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

    Gene ID: 57511, updated on 27-Nov-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
    mouse all
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    Genomic context

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    See COG6 in Genome Data Viewer
    Location:
    13q14.11
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (39655627..39791666)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (38874034..39010137)
    RS_2024_09 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. A novel syndrome of hypohidrosis and intellectual disability is linked to COG6 deficiency. Shaheen R, et al. J Med Genet, 2013 Jul. PMID 23606727
    2. 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
    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. 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
    5. 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

    See all (55) 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-congenital 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)

    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, ENST00000416691.6
      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_2024_08

    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

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

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