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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SLX4
SLX4 structure-specific endonuclease subunit
Chromosome 16 · 16p13.3
NCBI Gene: 84464Ensembl: ENSG00000188827.12HGNC: HGNC:23845UniProt: Q8IY92
114PubMed Papers
21Diseases
0Drugs
154Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHomologous RecombinationHub Gene
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
response to intra-S DNA damage checkpoint signalingchromosome, telomeric regionHolliday junction resolvase complexERCC4-ERCC1 complexFanconi anemia complementation group PFanconi anemiaBone marrow hypocellularityacute myeloid leukemia
✦AI Summary

SLX4 is a multifunctional scaffolding protein that coordinates structure-selective endonucleases to maintain genome stability 1. It acts as a regulatory platform for three endonucleases—XPF-ERCC1, MUS81-EME1, and SLX1—directing their nucleolytic activities toward specific DNA substrates 2. SLX4 resolves DNA secondary structures arising from replication and recombination, including Holliday junctions and DNA flap structures, and is essential for interstrand crosslink repair and homologous recombination 1. The protein also coordinates with MutSβ in mismatch repair and trinucleotide repeat stability 3. Beyond DNA repair, SLX4 regulates telomere maintenance and responds to replication stress 1. Pathologically, SLX4 contributes to Fanconi anemia (FANCP) when mutated 4, and recent evidence links SLX4 variants to premature ovarian insufficiency through impaired meiotic function 5. Notably, the FA pathway—including SLX4—paradoxically drives chr16 in cancer cells, generating complex genomic rearrangements that confer drug resistance 4. SLX4 is also transcriptionally regulated during DNA damage responses, with SOX9 binding its promoter to enhance expression in cancer contexts 6. These diverse roles establish SLX4 as a critical hub for genome stability maintenance.

Sources cited
1
SLX4 acts as a scaffold coordinating XPF-ERCC1, MUS81-EME1, and SLX1 endonucleases in DNA repair, interstrand crosslink repair, homologous recombination, and replication stress response
PMID: 30284473
2
SLX4 is a multidomain platform regulating three structure-selective nucleases with distinct substrate specificities and activation mechanisms
PMID: 26827285
3
SLX4 coordinates with MutSβ in DNA mismatch repair, trinucleotide repeat stability, crosslink repair and recombination
PMID: 33596761
4
SLX4-XPF-ERCC1 endonuclease induces chromothripsis in cancer cells, generating complex rearrangements and drug resistance
PMID: 39181133
5
SLX4 variants are associated with premature ovarian insufficiency through impaired meiosis
PMID: 36732629
6
SOX9 transcriptionally regulates SLX4 to enhance DNA damage repair in ovarian cancer
PMID: 40240356
Disease Associationsⓘ21
Fanconi anemia complementation group POpen Targets
0.81Strong
Fanconi anemiaOpen Targets
0.78Strong
Bone marrow hypocellularityOpen Targets
0.50Moderate
acute myeloid leukemiaOpen Targets
0.50Moderate
Menkes diseaseOpen Targets
0.50Moderate
myelodysplastic syndromeOpen Targets
0.50Moderate
Fanconi anemia complementation group AOpen Targets
0.49Moderate
type 2 diabetes mellitusOpen Targets
0.36Weak
liver diseaseOpen Targets
0.34Weak
restless legs syndromeOpen Targets
0.34Weak
diabetes mellitusOpen Targets
0.31Weak
glioblastoma multiformeOpen Targets
0.27Weak
genetic disorderOpen Targets
0.20Weak
hereditary neoplastic syndromeOpen Targets
0.16Weak
Inherited cancer-predisposing syndromeOpen Targets
0.16Weak
breast cancerOpen Targets
0.15Weak
Intellectual disabilityOpen Targets
0.15Weak
pituitary stalk interruption syndromeOpen Targets
0.12Weak
Hereditary breast cancerOpen Targets
0.12Weak
hereditary breast carcinomaOpen Targets
0.11Weak
Fanconi anemia complementation group PUniProt
Pathogenic Variants154
NM_032444.4(SLX4):c.2808_2809del (p.Ala938fs)Pathogenic
Fanconi anemia|Fanconi anemia complementation group P
★★☆☆2025→ Residue 938
NM_032444.4(SLX4):c.860del (p.Ser287fs)Pathogenic
Fanconi anemia|Fanconi anemia complementation group P
★★☆☆2025→ Residue 287
NM_032444.4(SLX4):c.4089_4090del (p.Asp1365fs)Pathogenic
not provided|Fanconi anemia|Fanconi anemia complementation group P
★★☆☆2025→ Residue 1365
NM_032444.4(SLX4):c.4823C>G (p.Ser1608Ter)Pathogenic
not provided|Fanconi anemia|SLX4-related disorder|Fanconi anemia complementation group P
★★☆☆2025→ Residue 1608
NM_032444.4(SLX4):c.2469G>A (p.Trp823Ter)Pathogenic
Fanconi anemia|Fanconi anemia complementation group P
★★☆☆2025→ Residue 823
NM_032444.4(SLX4):c.1163+2dupPathogenic
Fanconi anemia complementation group P|Fanconi anemia|not provided
★★☆☆2025
NM_032444.4(SLX4):c.3601C>T (p.Gln1201Ter)Pathogenic
Fanconi anemia complementation group P|Fanconi anemia
★★☆☆2025→ Residue 1201
NM_032444.4(SLX4):c.5229dup (p.Gln1744fs)Likely pathogenic
Fanconi anemia|not provided
★★☆☆2025→ Residue 1744
NM_032444.4(SLX4):c.2137C>T (p.Arg713Ter)Pathogenic
Fanconi anemia|Fanconi anemia complementation group P|not provided
★★☆☆2025→ Residue 713
NM_032444.4(SLX4):c.514del (p.Leu172fs)Pathogenic
Fanconi anemia complementation group P|Fanconi anemia
★★☆☆2025→ Residue 172
NM_032444.4(SLX4):c.59del (p.Leu20fs)Pathogenic
Fanconi anemia|not provided
★★☆☆2025→ Residue 20
NM_032444.4(SLX4):c.2384C>G (p.Ser795Ter)Pathogenic
not provided|Fanconi anemia
★★☆☆2025→ Residue 795
NM_032444.4(SLX4):c.1684-1G>ALikely pathogenic
Fanconi anemia|Fanconi anemia complementation group P
★★☆☆2025
NM_032444.4(SLX4):c.4761dup (p.Lys1588Ter)Pathogenic
Fanconi anemia complementation group P|Fanconi anemia
★★☆☆2025→ Residue 1588
NM_032444.4(SLX4):c.1125del (p.Ala376fs)Pathogenic
Fanconi anemia|not provided
★★☆☆2025→ Residue 376
NM_032444.4(SLX4):c.1116_1117insT (p.Leu373fs)Pathogenic
Fanconi anemia|not provided
★★☆☆2025→ Residue 373
NM_032444.4(SLX4):c.3895_3896del (p.Arg1299fs)Pathogenic
Fanconi anemia|Fanconi anemia complementation group P
★★☆☆2024→ Residue 1299
NM_032444.4(SLX4):c.425del (p.Gly142fs)Pathogenic
Fanconi anemia complementation group P|Fanconi anemia
★★☆☆2024→ Residue 142
NM_032444.4(SLX4):c.3619_3643del (p.Pro1207fs)Pathogenic
not provided|Fanconi anemia|Fanconi anemia complementation group P
★★☆☆2024→ Residue 1207
NM_032444.4(SLX4):c.1693C>T (p.Gln565Ter)Likely pathogenic
not provided
★★☆☆2024→ Residue 565
View on ClinVar ↗
Related Genes
ERCC1Protein interaction100%FANCAProtein interaction100%FANCCProtein interaction100%FANCD2Protein interaction100%FANCBProtein interaction100%FANCFProtein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
64%
Lung
61%
Liver
49%
Ovary
47%
Heart
34%
Gene Interaction Network
Click a node to explore
SLX4ERCC1FANCAFANCCFANCD2FANCBFANCF
PROTEIN STRUCTURE
Preparing viewer…
PDB7BU5 · 1.80 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.90LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.77 [0.66–0.90]
RankingsWhere SLX4 stands among ~20K protein-coding genes
  • #4,168of 20,598
    Most Researched114 · top quartile
  • #495of 5,498
    Most Pathogenic Variants154 · top 10%
  • #8,059of 17,882
    Most Constrained (LOEUF)0.90
Genes detectedSLX4
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Landscape of pathogenic mutations in premature ovarian insufficiency.
PMID: 36732629
Nat Med · 2023
1.00
2
The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance.
PMID: 39181133
Cell · 2024
0.90
3
Repeat expansions confer WRN dependence in microsatellite-unstable cancers.
PMID: 32999459
Nature · 2020
0.80
4
Coordinated roles of SLX4 and MutSβ in DNA repair and the maintenance of genome stability.
PMID: 33596761
Crit Rev Biochem Mol Biol · 2021
0.70
5
PMID: 20301575
0.60