SLX9

Chr 21

SLX9 ribosome biogenesis factor

Also known as: C21orf70, FAM207A, PRED56

NCBI Gene: 85395ENSG00000160256UniProt: Q9NSI2

The protein is predicted to be involved in ribosome biogenesis, specifically in the maturation of small ribosomal subunit RNA within the nucleolus as part of the 90S preribosome complex. However, no human diseases have been definitively associated with mutations in this gene to date. The gene shows relatively low constraint against loss-of-function variants (pLI = 0.08, LOEUF = 0.94), suggesting it may be more tolerant to functional disruption than many disease-causing genes.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
0
Pubs (1 yr)
94
P/LP submissions
0%
P/LP missense
0.94
LOEUF
DN
Mechanism· predicted
Clinical Summary— SLX9
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.08) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
89 unique Pathogenic / Likely Pathogenic· 66 VUS of 168 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.94LOEUF
pLI 0.076
Z-score 1.69
OE 0.36 (0.17–0.94)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.05Z-score
OE missense 1.01 (0.88–1.17)
136 obs / 134.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.36 (0.17–0.94)
0≤0.351.4
Missense OE1.01 (0.88–1.17)
0≤0.61.4
Synonymous OE1.03
0≤1.21.6
LoF obs/exp: 3 / 8.2Missense obs/exp: 136 / 134.3Syn Z: -0.16
DN
0.6841th %ile
GOF
0.5954th %ile
LOF
0.3454th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

168 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic85
Likely Pathogenic4
VUS66
Likely Benign5
Conflicting1
85
Pathogenic
4
Likely Pathogenic
66
VUS
5
Likely Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
85
0
85
Likely Pathogenic
0
0
4
0
4
VUS
0
48
18
0
66
Likely Benign
0
5
0
0
5
Benign
0
0
0
0
0
Conflicting
—1
Total0531070161

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

View in ClinVar →

Protein Context — Lollipop Plot

SLX9 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
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 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
A Novel G-Quadruplex Binding Protein in Yeast-Slx9.
Götz S et al.·Molecules
2019Open Access
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