ZSWIM1
protein-codingzinc finger SWIM-type containing 1, the group of Zinc fingers SWIM-type
Gene summary
Predicted to enable zinc ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- C20orf162
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.0 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 ZSWIM1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_080603.5. 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 | 0 | |||||
| missense | 60 | 1 | 61 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 60 | 1 | 0 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_542170.3 | 1 | MANE Select | |
| Ensembl | ENSP00000361601.1 | 1 | MANE Select | |
| Ensembl | ENSP00000523481.1 | 1 | Standard | |
| Ensembl | ENSP00000523481.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- zinc ion binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000372523
- Coding exons
- 1
- Length
- 4040
- Individuals with no LoFs
- 122713
- Homozygous LoFs
- 21
- Heterozygous LoFs
- 3013
- Defined
- 125747
- p
- 0.0121
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.22 | 214 | 270 | 0.792 | 0.0000145 | 3189 |
| Missense (PolyPhen) | 56 | 71.858 | 0.77932 | 837 | ||
| Synonymous | -0.197 | 115 | 112 | 1.02 | 0.00000599 | 988 |
| Loss of Function | -0.345 | 16 | 14.6 | 1.10 | 7.98e-7 | 155 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0017 | 0.0017 | notable |
| Latino/Admixed American | 0.0095 | 0.0094 | notable |
| Ashkenazi Jewish | 0.023 | 0.023 | notable |
| East Asian | 0.020 | 0.020 | notable |
| Finnish | 0.015 | 0.015 | notable |
| European (Non-Finnish) | 0.011 | 0.011 | notable |
| South Asian | 0.016 | 0.016 | notable |
| Other | 0.014 | 0.014 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.757
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 75.43
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.683
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |