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

Gene ID: 22796, updated on 3-Apr-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
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Genomic context

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Location:
1q42.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (230642481..230693982)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (230022982..230074527)
105.20220307 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
  • 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. The interaction of two tethering factors, p115 and COG complex, is required for Golgi integrity. Sohda M, et al. Traffic, 2007 Mar. PMID 17274799
  3. Retrograde transport on the COG railway. Ungar D, et al. Trends Cell Biol, 2006 Feb. PMID 16406524
  4. 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
  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 (40) 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
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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_2023_10

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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