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

Summary

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: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (70480567..70523554, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (76291598..76334735, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (70514470..70557457, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Growth in individuals with Saul-Wilson syndrome.
Title: Growth in individuals with Saul-Wilson syndrome.
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.
TMEM-COG4, COG7 and COG8 subunits restore endogenous COG localization to the Golgi membranes
Title: Membrane detachment is not essential for COG complex function.
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.
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.
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.

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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
COG4-congenital disorder of glycosylation MedGen: C4303552 OMIM: 613489 GeneReviews: Congenital Disorders of N-Linked Glycosylation and Multiple Pathway Overview	Compare labs
Microcephalic osteodysplastic dysplasia, Saul-Wilson type MedGen: C1300285 OMIM: 618150 GeneReviews: Saul-Wilson Syndrome	Compare labs

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16S2583E (e-PCR)
- UniSTS:37978

RH64977 (e-PCR)
- UniSTS:84318

D16S2587E (e-PCR)
- UniSTS:151659

STS-T86956 (e-PCR)
- UniSTS:15249

RH64922 (e-PCR)
- UniSTS:90289

SHGC-147852 (e-PCR)
- UniSTS:176051

STS-T95317 (e-PCR)
- UniSTS:78822

SHGC-33776 (e-PCR)
- UniSTS:78823

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
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

NG_027529.1 RefSeqGene

Range

5001..47984

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Status: REVIEWED

Source sequence(s)

AC106804

UniProtKB/TrEMBL

Q8N8L9
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

NR_158212.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC106804

Related

ENST00000703108.1

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

70480567..70523554 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

76291598..76334735 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.