COG1

component of oligomeric golgi complex 1, the group of Components of oligomeric golgi complex

Basic information

Region (hg38): 17:73193055-73208507

Previous symbols: [ "LDLB" ]

Links

ENSG00000166685NCBI:9382OMIM:606973HGNC:6545Uniprot:Q8WTW3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • COG1-congenital disorder of glycosylation (Strong), mode of inheritance: AR
  • COG1-congenital disorder of glycosylation (Strong), mode of inheritance: AR
  • COG1-congenital disorder of glycosylation (Definitive), mode of inheritance: AR
  • COG1-congenital disorder of glycosylation (Supportive), mode of inheritance: AR
  • COG1-congenital disorder of glycosylation (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Congenital disorder of glycosylation, type IIgARHematologicAwareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgeryBiochemical; Cardiovascular; Gastrointestinal; Musculoskeletal; Neurologic16537452; 19008299
The condition can include cardiac manifestations as well as other multi-system manifestations; Hepatic-metabolized agents should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COG1 gene.

  • COG1_congenital_disorder_of_glycosylation (355 variants)
  • Inborn_genetic_diseases (149 variants)
  • not_provided (58 variants)
  • COG1-related_disorder (12 variants)
  • not_specified (6 variants)
  • Prostate_cancer (2 variants)
  • Congenital_disorder_of_glycosylation (2 variants)
  • Nephrotic_syndrome (1 variants)
  • Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COG1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018714.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
108
clinvar
113
missense
245
clinvar
22
clinvar
1
clinvar
268
nonsense
4
clinvar
2
clinvar
2
clinvar
8
start loss
1
1
frameshift
6
clinvar
3
clinvar
1
clinvar
10
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 10 6 254 130 1

Highest pathogenic variant AF is 0.000010532263

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
COG1protein_codingprotein_codingENST00000299886 1415518
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.94e-81.001256850631257480.000251
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1815375251.020.00003066357
Missense in Polyphen130146.930.884761804
Synonymous-0.4442262181.040.00001311987
Loss of Function3.432044.80.4470.00000250495

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001210.00121
Ashkenazi Jewish0.000.00
East Asian0.0003260.000326
Finnish0.00004620.0000462
European (Non-Finnish)0.0002200.000220
Middle Eastern0.0003260.000326
South Asian0.0001630.000163
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for normal Golgi function. {ECO:0000250}.;
Disease
DISEASE: Congenital disorder of glycosylation 2G (CDG2G) [MIM:611209]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N- glycoproteins during embryonic development, differentiation, and maintenance of cell functions. Clinical features of CDG2G include failure to thrive, generalized hypotonia, growth retardation and mild psychomotor retardation. CDG2G is biochemically characterized by a defect in O-glycosylation as well as N-glycosylation. {ECO:0000269|PubMed:16537452}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec
0.134

Intolerance Scores

loftool
0.559
rvis_EVS
0.03
rvis_percentile_EVS
55.84

Haploinsufficiency Scores

pHI
0.164
hipred
N
hipred_score
0.426
ghis
0.537

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.933

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cog1
Phenotype

Gene ontology

Biological process
endoplasmic reticulum to Golgi vesicle-mediated transport;intra-Golgi vesicle-mediated transport;Golgi organization;protein transport
Cellular component
Golgi membrane;Golgi apparatus;Golgi transport complex;trans-Golgi network membrane
Molecular function
protein binding