SWI5
protein-codingSWI5 homologous recombination repair protein
Gene summary
Involved in cellular response to ionizing radiation and double-strand break repair via homologous recombination. Located in nucleoplasm. Part of Swi5-Sfr1 complex. [provided by Alliance of Genome Resources, Jun 2026]
- C9orf119
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~40.7 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 SWI5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001318089.2. 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 | 17 | 1 | 18 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 20 | 1 | 0 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001305018.2 | 5 | MANE Select | |
| Ensembl | ENSP00000411469.3 | 5 | MANE Select | |
| RefSeq | NP_001035100.2 | 5 | Standard | |
| RefSeq | NP_001305021.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- double-strand break repair via homologous recombination
- DNA recombinase assembly
- cellular response to ionizing radiation
Molecular Function
- protein binding
Cellular Component
- nucleus
- Swi5-Sfr1 complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000320188
- Coding exons
- 5
- Length
- 13612
- Individuals with no LoFs
- 124787
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 124796
- p
- 0.0000361
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.966 | 168 | 136 | 1.23 | 0.00000630 | 1495 |
| Missense (PolyPhen) | 46 | 42.44 | 1.0839 | 522 | ||
| Synonymous | -2.30 | 80 | 57.7 | 1.39 | 0.00000276 | 503 |
| Loss of Function | 1.34 | 6 | 10.8 | 0.558 | 5.53e-7 | 105 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000072 | 0.000071 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the SWI5-SFR1 complex, a complex required for double-strand break repair via homologous recombination. {ECO:0000269|PubMed:21252223}.;
Intolerance Scores
- RVIS EVS
- 0.71
- RVIS percentile EVS
- 85.53
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- 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 |