SLFN13
protein-codingschlafen family member 13, the group of Schlafen family
Gene summary
Enables RNA endonuclease activity. Involved in rRNA catabolic process and tRNA decay. Located in cytoplasm. [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 ~13.7 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 SLFN13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144682.6. 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 | 3 | 1 | 7 | ||
| missense | 155 | 18 | 173 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 162 | 21 | 1 | 184 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653283.3 | 4 | MANE Select | |
| Ensembl | ENSP00000285013.6 | 4 | MANE Select | |
| Ensembl | ENSP00000433181.1 | 1 | Standard | |
| Ensembl | ENSP00000434439.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- rRNA catabolic process
- tRNA catabolic process
- defense response to virus
- RNA phosphodiester bond hydrolysis, endonucleolytic
Molecular Function
- tRNA binding
- endoribonuclease activity
- ATP binding
- zinc ion binding
Cellular Component
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000285013
- Coding exons
- 4
- Length
- 13742
- Individuals with no LoFs
- 125717
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 30
- Defined
- 125747
- p
- 0.000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.688 | 500 | 459 | 1.09 | 0.0000235 | 5886 |
| Missense (PolyPhen) | 145 | 127.2 | 1.1399 | 1805 | ||
| Synonymous | -1.76 | 199 | 170 | 1.17 | 0.00000886 | 1715 |
| Loss of Function | -0.377 | 23 | 21.1 | 1.09 | 9.78e-7 | 306 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.00030 | 0.00029 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Endoribonuclease that cleaves tRNAs and rRNAs (PubMed:29563550). Cleaves tRNAs 11 nucleotides from the 3'- terminus at the acceptor stem (PubMed:29563550). Does not act on tRNA(Sec) (PubMed:29563550). Able to restrict HIV-1 virus replication; ability to inhibit HIV-1 replication is dependent on endoribonuclease activity (PubMed:29563550). {ECO:0000269|PubMed:29563550}.;
Recessive Scores
- pRec
- 0.0673
Intolerance Scores
- LoFtool
- 0.550
- RVIS EVS
- 2.76
- RVIS percentile EVS
- 99
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0835
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |