CCZ1
protein-codingCCZ1 homolog, vacuolar protein trafficking and biogenesis associated
Gene summary
Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in vacuolar transport and vesicle-mediated transport. Located in late endosome. Part of Mon1-Ccz1 complex. [provided by Alliance of Genome Resources, Jun 2026]
- C7orf28A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CCZ1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015622.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 74 | 3 | 77 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 83 | 4 | 0 | 87 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056437.4 | 15 | MANE Select | |
| Ensembl | ENSP00000325681.6 | 15 | MANE Select | |
| Ensembl | ENSP00000486988.1 | 3 | Standard | |
| Ensembl | ENSP00000557627.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Rab regulation of trafficking
- RAB GEFs exchange GTP for GDP on RABs
Biological Process
- vesicle-mediated transport
Molecular Function
- guanyl-nucleotide exchange factor activity
- protein binding
Cellular Component
- lysosomal membrane
- cytosol
- aggresome
- Mon1-Ccz1 complex
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000325974
- Coding exons
- 15
- Length
- 27250
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 33
- Defined
- 125746
- p
- 0.000147
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.194 | 199 | 191 | 1.04 | 0.00000990 | 3181 |
| Missense (PolyPhen) | 50 | 51.002 | 0.98035 | 869 | ||
| Synonymous | -0.867 | 79 | 69.8 | 1.13 | 0.00000405 | 798 |
| Loss of Function | 1.83 | 12 | 21.1 | 0.569 | 8.86e-7 | 356 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00051 | 0.00043 | rare |
| Latino/Admixed American | 0.000032 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000053 | 0.000046 | rare |
| European (Non-Finnish) | 0.00032 | 0.00022 | rare |
| South Asian | 0.000067 | 0.000065 | rare |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts in concert with MON1A, as a guanine exchange factor (GEF) for RAB7, promotes the exchange of GDP to GTP, converting it from an inactive GDP-bound form into an active GTP-bound form (PubMed:23084991). {ECO:0000269|PubMed:23084991}.;
Intolerance Scores
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.91
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |