ZACN
protein-codingzinc activated ion channel, the group of Zinc activated channels
Gene summary
LGICZ1 is a zinc-activated ligand-gated ion channel that defines a new subgroup of the cysteine-loop superfamily of ligand-gated ion channels (Davies et al., 2003 [PubMed 12381728]).[supplied by OMIM, Mar 2008]
- LGICZ1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.7 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 ZACN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_180990.4. 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 | ||||
| missense | 70 | 9 | 79 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 74 | 9 | 0 | 83 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_851321.2 | 9 | MANE Select | |
| Ensembl | ENSP00000334854.5 | 9 | MANE Select | |
| Ensembl | ENSP00000391936.1 | 3 | Standard | |
| Ensembl | ENSP00000397489.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- signal transduction
- chemical synaptic transmission
- response to zinc ion
- ion transmembrane transport
- regulation of membrane potential
Molecular Function
- transmembrane signaling receptor activity
- extracellular ligand-gated ion channel activity
- zinc ion binding
- ligand-gated ion channel activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- neuron projection
- synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000334586
- Coding exons
- 9
- Length
- 11706
- Individuals with no LoFs
- 80560
- Homozygous LoFs
- 6597
- Heterozygous LoFs
- 38590
- Defined
- 125747
- p
- 0.200
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.416 | 257 | 239 | 1.08 | 0.0000136 | 2635 |
| Missense (PolyPhen) | 71 | 61.877 | 1.1474 | 749 | ||
| Synonymous | -0.996 | 122 | 109 | 1.12 | 0.00000666 | 873 |
| Loss of Function | -2.13 | 27 | 17.4 | 1.55 | 8.63e-7 | 173 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.091 | 0.090 | notable |
| Latino/Admixed American | 0.40 | 0.39 | notable |
| Ashkenazi Jewish | 0.16 | 0.16 | notable |
| East Asian | 0.36 | 0.37 | notable |
| Finnish | 0.18 | 0.18 | notable |
| European (Non-Finnish) | 0.17 | 0.17 | notable |
| South Asian | 0.12 | 0.12 | notable |
| Other | 0.20 | 0.20 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Zinc-activated ligand-gated ion channel. {ECO:0000269|PubMed:12381728}.;
Intolerance Scores
- LoFtool
- 0.505
- RVIS EVS
- 0.62
- RVIS percentile EVS
- 83.53
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0524
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |