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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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GEN1
GEN1 structure-specific endonuclease
Chromosome 2 · 2p24.2
NCBI Gene: 348654Ensembl: ENSG00000178295.16HGNC: HGNC:26881UniProt: Q17RS7
54PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHomologous Recombination
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
resolution of DNA recombination intermediatespositive regulation of mitotic cell cycle spindle assembly checkpointfour-way junction DNA bindingresolution of mitotic recombination intermediatesstomach diseasesign or symptombenign prostatic hyperplasiaInherited cancer-predisposing syndrome
✦AI Summary

GEN1 is a structure-specific endonuclease that resolves Holliday junctions (HJs)—four-way DNA intermediates formed during homologous recombination and DNA repair—by introducing symmetrically related cuts to produce ligatable nicked duplex products 1. The enzyme functions as a largely monomeric protein that dimerizes on HJ substrates, with first-strand cleavage being rate-limiting and second-strand cleavage occurring rapidly 1. Beyond HJ resolution, GEN1 exhibits endonuclease activity on 5'-flap and replication fork substrates 2, and recently was shown to promote common fragile site (CFS) expression by cleaving under-replicated DNA, indicating a dual role in resolving both recombination and replication intermediates 3. GEN1 contains a unique chr2 that directly contacts DNA and is essential for catalytic activity, distinguishing it within the Rad2/XPG nuclease family 1. Functionally, GEN1 is required for cell viability in the absence of other HJ resolvase activities, operating redundantly with SLX4-associated nucleases 2. Clinically, rare deleterious GEN1 variants are associated with congenital anomalies of the kidney and urinary tract (CAKUT) through impaired protein stability and enzymatic activity 4, and GEN1 variants show nominal evidence of association with aggressive prostate cancer 5.

Sources cited
1
GEN1 structure, chromodomain function in DNA recognition, dimerization mechanism, and symmetrical HJ cleavage producing ligatable products
PMID: 26682650
2
GEN1 activity on HJs and replication fork substrates; redundancy with SLX4-associated nucleases for cell viability
PMID: 24080495
3
GEN1 promotes common fragile site expression and processes under-replicated DNA, indicating dual role in replication and recombination intermediates
PMID: 36729836
4
GEN1 rare variants impair protein stability and enzymatic activity, associated with human CAKUT
PMID: 38654324
5
GEN1 variants show nominal evidence of association with aggressive prostate cancer
PMID: 37733366
Disease Associationsⓘ20
stomach diseaseOpen Targets
0.32Weak
sign or symptomOpen Targets
0.27Weak
benign prostatic hyperplasiaOpen Targets
0.16Weak
hereditary neoplastic syndromeOpen Targets
0.15Weak
Inherited cancer-predisposing syndromeOpen Targets
0.15Weak
metabolic diseaseOpen Targets
0.08Suggestive
hyperlipidemiaOpen Targets
0.07Suggestive
congenital anomaly of kidney and urinary tractOpen Targets
0.07Suggestive
gastric cancerOpen Targets
0.07Suggestive
ovarian cancerOpen Targets
0.06Suggestive
breast cancerOpen Targets
0.06Suggestive
alcohol drinkingOpen Targets
0.06Suggestive
Genetic renal or urinary tract malformationOpen Targets
0.05Suggestive
familial vesicoureteral refluxOpen Targets
0.05Suggestive
hypothyroidismOpen Targets
0.05Suggestive
renal hypodysplasia/aplasia 3Open Targets
0.05Suggestive
congenital hydronephrosisOpen Targets
0.04Suggestive
urofacial syndrome 2Open Targets
0.04Suggestive
congenital anomalies of kidney and urinary tract 1Open Targets
0.04Suggestive
Ochoa syndromeOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
BARD1Protein interaction100%WRNProtein interaction91%DNA2Protein interaction89%MUS81Protein interaction89%SLX4Protein interaction89%EME1Protein interaction89%
Tissue Expression6 tissues
Bone Marrow
100%
Liver
44%
Heart
18%
Lung
14%
Brain
7%
Ovary
6%
Gene Interaction Network
Click a node to explore
GEN1BARD1WRNDNA2MUS81SLX4EME1
PROTEIN STRUCTURE
Preparing viewer…
PDB5T9J · 3.00 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.42LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.98 [0.69–1.42]
RankingsWhere GEN1 stands among ~20K protein-coding genes
  • #8,318of 20,598
    Most Researched54
  • #14,656of 17,882
    Most Constrained (LOEUF)1.42
Genes detectedGEN1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
GEN1 as a risk factor for human congenital anomalies of the kidney and urinary tract.
PMID: 38654324
Hum Genomics · 2024
1.00
2
Holliday junction resolvases.
PMID: 25183833
Cold Spring Harb Perspect Biol · 2014
0.90
3
Germline Sequencing Analysis to Inform Clinical Gene Panel Testing for Aggressive Prostate Cancer.
PMID: 37733366
JAMA Oncol · 2023
0.80
4
Human GEN1 and the SLX4-associated nucleases MUS81 and SLX1 are essential for the resolution of replication-induced Holliday junctions.
PMID: 24080495
Cell Rep · 2013
0.70
5
Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage.
PMID: 26682650
Elife · 2015
0.60