ZCCHC18
protein-codingzinc finger CCHC-type containing 18, the group of Zinc fingers CCHC-type|Paraneoplastic Ma antigens
Gene summary
Predicted to enable zinc ion binding activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.7 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 ZCCHC18 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001143978.3. 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 | 3 | 1 | 4 | |||
| missense | 50 | 4 | 54 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 5 | 0 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001137450.1 | 1 | MANE Select | |
| Ensembl | ENSP00000498828.1 | 1 | MANE Select | |
| Ensembl | ENSP00000473824.1 | 1 | Standard | |
| Ensembl | ENSP00000473824.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- metal ion binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000537356
- Coding exons
- 1
- Length
- 3712
- Individuals with no LoFs
- 125433
- Homozygous LoFs
- 100
- Heterozygous LoFs
- 90
- Defined
- 125623
- p
- 0.000757
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.747 | 132 | 158 | 0.833 | 0.0000122 | 2644 |
| Missense (PolyPhen) | 28 | 29.423 | 0.95165 | 674 | ||
| Synonymous | 1.01 | 49 | 58.8 | 0.833 | 0.00000425 | 808 |
| Loss of Function | 1.70 | 1 | 5.18 | 0.193 | 3.25e-7 | 105 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0021 | 0.0016 | notable |
| Latino/Admixed American | 0.00018 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00029 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00012 | 0.000079 | rare |
| South Asian | 0.0075 | 0.0047 | notable |
| Other | 0.00067 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
Essentials
- Essential (CRISPR2)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |