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COG5 component of oligomeric golgi complex 5 [ Homo sapiens (human) ]

Gene ID: 10466, updated on 5-Mar-2024

Summary

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Official Symbol
COG5provided by HGNC
Official Full Name
component of oligomeric golgi complex 5provided by HGNC
Primary source
HGNC:HGNC:14857
See related
Ensembl:ENSG00000164597 MIM:606821; AllianceGenome:HGNC:14857
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
CDG2I; GTC90; GOLTC1
Summary
The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. The encoded protein is organized with conserved oligomeric Golgi complex components 6, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants. Mutations in this gene result in congenital disorder of glycosylation type 2I.[provided by RefSeq, Jan 2011]
Expression
Ubiquitous expression in thyroid (RPKM 12.7), prostate (RPKM 10.2) and 25 other tissues See more
Orthologs
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Genomic context

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See COG5 in Genome Data Viewer
Location:
7q22.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (107201372..107563920, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (108517426..108879966, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (106841817..107204365, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26490 Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma Neighboring gene CRISPRi-validated cis-regulatory element chr7.4040 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4041 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4042 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4045 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4046 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4048 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4050 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:106681203-106681414 Neighboring gene Sharpr-MPRA regulatory region 8060 Neighboring gene PRKAR2B antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12069 Neighboring gene protein kinase cAMP-dependent type II regulatory subunit beta Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:106792322-106793521 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:106808976-106809549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18538 Neighboring gene uncharacterized LOC124901720 Neighboring gene uncharacterized LOC124901721 Neighboring gene HMG-box transcription factor 1 Neighboring gene MPRA-validated peak6677 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr7:107031303-107031825 Neighboring gene MPRA-validated peak6680 silencer Neighboring gene ribosomal protein L37a pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:107148389-107148890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:107148891-107149390 Neighboring gene G protein-coupled receptor 22 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:107204244-107204454 Neighboring gene DUS4L-BCAP29 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18539 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:107204943-107206142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26493 Neighboring gene uncharacterized LOC124901856 Neighboring gene dihydrouridine synthase 4 like Neighboring gene B cell receptor associated protein 29

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. Deficiency in COG5 causes a moderate form of congenital disorders of glycosylation. Paesold-Burda P, et al. Hum Mol Genet, 2009 Nov 15. PMID 19690088
  2. COG5 variants lead to complex early onset retinal degeneration, upregulation of PERK and DNA damage. Tabbarah S, et al. Sci Rep, 2020 Dec 4. PMID 33277529, Free PMC Article
  3. Fetal glycosylation defect due to ALG3 and COG5 variants detected via amniocentesis: Complex glycosylation defect with embryonic lethal phenotype. Ferrer A, et al. Mol Genet Metab, 2020 Dec. PMID 33187827
  4. Fusion of HMGA2 to COG5 in uterine leiomyoma. Velagaleti GV, et al. Cancer Genet Cytogenet, 2010 Oct 1. PMID 20804914
  5. A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22. Kerkhof HJ, et al. Arthritis Rheum, 2010 Feb. PMID 20112360, Free PMC Article

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Fetal glycosylation defect due to ALG3 and COG5 variants detected via amniocentesis: Complex glycosylation defect with embryonic lethal phenotype.
    Title: Fetal glycosylation defect due to ALG3 and COG5 variants detected via amniocentesis: Complex glycosylation defect with embryonic lethal phenotype.
  2. COG5 variants lead to complex early onset retinal degeneration, upregulation of PERK and DNA damage.
    Title: COG5 variants lead to complex early onset retinal degeneration, upregulation of PERK and DNA damage.
  3. Targeted silencing of components of lobe B of the COG complex, namely COG5, COG6, COG7 and COG8, inhibited HIV-1 replication
    Title: Target silencing of components of the conserved oligomeric Golgi complex impairs HIV-1 replication.
  4. Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex.
    Title: Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex.
  5. In conclusion, we find that GDF5, but not COG5 or MCF2L, influence the extent of radiographic damage in knee osteoarthritis
    Title: Genetic contribution to radiographic severity in osteoarthritis of the knee.
  6. Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Meta-analysis of genome-wide association studies confirms a susceptibility locus for knee osteoarthritis on chromosome 7q22.
  7. Report on a uterine leiomyoma with a novel HMGA2 fusion gene in a 44-year-old woman.
    Title: Fusion of HMGA2 to COG5 in uterine leiomyoma.
  8. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22.
  9. Sec34 is implicated in traffic from the endoplasmic reticulum to the Golgi and exists in a complex with GTC-90 and ldlBp
    Title: Sec34 is implicated in traffic from the endoplasmic reticulum to the Golgi and exists in a complex with GTC-90 and ldlBp.
  10. COG5- and COG7 subunits play distinctive roles in controlling Golgi structure and function
    Title: Genetic analysis of the subunit organization and function of the conserved oligomeric golgi (COG) complex: studies of COG5- and COG7-deficient mammalian cells.
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
A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22.
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

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

  • FLJ41732, FLJ44289

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in glycosylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within inter-Golgi cisterna vesicle-mediated transport IDA
Inferred from Direct Assay
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 NAS
Non-traceable Author Statement
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 apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
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 membrane HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
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 5
Names
13S golgi transport complex 1 90 kDa subunit
COG complex subunit 5
conserved oligomeric Golgi complex protein 5

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_028095.2 RefSeqGene

    Range
    5595..368143
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001161520.2 → NP_001154992.2  conserved oligomeric Golgi complex subunit 5 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and lacks a portion of the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC004492, AK022835, AK314270, BC068540
    Consensus CDS
    CCDS55152.2
    UniProtKB/Swiss-Prot
    A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
    Related
    ENSP00000377228.3, ENST00000393603.7
    Conserved Domains (1) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5

  2. NM_001379511.1 → NP_001366440.1  conserved oligomeric Golgi complex subunit 5 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492, AC004855
    UniProtKB/Swiss-Prot
    A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
    Conserved Domains (1) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5

  3. NM_001379512.1 → NP_001366441.1  conserved oligomeric Golgi complex subunit 5 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492, AC004855
    UniProtKB/Swiss-Prot
    A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
    Conserved Domains (1) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5

  4. NM_001379513.1 → NP_001366442.1  conserved oligomeric Golgi complex subunit 5 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492, AC004855
    UniProtKB/Swiss-Prot
    A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
    Conserved Domains (1) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5

  5. NM_001379514.1 → NP_001366443.1  conserved oligomeric Golgi complex subunit 5 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492, AC004855
    UniProtKB/Swiss-Prot
    A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
    Conserved Domains (1) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5

  6. NM_001379515.1 → NP_001366444.1  conserved oligomeric Golgi complex subunit 5 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492
    Conserved Domains (2) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5
    cl00549
    Location:481 → 559
    ABC_membrane; ABC transporter transmembrane region

  7. NM_001379516.1 → NP_001366445.1  conserved oligomeric Golgi complex subunit 5 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492, AC004855
    Conserved Domains (1) summary
    cl22951
    Location:35 → 81
    Vps51; Vps51/Vps67

  8. NM_006348.5 → NP_006339.4  conserved oligomeric Golgi complex subunit 5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492, AC004855
    Consensus CDS
    CCDS5742.2
    UniProtKB/Swiss-Prot
    A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
    Related
    ENSP00000297135.4, ENST00000297135.9
    Conserved Domains (1) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5

  9. NM_181733.4 → NP_859422.3  conserved oligomeric Golgi complex subunit 5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC002381, AC004492, AC004855
    Consensus CDS
    CCDS5743.2
    UniProtKB/Swiss-Prot
    A4D0R6, A4D0R7, O14555, O95008, Q6NUL5, Q9UP83
    Related
    ENSP00000334703.3, ENST00000347053.8
    Conserved Domains (1) summary
    pfam10392
    Location:35 → 158
    COG5; Golgi transport complex subunit 5

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    107201372..107563920 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446634.2 → XP_024302402.2  conserved oligomeric Golgi complex subunit 5 isoform X1

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017852930.1 Reference GRCh38.p14 PATCHES

    Range
    46894..409575 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332128.1 → XP_054188103.1  conserved oligomeric Golgi complex subunit 5 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    108517426..108879966 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357090.1 → XP_054213065.1  conserved oligomeric Golgi complex subunit 5 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UP83.4 GenPept UniProtKB/Swiss-Prot:Q9UP83

Gene LinkOut

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

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