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COG6 component of oligomeric golgi complex 6 [ Homo sapiens (human) ]

Gene ID: 57511, updated on 3-Apr-2024

Summary

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Official Symbol
COG6provided by HGNC
Official Full Name
component of oligomeric golgi complex 6provided by HGNC
Primary source
HGNC:HGNC:18621
See related
Ensembl:ENSG00000133103 MIM:606977; AllianceGenome:HGNC:18621
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
COD2; SHNS; CDG2L
Summary
This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi apparatus. The encoded protein is organized with conserved oligomeric Golgi complex components 5, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2009]
Expression
Ubiquitous expression in testis (RPKM 7.0), thyroid (RPKM 5.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
13q14.11
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (39655627..39791666)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (38874034..39010137)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (40229764..40365803)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene LHFPL tetraspan subfamily member 6 Neighboring gene uncharacterized LOC105370170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:40086605-40087104 Neighboring gene NANOG hESC enhancer GRCh37_chr13:40089286-40089967 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:40137620-40138120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:40138121-40138621 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:40139174-40140373 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:40145310-40145877 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:40145878-40146444 Neighboring gene protein SPT2 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5277 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5278 Neighboring gene microRNA 4305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:40341964-40342464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:40342465-40342965 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:40377804-40378420 Neighboring gene CDKN2A interacting protein N-terminal like pseudogene 3 Neighboring gene RNY4 pseudogene 14 Neighboring gene azurocidin 1 pseudogene 1

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. Disorder of sex development associated with a novel homozygous nonsense mutation in COG6 expands the phenotypic spectrum of COG6-CDG. Lugli L, et al. Am J Med Genet A, 2021 Apr. PMID 33394555
  2. COG6-CDG: Expanding the phenotype with emphasis on glycosylation defects involved in the causation of male disorders of sex development. Mandel H, et al. Clin Genet, 2020 Oct. PMID 32683677
  3. Compound heterozygous variants of the COG6 gene in a Chinese patient with deficiency of subunit 6 of the conserved oligomeric Golgi complex (COG6-CDG). Li G, et al. Eur J Med Genet, 2019 Jan. PMID 29709711
  4. A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus. Márquez A, et al. Ann Rheum Dis, 2017 Jan. PMID 27193031
  5. Key features and clinical variability of COG6-CDG. Rymen D, et al. Mol Genet Metab, 2015 Nov. PMID 26260076

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Disorder of sex development associated with a novel homozygous nonsense mutation in COG6 expands the phenotypic spectrum of COG6-CDG.
    Title: Disorder of sex development associated with a novel homozygous nonsense mutation in COG6 expands the phenotypic spectrum of COG6-CDG.
  2. COG6-CDG: Expanding the phenotype with emphasis on glycosylation defects involved in the causation of male disorders of sex development.
    Title: COG6-CDG: Expanding the phenotype with emphasis on glycosylation defects involved in the causation of male disorders of sex development.
  3. Ptahogenic compound heterozygous variants of the COG6 gene were identified in a neonatal patient.
    Title: Compound heterozygous variants of the COG6 gene in a Chinese patient with deficiency of subunit 6 of the conserved oligomeric Golgi complex (COG6-CDG).
  4. COG6 is a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus.
    Title: A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus.
  5. study presents 7 additional patients with 4 novel COG6 mutations; genotype-phenotype correlation can be discerned ranging from deep intronic mutations found in Shaheen syndrome as the mildest form to loss-of-function mutations leading to early lethal congenital disorders of glycosylation phenotypes
    Title: Key features and clinical variability of COG6-CDG.
  6. The aim of this study was to investigate whether the HCP5, TNIP1, TNFAIP3, SPATA2 and COG6 genes were genetic risk factors for psoriasis in Chinese population.
    Title: Investigating the genetic association of HCP5, SPATA2, TNIP1, TNFAIP3 and COG6 with psoriasis in Chinese population.
  7. Our findings implicate COG6 rs9548934C-->T genotypes and circulating miRNA-1 phenotype in modulating the occurrence and major adverse cardiovascular events of coronary artery disease.
    Title: Polymorphism in miRNA-1 target site and circulating miRNA-1 phenotype are associated with the decreased risk and prognosis of coronary artery disease.
  8. 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.
  9. data implicate COG6 in the pathogenesis of a novel hypohidrotic disorder in humans that is distinct from congenital disorders of glycosylation.
    Title: A novel syndrome of hypohidrosis and intellectual disability is linked to COG6 deficiency.
  10. COG6 interaction with SNARE proteins via universal SNARE-binding motif of COG6 is important for Golgi complex intergrity.
    Title: COG6 interacts with a subset of the Golgi SNAREs and is important for the Golgi complex integrity.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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
COG6-ongenital disorder of glycosylation
MedGen: C3553230 OMIM: 614576 GeneReviews: Not available
Compare labs
Hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome
MedGen: C3809160 OMIM: 615328 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci.
EBI GWAS Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
EBI GWAS Catalog
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

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

  • KIAA1134, DKFZp313D191

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 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 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
  
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 trans-Golgi network membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
conserved oligomeric Golgi complex subunit 6
Names
COG complex subunit 6
complexed with Dor1p 2
conserved oligomeric Golgi complex protein 6
testicular tissue protein Li 41

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_028352.1 RefSeqGene

    Range
    5036..102002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145079.2 → NP_001138551.1  conserved oligomeric Golgi complex subunit 6 isoform 2

    See identical proteins and their annotated locations for NP_001138551.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 3' most exon, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB032960, AL596306, DC317375
    Consensus CDS
    CCDS45042.1
    UniProtKB/TrEMBL
    A0A140VJG7, B4DG73
    Related
    ENSP00000403733.1, ENST00000416691.5
    Conserved Domains (1) summary
    pfam06419
    Location:56 → 610
    COG6; Conserved oligomeric complex COG6

  2. NM_020751.3 → NP_065802.1  conserved oligomeric Golgi complex subunit 6 isoform 1

    See identical proteins and their annotated locations for NP_065802.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL512505, BC051723, BU675177, DC317375
    Consensus CDS
    CCDS9370.1
    UniProtKB/Swiss-Prot
    Q5T0U1, Q6AI19, Q86V49, Q9ULT5, Q9Y2V7
    UniProtKB/TrEMBL
    B4DG73
    Related
    ENSP00000397441.2, ENST00000455146.8
    Conserved Domains (1) summary
    smart01087
    Location:68 → 656
    COG6; Conserved oligomeric complex COG6

RNA

  1. NR_026745.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an additional exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF116827, AL512505, BU675177, DC317375
    Related
    ENST00000356576.8

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    39655627..39791666
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535168.2 → XP_011533470.1  conserved oligomeric Golgi complex subunit 6 isoform X1

    UniProtKB/TrEMBL
    B4DG73
    Conserved Domains (1) summary
    pfam06419
    Location:56 → 697
    COG6; Conserved oligomeric complex COG6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    38874034..39010137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374771.1 → XP_054230746.1  conserved oligomeric Golgi complex subunit 6 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2V7.2 GenPept UniProtKB/Swiss-Prot:Q9Y2V7

Gene LinkOut

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