SLFN13

Chr 17

schlafen family member 13

Also known as: SLFN10, hSLFN13

NCBI Gene: 146857UniProt: Q68D06

Enables RNA endonuclease activity. Involved in rRNA catabolic process and tRNA decay. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

0
Active trials
93
ClinVar variants
4
Pathogenic / LP
-0.7
Missense Z
1.54
LOEUF
2
Pubs (2 yr)
Clinical Summary— SLFN13
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
4 Pathogenic / Likely Pathogenic· 78 VUS of 93 total submissions
Some data sources returned errors (2)

ensembl: Error: Ensembl fetch failed: 500 for https://rest.ensembl.org/lookup/symbol/homo_sapiens/SLFN13?content-type=application/json&expand=1

pubmed: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.54LOEUF
pLI 0.000
Z-score -0.38
OE 1.09 (0.78–1.54)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.69Z-score
OE missense 1.09 (1.01–1.17)
500 obs / 458.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.09 (0.78–1.54)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.09 (1.01–1.17)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.17
0≤1.21.6
LoF obs/exp: 23 / 21.1Missense obs/exp: 500 / 458.5Syn Z: -1.76

ClinVar Variant Classifications

93 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
VUS78
Likely Benign9
Benign2
4
Pathogenic
78
VUS
9
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
0
0
0
VUS
0
75
3
0
78
Likely Benign
0
6
2
1
9
Benign
0
1
0
1
2
Total0829293

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLFN13 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Insights into Gene Regulation under Temozolomide-Promoted Cellular Dormancy and Its Connection to Stemness in Human Glioblastoma
Kubelt C et al.·Cells
2023
Schlafen Family Intra-Regulation by IFN-alpha2 in Triple-Negative Breast Cancer
Brown SR et al.·Cancers (Basel)
2023
Screening for aberrantly methylated and differentially expressed genes in nonalcoholic fatty liver disease of hepatocellular carcinoma patients with cirrhosis
Zhang G et al.·World J Surg Oncol
2022Cohort
The crucial role of single-stranded DNA binding in enhancing sensitivity to DNA-damaging agents for Schlafen 11 and Schlafen 13
Fujiwara K et al.·iScience
2023
Structural and biochemical characterization of human Schlafen 5
Metzner FJ et al.·Nucleic Acids Res
2022
Prognostic factors and Doxorubicin involved in malignant progression of meningioma
Huo X et al.·Sci Rep
2023
Research progress of the SLFN family in malignant tumors
Yu J et al.·Front Oncol
2024
Histone acetyltransferase inhibition reverses opacity in rat galactose-induced cataract
Nagaya M et al.·PLoS One
2022
Epigenome-wide DNA methylation signature of benzo[a]pyrene exposure and their mediation roles in benzo[a]pyrene-associated lung cancer development.
Meng H et al.·J Hazard Mater
2021
Comprehensive analysis of bulk and single-cell RNA sequencing data reveals Schlafen-5 (SLFN5) as a novel prognosis and immunity.
Wu YJ et al.·Int J Med Sci
2024
Top 10 full-text resultsSearch PubTator3 ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients