COG1
Chr 17ARcomponent of oligomeric golgi complex 1
Also known as: CDG2G, LDLB
The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. It is thought that this protein is required for steps in the normal medial and trans Golgi-associated processing of glycoconjugates and plays a role in the organization of the Golgi-localized complex. [provided by RefSeq, Jul 2008]
Primary Disease Associations & Inheritance
Congenital disorder of glycosylation, type IIgMIM #611209
AR
Clinical Summary— COG1
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Gene-Disease Validity (ClinGen)
COG1-congenital disorder of glycosylation · ARModerate
Moderate evidence — consider for supplementary testing
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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
32 Pathogenic / Likely Pathogenic· 244 VUS of 464 total submissions
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Open GeneReview ↗GeneReview available — COG1
Authoritative clinical overview · Recommended first read
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.65LOEUF
pLI 0.000
Z-score 3.43
OE 0.45 (0.31–0.65)
Typical tolerance to LoF variation
Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.18Z-score
OE missense 1.02 (0.95–1.10)
537 obs / 525.3 exp
Tolerant to missense variation
Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.45 (0.31–0.65)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.02 (0.95–1.10)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.04
0≤1.21.6
LoF obs/exp: 20 / 44.8Missense obs/exp: 537 / 525.3Syn Z: -0.44
ClinVar Variant Classifications
464 submitted variants in ClinVar
Classification Summary
Pathogenic28
Likely Pathogenic4
VUS244
Likely Benign161
Benign11
Conflicting16
28
Pathogenic
4
Likely Pathogenic
244
VUS
161
Likely Benign
11
Benign
16
Conflicting
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 7 | 0 | 21 | 0 | 28 |
Likely Pathogenic | 2 | 0 | 2 | 0 | 4 |
VUS | 3 | 225 | 15 | 1 | 244 |
Likely Benign | 0 | 11 | 48 | 102 | 161 |
Benign | 0 | 3 | 4 | 4 | 11 |
Conflicting | — | 16 | |||
| Total | 12 | 239 | 90 | 107 | 464 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
COG1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
Gene2Phenotype Curations
COG1-related congenital disorder of glycosylation
definitiveGene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org
OMIM — Genotype-Phenotype Relationships
1 OMIM entry
COMPONENT OF OLIGOMERIC GOLGI COMPLEX 1; COG1
MIM #606973 · *
Autosomal recessive
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →📖
Open GeneReview ↗GeneReview available — COG1
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
Metabolic Cardiomyopathies and Cardiac Defects in Inherited Disorders of Carbohydrate Metabolism: A Systematic Review.
Conte F et al.·Int J Mol Sci
2023Review
COG1-congenital disorders of glycosylation: Milder presentation and review.
Salazar M et al.·Clin Genet
2021Review
Role of the conserved oligomeric Golgi (COG) complex in protein glycosylation.
Smith RD et al.·Carbohydr Res
2008Review
Hypothesis: lobe A (COG1-4)-CDG causes a more severe phenotype than lobe B (COG5-8)-CDG.
Haijes HA et al.·J Med Genet
2018
COG6-CDG: Novel variants and novel malformation.
Cirnigliaro L et al.·Birth Defects Res
2022Case report
Congenital Disorders of Glycosylation in Portugal-Two Decades of Experience.
Quelhas D et al.·J Pediatr
2021
Component of oligomeric Golgi complex 1 deficiency leads to hypoglycemia: a case report and literature review.
Huang Y et al.·BMC Pediatr
2021Review
Identification of novel fusion genes with 28S ribosomal DNA in hematologic malignancies.
Kobayashi S et al.·Int J Oncol
2014
Conserved Oligomeric Golgi (COG) Complex Proteins Facilitate Orthopoxvirus Entry, Fusion and Spread.
Realegeno S et al.·Viruses
2020
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
The Dof transcription factor COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch accumulation.
Wei Z et al.·Mol Plant
2023
The COG1-OsSERL2 complex senses cold to trigger signaling network for chilling tolerance in japonica rice.
Xia C et al.·Nat Commun
2023Open Access
PRX2 and PRX25, peroxidases regulated by COG1, are involved in seed longevity in Arabidopsis.
Renard J et al.·Plant Cell Environ
2020
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
Author Correction: The COG1-OsSERL2 complex senses cold to trigger signaling network for chilling tolerance in japonica rice.
Xia C et al.·Nat Commun
2024
Great Abilities of Shinella zoogloeoides Strain from a Landfarming Soil for Crude Oil Degradation and a Synergy Model for Alginate-Bead-Entrapped Consortium Efficiency
Goma-Tchimbakala EJCD et al.·Microorganisms
2022Functional
The Mini-Cog, Clock Drawing Test, and Three-Item Recall Test: Rapid Cognitive Screening Tools with Comparable Performance in Detecting Mild NCD in Older Patients
Limpawattana P et al.·Geriatrics (Basel)
2021Cohort
The Mini-Cog: A Community Screening Tool for Dementia in Indonesia.
Turana Y et al.·Int J Geriatr Psychiatry
2024
Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes
Novikova SV et al.·Int J Mol Sci
2023
Top 6 full-text resultsSearch PubTator3 ↗
External Resources
Links to major genomics databases and tools