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COG4 component of oligomeric golgi complex 4 [ Homo sapiens (human) ]

Gene ID: 25839, updated on 11-Apr-2024

Summary

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Official Symbol
COG4provided by HGNC
Official Full Name
component of oligomeric golgi complex 4provided by HGNC
Primary source
HGNC:HGNC:18620
See related
Ensembl:ENSG00000103051 MIM:606976; AllianceGenome:HGNC:18620
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
COD1; CDG2J; SWILS
Summary
The protein encoded by this gene is a component of an oligomeric protein complex involved in the structure and function of the Golgi apparatus. Defects in this gene may be a cause of congenital disorder of glycosylation type IIj. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2010]
Expression
Ubiquitous expression in testis (RPKM 19.4), skin (RPKM 14.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q22.1
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (70480567..70523554, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (76291598..76334735, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70514470..70557457, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70500319-70500820 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70500821-70501320 Neighboring gene fucose kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:70504733-70505668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11065 Neighboring gene Sharpr-MPRA regulatory region 8991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11066 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70558263-70559000 Neighboring gene small nucleolar RNA, C/D box 111B Neighboring gene splicing factor 3b subunit 3 Neighboring gene small nucleolar RNA, C/D box 111

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. Growth in individuals with Saul-Wilson syndrome. Ferreira CR, et al. Am J Med Genet A, 2020 Sep. PMID 32652690, Free PMC Article
  2. Saul-Wilson Syndrome. Adam MP, et al. , 1993. PMID 32078278
  3. Golgi function and dysfunction in the first COG4-deficient CDG type II patient. Reynders E, et al. Hum Mol Genet, 2009 Sep 1. PMID 19494034, Free PMC Article
  4. A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation. Ferreira CR, et al. Am J Hum Genet, 2018 Oct 4. PMID 30290151, Free PMC Article
  5. Membrane detachment is not essential for COG complex function. Climer LK, et al. Mol Biol Cell, 2018 Apr 15. PMID 29467253, Free PMC Article

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Growth in individuals with Saul-Wilson syndrome.
    Title: Growth in individuals with Saul-Wilson syndrome.
  2. A specific heterozygous COG4 substitution as the molecular basis of Saul-Wilson syndrome.
    Title: A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation.
  3. TMEM-COG4, COG7 and COG8 subunits restore endogenous COG localization to the Golgi membranes
    Title: Membrane detachment is not essential for COG complex function.
  4. A novel R729W missense mutation in COG4 was associated with the congenital disorder of glycosylation type II.
    Title: Golgi function and dysfunction in the first COG4-deficient CDG type II patient.
  5. The 1.9 A crystal structure of a Cog4 C-terminal fragment, was determined. Arg 729 is found to occupy a key position at the center of a salt bridge network, thereby stabilizing Cog4's small C-terminal domain.
    Title: Structural basis for a human glycosylation disorder caused by mutation of the COG4 gene.
  6. Study shows that the SM protein, Sly1, interacts directly with the conserved oligomeric Golgi (COG) tethering complex; Sly1-COG interaction is mediated by the Cog4 subunit, which also interacts with Syntaxin 5 through a different binding site.
    Title: Direct interaction between the COG complex and the SM protein, Sly1, is required for Golgi SNARE pairing.
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

EBI GWAS Catalog

Description
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

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 4 (COG4) 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

Clone Names

  • DKFZp586E1519

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 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 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 
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum 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
  
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 NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
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 4
Names
COG complex subunit 4
complexed with Dor1p
conserved oligomeric Golgi complex protein 4

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_027529.1 RefSeqGene

    Range
    5001..47984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001195139.2 → NP_001182068.2  conserved oligomeric Golgi complex subunit 4 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC106804, AK096557, AL050101, AU125729, BP282697
    Consensus CDS
    CCDS73909.2
    UniProtKB/TrEMBL
    A0A6I8PIQ6, Q6PIW8
    Related
    ENSP00000501405.1, ENST00000674443.1

  2. NM_001365426.1 → NP_001352355.1  conserved oligomeric Golgi complex subunit 4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC106804
    UniProtKB/TrEMBL
    Q8N8L9

  3. NM_015386.3 → NP_056201.2  conserved oligomeric Golgi complex subunit 4 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AK096557, AL050101, AU125729, BP282697
    Consensus CDS
    CCDS10892.2
    UniProtKB/Swiss-Prot
    B4DMN8, C9JS23, Q96D40, Q9BRF0, Q9BVZ2, Q9H5Y4, Q9H9E3, Q9Y3W3
    UniProtKB/TrEMBL
    J3KNI1
    Related
    ENSP00000315775.5, ENST00000323786.10
    Conserved Domains (2) summary
    pfam08318
    Location:192 → 501
    COG4; COG4 transport protein
    cl19885
    Location:551 → 788
    Sec6; Exocyst complex component Sec6

RNA

  1. NR_158212.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC106804
    Related
    ENST00000703108.1

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    70480567..70523554 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    76291598..76334735 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_145818.1: Suppressed sequence

    Description
    NM_145818.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H9E3.3 GenPept UniProtKB/Swiss-Prot:Q9H9E3

Gene LinkOut

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

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