.6 → NP_055378.1  trafficking protein particle complex subunit 2 isoform 1

      See identical proteins and their annotated locations for NP_055378.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AA770629, AC003037, BC052618, DA344866
      Consensus CDS
      CCDS48082.1
      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
      Related
      ENSP00000352708.5, ENST00000359680.9
      Conserved Domains (1) summary
      cd14825
      Location:4 → 138
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      13712245..13734620 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545566.3 → XP_011543868.1  trafficking protein particle complex subunit 2 isoform X1

      See identical proteins and their annotated locations for XP_011543868.1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
      Related
      ENSP00000392495.3, ENST00000458511.7
      Conserved Domains (1) summary
      cd14825
      Location:4 → 138
      TRAPPC2_sedlin; Trafficking protein particle complex subunit 2

    2. XM_047442351.1 → XP_047298307.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5

    3. XM_047442352.1 → XP_047298308.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      13293643..13316052 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327565.1 → XP_054183540.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5

    2. XM_054327564.1 → XP_054183539.1  trafficking protein particle complex subunit 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NEG0, O14582, P0DI81, P0DI82, Q9HD16
      UniProtKB/TrEMBL
      Q6IBE5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DI81.1 GenPept UniProtKB/Swiss-Prot:P0DI81

    Gene LinkOut

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

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