GCC1

Chr 7

GRIP and coiled-coil domain containing 1

Also known as: GCC1P, GCC88

NCBI Gene: 79571ENSG00000179562UniProt: Q96CN9

The protein encoded by this gene is a peripheral membrane protein. It is sensitive to brefeldin A. This encoded protein contains a GRIP domain which is thought to be used in targeting. It may play a role in the organization of trans-Golgi network subcompartment involved with membrane transport. [provided by RefSeq, Jul 2008]

140
ClinVar variants
24
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— GCC1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
24 Pathogenic / Likely Pathogenic· 113 VUS of 140 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
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.
0.80LOEUF
pLI 0.000
Z-score 2.37
OE 0.51 (0.34–0.80)
Tolerant

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.
0.63Z-score
OE missense 0.91 (0.84–0.99)
399 obs / 436.2 exp
Tolerant

Mild missense constraint

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.0.51 (0.34–0.80)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.91 (0.84–0.99)
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.1.01
0≤1.21.6
LoF obs/exp: 14 / 27.4Missense obs/exp: 399 / 436.2Syn Z: -0.13

ClinVar Variant Classifications

140 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic1
VUS113
Likely Benign3
23
Pathogenic
1
Likely Pathogenic
113
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
23
0
23
Likely Pathogenic
0
0
1
0
1
VUS
0
109
4
0
113
Likely Benign
0
2
0
1
3
Benign
0
0
0
0
0
Total0111281140

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

View in ClinVar →

Protein Context — Lollipop Plot

GCC1 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Systematic and comprehensive analysis of major localizations of alpha-dystroglycan-specific modifying enzymes.
Aso S et al.·Glycobiology
2025
Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.
Cho YS et al.·Nat Genet
2011Meta-analysis
The Golgi ribbon in mammalian cells negatively regulates autophagy by modulating mTOR activity.
Gosavi P et al.·J Cell Sci
2018
Transcriptional changes common to human cocaine, cannabis and phencyclidine abuse.
Lehrmann E et al.·PLoS One
2006
Golgi-58K can re-localize to late endosomes upon cellular uptake of PS-ASOs and facilitates endosomal release of ASOs.
Liang XH et al.·Nucleic Acids Res
2021
Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers.
Shin JJH et al.·Nat Commun
2020
Intersectin-1 interacts with the golgin GCC88 to couple the actin network and Golgi architecture.
Makhoul C et al.·Mol Biol Cell
2019
Retromer has a selective function in cargo sorting via endosome transport carriers.
Cui Y et al.·J Cell Biol
2019
A role of GCC88 in the retrograde transport of CI-M6PR and the maintenance of lysosomal activity.
Cui Y et al.·Cell Biol Int
2019
Membrane trafficking. The specificity of vesicle traffic to the Golgi is encoded in the golgin coiled-coil proteins.
Wong M et al.·Science
2014
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools