SLFNL1
protein-codingschlafen like 1, the group of Schlafen family
Gene summary
Predicted to enable ATP binding activity. [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 ~7.6 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 SLFNL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144990.4. 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 | 2 | 2 | ||||
| missense | 99 | 6 | 105 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 101 | 6 | 0 | 107 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_659427.3 | 4 | MANE Select | |
| Ensembl | ENSP00000304401.8 | 4 | MANE Select | |
| RefSeq | NP_001161719.1 | 4 | Standard | |
| RefSeq | NP_001287788.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- ATP binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359345
- Coding exons
- 4
- Length
- 7641
- Individuals with no LoFs
- 124213
- Homozygous LoFs
- 14
- Heterozygous LoFs
- 1521
- Defined
- 125748
- p
- 0.00612
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.604 | 288 | 261 | 1.11 | 0.0000178 | 2612 |
| Missense (PolyPhen) | 83 | 82.888 | 1.0014 | 817 | ||
| Synonymous | 0.0899 | 115 | 116 | 0.989 | 0.00000827 | 837 |
| Loss of Function | 1.34 | 9 | 14.5 | 0.620 | 7.10e-7 | 151 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.0018 | 0.0017 | notable |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0.025 | 0.024 | notable |
| European (Non-Finnish) | 0.0076 | 0.0076 | notable |
| South Asian | 0.00047 | 0.00046 | rare |
| Other | 0.0089 | 0.0087 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.927
- RVIS EVS
- 0.98
- RVIS percentile EVS
- 90.46
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.387
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |