SLF2

Chr 10AR

SMC5/6 complex localization factor 2

Also known as: ATELS1, C10orf6, FAM178A, hNSE6

NCBI Gene: 55719ENSG00000119906UniProt: Q8IX21

Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in PML body; chromatin; and site of double-strand break. Implicated in mosaic variegated aneuploidy syndrome. [provided by Alliance of Genome Resources, Jul 2025]

Primary Disease Associations & Inheritance

Atelis syndrome 1MIM #620184
AR
0
Active trials
18
Pathogenic / LP
108
ClinVar variants
3
Pubs (1 yr)
1.0
Missense Z
0.54
LOEUF
Clinical Summary— SLF2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
18 Pathogenic / Likely Pathogenic· 82 VUS of 108 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.54LOEUF
pLI 0.000
Z-score 4.17
OE 0.37 (0.26–0.54)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.97Z-score
OE missense 0.89 (0.83–0.95)
528 obs / 594.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.37 (0.26–0.54)
0≤0.351.4
Missense OE0.89 (0.83–0.95)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 19 / 51.2Missense obs/exp: 528 / 594.6Syn Z: 0.07

ClinVar Variant Classifications

108 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic17
Likely Pathogenic1
VUS82
Likely Benign6
Benign1
Conflicting1
17
Pathogenic
1
Likely Pathogenic
82
VUS
6
Likely Benign
1
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
1
13
0
17
Likely Pathogenic
0
0
1
0
1
VUS
0
80
2
0
82
Likely Benign
0
6
0
0
6
Benign
0
1
0
0
1
Conflicting
—1
Total388160108

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

View in ClinVar →

SLF2 · protein map & ClinVar variants

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

Gene2Phenotype Curations

SLF2-related developmental disorder

moderate
ARUndeterminedUncertain
Dev. Disorders
G2P ↗
splice region variantstop gained NMD triggeringsplice donor variant NMD triggeringframeshift variant NMD triggering

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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