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    TRAPPC11 trafficking protein particle complex subunit 11 [ Homo sapiens (human) ]

    Gene ID: 60684, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TRAPPC11provided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 11provided by HGNC
    Primary source
    HGNC:HGNC:25751
    See related
    Ensembl:ENSG00000168538 MIM:614138; AllianceGenome:HGNC:25751
    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
    GRY; FOIGR; LGMD2S; C4orf41; LGMDR18
    Summary
    The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2013]
    Expression
    Ubiquitous expression in adrenal (RPKM 9.6), thyroid (RPKM 9.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRAPPC11 in Genome Data Viewer
    Location:
    4q35.1
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (183659293..183713589)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (187002489..187056786)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (184580446..184634742)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22185 Neighboring gene RWD domain containing 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:184579545-184580333 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:184580334-184581121 Neighboring gene RNA, U6 small nuclear 479, pseudogene Neighboring gene RNA, U6 small nuclear 335, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:184614366-184615565 Neighboring gene RNA, U6 small nuclear 1053, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15833 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:184644336-184645097 Neighboring gene uncharacterized LOC105377581 Neighboring gene uncharacterized LOC124900824

    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. Expanding the phenotypic spectrum of TRAPPC11-related muscular dystrophy: 25 Roma individuals carrying a founder variant. Justel M, et al. J Med Genet, 2023 Oct. PMID 37197784, Free PMC Article
    2. TRAPPC11 functions in autophagy by recruiting ATG2B-WIPI4/WDR45 to preautophagosomal membranes. Stanga D, et al. Traffic, 2019 May. PMID 30843302
    3. Large TRAPPC11 gene deletions as a cause of muscular dystrophy and their estimated genesis. Kopčilová J, et al. J Med Genet, 2024 Aug 29. PMID 38955476
    4. A novel TRAPPC11 mutation in two Turkish families associated with cerebral atrophy, global retardation, scoliosis, achalasia and alacrima. Koehler K, et al. J Med Genet, 2017 Mar. PMID 27707803
    5. Recessive TRAPPC11 mutations cause a disease spectrum of limb girdle muscular dystrophy and myopathy with movement disorder and intellectual disability. Bögershausen N, et al. Am J Hum Genet, 2013 Jul 11. PMID 23830518, Free PMC Article

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Large TRAPPC11 gene deletions as a cause of muscular dystrophy and their estimated genesis.
      Title: Large TRAPPC11 gene deletions as a cause of muscular dystrophy and their estimated genesis.
    2. Expanding the phenotypic spectrum of TRAPPC11-related muscular dystrophy: 25 Roma individuals carrying a founder variant.
      Title: Expanding the phenotypic spectrum of TRAPPC11-related muscular dystrophy: 25 Roma individuals carrying a founder variant.
    3. TRAPPC11 recruits ATG2B-WIPI4/WDR45 to preautophagosomal membranes. Fibroblasts from a patient with TRAPPC11 mutations failed to recruit ATG2B-WIPI4.
      Title: TRAPPC11 functions in autophagy by recruiting ATG2B-WIPI4/WDR45 to preautophagosomal membranes.
    4. Recessive mutations in TRAPPC11 and GOSR2 are associated with congenital muscular dystrophy and hypoglycosylation of alpha-dystroglycan.
      Title: TRAPPC11 and GOSR2 mutations associate with hypoglycosylation of α-dystroglycan and muscular dystrophy.
    5. The identified novel TRAPPC11 mutation represents an expansion of the myopathy phenotype described before and is characterised particularly by achalasia, alacrima, neurological and muscular phenotypes.
      Title: A novel TRAPPC11 mutation in two Turkish families associated with cerebral atrophy, global retardation, scoliosis, achalasia and alacrima.
    6. TRAPPC11 role in protein glycosylation and lipid-linked oligosaccharides biosynthesis
      Title: trappc11 is required for protein glycosylation in zebrafish and humans.
    7. Homozygous mutations in the membrane trafficking component TRAPPC11 causes a form of autosomal-recessive, slowly progressive limb girdle muscular dystrophy with childhood onset and high serum creatine kinase.
      Title: Recessive TRAPPC11 mutations cause a disease spectrum of limb girdle muscular dystrophy and myopathy with movement disorder and intellectual disability.
    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
    Autosomal recessive limb-girdle muscular dystrophy type R18
    MedGen: C4517996 OMIM: 615356 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

    • FLJ12716

    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 Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in constitutive secretory pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of protein complex stability IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle tethering NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of TRAPP complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of TRAPPIII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    trafficking protein particle complex subunit 11
    Names
    foie gras homolog
    gryzun homolog
    trafficking protein particle complex 11

    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_033102.1 RefSeqGene

      Range
      5027..59323
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_021942.6 → NP_068761.4  trafficking protein particle complex subunit 11 isoform a

      See identical proteins and their annotated locations for NP_068761.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AI034264, BX647127, BX648499
      Consensus CDS
      CCDS34112.1
      UniProtKB/Swiss-Prot
      A4QPB8, B2RCD6, Q5U5I7, Q6FI73, Q7Z392, Q86T25, Q9H0L1, Q9H5K9, Q9H8Q1, Q9H9I7
      UniProtKB/TrEMBL
      B3KU05
      Related
      ENSP00000335371.6, ENST00000334690.11
      Conserved Domains (2) summary
      pfam12742
      Location:1036 → 1095
      Gryzun-like; Gryzun, putative Golgi trafficking
      pfam11817
      Location:263 → 522
      Foie-gras_1; Foie gras liver health family 1

    2. NM_199053.3 → NP_951008.1  trafficking protein particle complex subunit 11 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains alternate exon structure in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      BC051724, BX648499
      Consensus CDS
      CCDS47166.1
      UniProtKB/TrEMBL
      B3KU05
      Related
      ENSP00000349738.4, ENST00000357207.8
      Conserved Domains (2) summary
      pfam11817
      Location:263 → 522
      Foie-gras_1; Foie gras liver health family 1
      pfam12742
      Location:1036 → 1066
      Gryzun-like; Gryzun, putative Golgi trafficking

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      183659293..183713589
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024454180.2 → XP_024309948.1  trafficking protein particle complex subunit 11 isoform X1

      UniProtKB/Swiss-Prot
      A4QPB8, B2RCD6, Q5U5I7, Q6FI73, Q7Z392, Q86T25, Q9H0L1, Q9H5K9, Q9H8Q1, Q9H9I7
      UniProtKB/TrEMBL
      B3KU05
      Conserved Domains (2) summary
      pfam12742
      Location:1036 → 1095
      Gryzun-like; Gryzun, putative Golgi trafficking
      pfam11817
      Location:263 → 522
      Foie-gras_1; Foie gras liver health family 1

    2. XM_047416069.1 → XP_047272025.1  trafficking protein particle complex subunit 11 isoform X2

    3. XM_024454179.2 → XP_024309947.1  trafficking protein particle complex subunit 11 isoform X1

      UniProtKB/Swiss-Prot
      A4QPB8, B2RCD6, Q5U5I7, Q6FI73, Q7Z392, Q86T25, Q9H0L1, Q9H5K9, Q9H8Q1, Q9H9I7
      UniProtKB/TrEMBL
      B3KU05
      Conserved Domains (2) summary
      pfam12742
      Location:1036 → 1095
      Gryzun-like; Gryzun, putative Golgi trafficking
      pfam11817
      Location:263 → 522
      Foie-gras_1; Foie gras liver health family 1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      187002489..187056786
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350702.1 → XP_054206677.1  trafficking protein particle complex subunit 11 isoform X1

      UniProtKB/Swiss-Prot
      A4QPB8, B2RCD6, Q5U5I7, Q6FI73, Q7Z392, Q86T25, Q9H0L1, Q9H5K9, Q9H8Q1, Q9H9I7

    2. XM_054350703.1 → XP_054206678.1  trafficking protein particle complex subunit 11 isoform X2

    3. XM_054350701.1 → XP_054206676.1  trafficking protein particle complex subunit 11 isoform X1

      UniProtKB/Swiss-Prot
      A4QPB8, B2RCD6, Q5U5I7, Q6FI73, Q7Z392, Q86T25, Q9H0L1, Q9H5K9, Q9H8Q1, Q9H9I7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z392.2 GenPept UniProtKB/Swiss-Prot:Q7Z392

    Gene LinkOut

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

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