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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
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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

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