CCZ1B
protein-codingCCZ1 homolog B, 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]
- C7orf28B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~32.6 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 CCZ1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198097.5. 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 | 3 | 4 | |||
| missense | 61 | 3 | 64 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 68 | 6 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_932765.1 | 15 | MANE Select | |
| Ensembl | ENSP00000314544.8 | 15 | MANE Select | |
| Ensembl | ENSP00000390078.1 | 3 | Standard | |
| Ensembl | ENSP00000487253.1 | 3 | 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
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
- ENST00000316731
- Coding exons
- 15
- Length
- 32637
- Individuals with no LoFs
- 125705
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 29
- Defined
- 125735
- p
- 0.000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.350 | 178 | 192 | 0.929 | 0.00000971 | 3205 |
| Missense (PolyPhen) | 35 | 49.408 | 0.70839 | 868 | ||
| Synonymous | 0.651 | 62 | 68.9 | 0.900 | 0.00000391 | 802 |
| Loss of Function | 0.484 | 20 | 22.5 | 0.890 | 0.00000102 | 357 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00020 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000094 | 0.000092 | rare |
| European (Non-Finnish) | 0.000092 | 0.000079 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0.00020 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.88
- RVIS percentile EVS
- 89.02
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |