Gene Gene information from NCBI Gene database.
Entrez ID 25839
Gene name Component of oligomeric golgi complex 4
Gene symbol COG4
Synonyms (NCBI Gene)
CDG2JCOD1SWILS
Chromosome 16
Chromosome location 16q22.1
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 e
SNPs SNP information provided by dbSNP.
13
SNP ID Visualize variation Clinical significance Consequence
rs267606740 G>A Pathogenic Downstream transcript variant, missense variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs372362031 C>T Likely-pathogenic Non coding transcript variant, missense variant, coding sequence variant
rs376663459 G>A Likely-pathogenic Non coding transcript variant, 5 prime UTR variant, coding sequence variant, stop gained
rs376885733 A>G Conflicting-interpretations-of-pathogenicity, likely-benign Non coding transcript variant, 5 prime UTR variant, synonymous variant, coding sequence variant
rs387907202 C>A,T Pathogenic Non coding transcript variant, stop gained, coding sequence variant, missense variant, 5 prime UTR variant
miRNA miRNA information provided by mirtarbase database.
189
miRTarBase ID miRNA Experiments Reference
MIRT040817 hsa-miR-18a-3p CLASH 23622248
MIRT039829 hsa-miR-615-3p CLASH 23622248
MIRT902158 hsa-miR-122 CLIP-seq
MIRT902159 hsa-miR-1224-3p CLIP-seq
MIRT902160 hsa-miR-1260 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
20
GO ID Ontology Definition Evidence Reference
GO:0000139 Component Golgi membrane IEA
GO:0000139 Component Golgi membrane NAS 27066481
GO:0000139 Component Golgi membrane TAS
GO:0000301 Process Retrograde transport, vesicle recycling within Golgi IMP 27066481
GO:0005515 Function Protein binding IPI 15047703, 19536132, 32296183, 33961781
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606976 18620 ENSG00000103051
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9H9E3
Protein name Conserved oligomeric Golgi complex subunit 4 (COG complex subunit 4) (Component of oligomeric Golgi complex 4)
Protein function Required for normal Golgi function (PubMed:19536132, PubMed:30290151). Plays a role in SNARE-pin assembly and Golgi-to-ER retrograde transport via its interaction with SCFD1 (PubMed:19536132). {ECO:0000269|PubMed:19536132, ECO:0000269|PubMed:302
PDB 3HR0
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF08318 COG4 188 497 COG4 transport protein Domain
Sequence
MADLDSPPKLSGVQQPSEGVGGGRCSEISAELIRSLTELQELEAVYERLCGEEKVVEREL
DALLEQQNTIESKMVTLHRMGPNLQLIEGDAKQLAGMITFTCNLAENVSSKVRQLDLAKN
RLYQAIQRADDILDLKFCMDGVQTALRSEDYEQAAAHTHRYLCLDKSVIELSRQGKEGSM
IDANLKLLQEAEQRLKAIVAEKFAIATKEGDLPQVERFFKIFPLLGLHEEGLRKFSEYLC
KQVASKAEENLLMVLGTDMSDRRAAVIFADTLTLLFEGIARIVETHQPIVETYYGPGRLY
TLIKYLQVECDRQVEKVVDKFIKQRDYHQQFRHVQNNLMRNSTTEKIEPRELDPILTEVT
LMNARSELYLRFLKKRISSDFEVGDSMASEEVKQEHQKCLDKLLNNCLLSCTMQELIGLY
VTMEEYFMRETVNKAVALDTYEKGQLTSSMVDDVFYIVKKCIGRALSSSSIDCLCAMINL
ATTELESDFRDVLCNKL
RMGFPATTFQDIQRGVTSAVNIMHSSLQQGKFDTKGIESTDEA
KMSFLVTLNNVEVCSENISTLKKTLESDCTKLFSQGIGGEQAQAKFDSCLSDLAAVSNKF
RDLLQEGLTELNSTAIKPQVQPWINSFFSVSHNIEEEEFNDYEANDPWVQQFILNLEQQM
AEFKASLSPVIYDSLTGLMTSLVAVELEKVVLKSTFNRLGGLQFDKELRSLIAYLTTVTT
WTIRDKFARLSQMATILNLERVTEILDYWGPNSGPLTWRLTPAEVRQVLALRIDFRSEDI
KRLRL
Sequence length 785
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    COPI-mediated anterograde transport
Intra-Golgi traffic
Retrograde transport at the Trans-Golgi-Network
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
26
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
COG4-congenital disorder of glycosylation Pathogenic; Likely pathogenic rs2151749755, rs2151758141, rs2151758219, rs540632609, rs267606740, rs376663459, rs926950737, rs387907202, rs387907203, rs1555575860, rs937887233, rs1048764460, rs2049726544, rs1249789100, rs1311924956 RCV001647345
RCV001647344
RCV001962877
RCV002021735
RCV000003837
View all (10 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
COG4-related disorder Likely pathogenic; Pathogenic rs1333878137 RCV005223078
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Delayed gross motor development Pathogenic rs1048764460 RCV000782124
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hepatocellular carcinoma Likely pathogenic rs540632609 RCV005925664
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
COG4-CDG Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Apraxia of Phonation Apraxia CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Apraxias Apraxia CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Blood Coagulation Disorders Blood Coagulation Disorders HPO_DG
★☆☆☆☆
Found in Text Mining only
Carcinoma Renal Cell Renal cell carcinoma Pubtator 34539936 Stimulate
★☆☆☆☆
Found in Text Mining only
Cataract Cataract HPO_DG
★☆☆☆☆
Found in Text Mining only
CATARACT 5, MULTIPLE TYPES Cataract CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Cerebral atrophy Cerebral Atrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
Cirrhosis Cirrhosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Clumsiness - motor delay Motor delay HPO_DG
★☆☆☆☆
Found in Text Mining only
COG4-CDG Congenital Disorder Of Glycosylation Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations