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    COG2 component of oligomeric golgi complex 2 [ Homo sapiens (human) ]

    Gene ID: 22796, updated on 28-Oct-2024

    Summary

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    Official Symbol
    COG2provided by HGNC
    Official Full Name
    component of oligomeric golgi complex 2provided by HGNC
    Primary source
    HGNC:HGNC:6546
    See related
    Ensembl:ENSG00000135775 MIM:606974; AllianceGenome:HGNC:6546
    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
    LDLC; CDG2Q
    Summary
    This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi complex. The encoded protein specifically interacts with the USO1 vesicle docking protein and may be necessary for normal Golgi ribbon formation and trafficking of Golgi enzymes. Mutations of this gene are associated with abnormal glycosylation within the Golgi apparatus. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2009]
    Expression
    Ubiquitous expression in adrenal (RPKM 11.3), colon (RPKM 11.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COG2 in Genome Data Viewer
    Location:
    1q42.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (230642481..230693982)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (230022982..230074527)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (230778227..230829728)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S24 pseudogene 4 Neighboring gene uncharacterized LOC124904545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1942 Neighboring gene uncharacterized LOC107985358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230844373-230845194 Neighboring gene Sharpr-MPRA regulatory region 2465 Neighboring gene angiotensinogen Neighboring gene VISTA enhancer hs2133 Neighboring gene calpain 9 Neighboring gene uncharacterized LOC107985359 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:230914014-230914159 Neighboring gene NANOG hESC enhancer GRCh37_chr1:230919761-230920350

    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. Mutations in COG2 encoding a subunit of the conserved oligomeric golgi complex cause a congenital disorder of glycosylation. Kodera H, et al. Clin Genet, 2015 May. PMID 24784932
    2. LDLC encodes a brefeldin A-sensitive, peripheral Golgi protein required for normal Golgi function. Podos SD, et al. J Cell Biol, 1994 Nov. PMID 7962052, Free PMC Article
    3. Retrograde transport on the COG railway. Ungar D, et al. Trends Cell Biol, 2006 Feb. PMID 16406524
    4. The interaction of two tethering factors, p115 and COG complex, is required for Golgi integrity. Sohda M, et al. Traffic, 2007 Mar. PMID 17274799
    5. Identification of novel genes from stomach cancer cell lines by differential display. Salesiotis AN, et al. Cancer Lett, 1995 May 4. PMID 7750094

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our data strongly suggest that these compound heterozygous mutations in COG2 are causative of CDG.
      Title: Mutations in COG2 encoding a subunit of the conserved oligomeric golgi complex cause a congenital disorder of glycosylation.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3.
    3. The interaction between p115 and Cog2 was found to be essential for Golgi ribbon reformation after the disruption of the ribbon by p115 KD or brefeldin A treatment and recovery by re-expression of p115 or drug wash out, respectively.
      Title: The interaction of two tethering factors, p115 and COG complex, is required for Golgi integrity.
    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
    Congenital disorder of glycosylation, type IIq
    MedGen: C4479353 OMIM: 617395 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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of component of oligomeric golgi complex 2 (COG2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    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 protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intra-Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intra-Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde transport, vesicle recycling within Golgi IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in Golgi stack IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Golgi transport complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Golgi transport complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Golgi transport complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of Golgi transport complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    conserved oligomeric Golgi complex subunit 2
    Names
    COG complex subunit 2
    brefeldin A-sensitive, peripheral Golgi protein
    conserved oligomeric Golgi complex protein 2
    low density lipoprotein receptor defect C complementing
    low density lipoprotein receptor defect C-complementing protein

    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_001145036.2 → NP_001138508.1  conserved oligomeric Golgi complex subunit 2 isoform 2

      See identical proteins and their annotated locations for NP_001138508.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region compared to variant 1. This results in a shorter isoform (2) compared to isoform 1.
      Source sequence(s)
      AL158214, BC051906, DB449302, DC349417
      Consensus CDS
      CCDS44329.1
      UniProtKB/TrEMBL
      B7Z2Y2
      Related
      ENSP00000355628.3, ENST00000366668.7
      Conserved Domains (2) summary
      pfam06148
      Location:15 → 147
      COG2; COG (conserved oligomeric Golgi) complex component, COG2
      pfam12022
      Location:573 → 698
      DUF3510; Domain of unknown function (DUF3510)

    2. NM_007357.3 → NP_031383.1  conserved oligomeric Golgi complex subunit 2 isoform 1

      See identical proteins and their annotated locations for NP_031383.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK312678, AL158214, BC051906, DB449302, DC349417
      Consensus CDS
      CCDS1584.1
      UniProtKB/Swiss-Prot
      Q14746, Q86U99
      UniProtKB/TrEMBL
      B1ALW7, B7Z2Y2
      Related
      ENSP00000355629.4, ENST00000366669.9
      Conserved Domains (2) summary
      pfam06148
      Location:15 → 147
      COG2; COG (conserved oligomeric Golgi) complex component, COG2
      pfam12022
      Location:574 → 699
      DUF3510; Domain of unknown function (DUF3510)

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      230642481..230693982
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449445.1 → XP_047305401.1  conserved oligomeric Golgi complex subunit 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      230022982..230074527
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335140.1 → XP_054191115.1  conserved oligomeric Golgi complex subunit 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14746.1 GenPept UniProtKB/Swiss-Prot:Q14746

    Gene LinkOut

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