COG6

Chr 13AR

component of oligomeric golgi complex 6

Also known as: CDG2L, COD2, SHNS

NCBI Gene: 57511ENSG00000133103UniProt: Q9Y2V7

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]

Primary Disease Associations & Inheritance

Congenital disorder of glycosylation, type IIlMIM #614576
AR
Shaheen syndromeMIM #615328
AR
0
Active trials
80
Pathogenic / LP
476
ClinVar variants
5
Pubs (1 yr)
-0.2
Missense Z
1.02
LOEUF
Clinical Summary— COG6
🧬
Gene-Disease Validity (ClinGen)
COG6-congenital disorder of glycosylation · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
80 Pathogenic / Likely Pathogenic· 199 VUS of 476 total submissions
📖
GeneReview available — COG6
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.02LOEUF
pLI 0.000
Z-score 1.46
OE 0.75 (0.56–1.02)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.18Z-score
OE missense 1.03 (0.94–1.12)
371 obs / 361.2 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.75 (0.56–1.02)
0≤0.351.4
Missense OE1.03 (0.94–1.12)
0≤0.61.4
Synonymous OE0.94
0≤1.21.6
LoF obs/exp: 29 / 38.8Missense obs/exp: 371 / 361.2Syn Z: 0.54

ClinVar Variant Classifications

476 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic61
Likely Pathogenic19
VUS199
Likely Benign102
Benign81
Conflicting14
61
Pathogenic
19
Likely Pathogenic
199
VUS
102
Likely Benign
81
Benign
14
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
6
1
54
0
61
Likely Pathogenic
11
1
6
1
19
VUS
4
146
42
7
199
Likely Benign
0
5
52
45
102
Benign
0
4
76
1
81
Conflicting
—14
Total2115723054476

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

COG6 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients