CCZ1

Chr 7

CCZ1 vacuolar protein trafficking and biogenesis associated

Also known as: C7orf28A, CCZ1A, CGI-43, H_DJ1163J12.2

NCBI Gene: 51622ENSG00000122674UniProt: P86791

Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in vesicle-mediated transport. Located in intracellular membrane-bounded organelle. Part of Mon1-Ccz1 complex. [provided by Alliance of Genome Resources, Apr 2025]

164
ClinVar variants
45
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CCZ1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
45 Pathogenic / Likely Pathogenic· 108 VUS of 164 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.
0.92LOEUF
pLI 0.000
Z-score 1.83
OE 0.57 (0.36–0.92)
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.
-0.19Z-score
OE missense 1.04 (0.93–1.17)
199 obs / 191.5 exp
Tolerant

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.0.57 (0.36–0.92)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.04 (0.93–1.17)
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.1.13
0≤1.21.6
LoF obs/exp: 12 / 21.1Missense obs/exp: 199 / 191.5Syn Z: -0.87

ClinVar Variant Classifications

164 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic40
Likely Pathogenic5
VUS108
Likely Benign8
Benign3
40
Pathogenic
5
Likely Pathogenic
108
VUS
8
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
40
0
40
Likely Pathogenic
0
0
5
0
5
VUS
0
92
16
0
108
Likely Benign
0
3
4
1
8
Benign
0
1
2
0
3
Total096671164

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

View in ClinVar →

Protein Context — Lollipop Plot

CCZ1 · 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
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
SH3P2-mediated autophagosomal targeting of the CCZ1-MON1-RABG3e module regulates autophagosome-vacuole fusion in Arabidopsis.
Zheng X et al.·Autophagy
2026
Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned.
Wilmes S et al.·Sci Adv
2025🔓 Open Access
Cryo-EM structure of the human MON1A-CCZ1-RAB7A complex provides insights into nucleotide exchange mechanism.
Li X et al.·Life Metab
2025🔓 Open AccessFunctional
The MON1-CCZ1 complex plays dual roles in autophagic degradation and vacuolar protein transport in rice.
Zhang B et al.·J Integr Plant Biol
2025🔓 Open Access
Tissue-Specific Regulation of Vesicular Trafficking Mediated by Rab-GEF Complex MON1/CCZ1 From Solanum chilense Increases Salt Stress Tolerance in Arabidopsis thaliana.
Madrid-Espinoza J et al.·Plant Cell Environ
2025
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