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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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FAN1
FANCD2 and FANCI associated nuclease 1
Chromosome 15 Β· 15q13.3
NCBI Gene: 22909Ensembl: ENSG00000198690.11HGNC: HGNC:29170UniProt: Q9Y2M0
62PubMed Papers
1Diseases
0Drugs
60Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHomologous Recombination
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
double-strand break repair via homologous recombinationnucleoplasmnucleusinterstrand cross-link repairInterstitial nephritis, karyomegalic
✦AI Summary

FAN1 is a 5'-3' exonuclease and endonuclease that functions as a critical nuclease in DNA interstrand crosslink (ICL) repair 1. The protein is recruited to DNA damage sites by monoubiquitinated FANCD2 and operates through a strand-directed nuclease mechanism that cleaves DNA at intervals to excise ICLs from one strand via flanking incisions 2. FAN1 also removes triplet repeat extrusions through a PCNA- and RFC-dependent mechanism, with PCNA conferring strand directionality to the nuclease and requiring physical interaction between these proteins 3. This function is particularly relevant to Huntington's disease, where FAN1 prevents somatic CAG repeat expansion through very short patch excision-repair that competes with mismatch repair proteins 3. Genome-wide association studies identified FAN1 as a genetic modifier of Huntington's disease age of onset, with effects differentially influencing motor and cognitive domains 4. Cell-type-specific analysis reveals that elevated MSH2/MSH3 levels in striatal neurons inhibit FAN1-mediated nucleolytic excision of CAG slip-outs, suggesting a key antagonistic relationship in repeat expansion control 5. FAN1 mutations associate with various cancers and degenerative diseases, underscoring its importance in maintaining chr15 stability 1.

Sources cited
1
FAN1 is a 5' flap structure-specific endonuclease and 5' to 3' exonuclease that resolves ICLs and controls replication fork progression
PMID: 28623094
2
FAN1 acts as a 5'-3' exonuclease anchoring at DNA cut ends, cleaving successively at every third nucleotide to excise ICLs via flanking incisions
PMID: 25430771
3
FAN1 removes triplet repeat extrusions via PCNA- and RFC-dependent mechanism using very short patch excision-repair that competes with mismatch repair
PMID: 37549289
4
FAN1 is a genetic modifier of Huntington's disease age of onset with differential effects on motor and cognitive domains
PMID: 35325614
5
MSH2/MSH3 elevation in striatal neurons inhibits FAN1-mediated excision of CAG slip-outs, antagonistically controlling CAG expansions
PMID: 38291334
Disease Associationsβ“˜1
Interstitial nephritis, karyomegalicUniProt
Pathogenic Variants60
NM_014967.5(FAN1):c.2120G>A (p.Trp707Ter)Pathogenic
Karyomegalic interstitial nephritis
β˜…β˜…β˜†β˜†2025β†’ Residue 707
NM_014967.5(FAN1):c.2616del (p.Asp873fs)Pathogenic
Karyomegalic interstitial nephritis|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 873
NM_014967.5(FAN1):c.1943+1G>APathogenic
Karyomegalic interstitial nephritis|not provided
β˜…β˜…β˜†β˜†2025
NM_014967.5(FAN1):c.922_923del (p.Val308fs)Pathogenic
not provided|Karyomegalic interstitial nephritis
β˜…β˜…β˜†β˜†2025β†’ Residue 308
NM_014967.5(FAN1):c.2128C>T (p.Arg710Ter)Pathogenic
not provided|Karyomegalic interstitial nephritis
β˜…β˜…β˜†β˜†2025β†’ Residue 710
NM_014967.5(FAN1):c.1369C>T (p.Gln457Ter)Pathogenic
Karyomegalic interstitial nephritis
β˜…β˜…β˜†β˜†2025β†’ Residue 457
NM_014967.5(FAN1):c.2260C>T (p.Arg754Ter)Pathogenic
not provided|Karyomegalic interstitial nephritis
β˜…β˜…β˜†β˜†2024β†’ Residue 754
NM_014967.5(FAN1):c.141C>A (p.Cys47Ter)Pathogenic
FAN1-related disorder|Karyomegalic interstitial nephritis
β˜…β˜…β˜†β˜†2024β†’ Residue 47
NM_014967.5(FAN1):c.2245C>T (p.Arg749Ter)Pathogenic
Karyomegalic interstitial nephritis|not provided|FAN1-related disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 749
NM_014967.5(FAN1):c.1899del (p.Cys633fs)Pathogenic
not provided|Kidney failure|Karyomegalic interstitial nephritis
β˜…β˜…β˜†β˜†2024β†’ Residue 633
NM_014967.5(FAN1):c.1480C>T (p.Gln494Ter)Pathogenic
Karyomegalic interstitial nephritis
β˜…β˜†β˜†β˜†2025β†’ Residue 494
NM_014967.5(FAN1):c.2241del (p.Gln748fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 748
NM_014967.5(FAN1):c.289del (p.Asp96_Val97insTer)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 96
NM_014967.5(FAN1):c.2542del (p.Asp848fs)Likely pathogenic
Karyomegalic interstitial nephritis
β˜…β˜†β˜†β˜†2025β†’ Residue 848
NM_014967.5(FAN1):c.2421del (p.Thr808fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 808
NM_014967.5(FAN1):c.322_323del (p.Asn108fs)Pathogenic
Karyomegalic interstitial nephritis
β˜…β˜†β˜†β˜†2024β†’ Residue 108
NM_014967.5(FAN1):c.1606C>T (p.Arg536Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 536
NM_014967.5(FAN1):c.2123G>A (p.Trp708Ter)Likely pathogenic
Karyomegalic interstitial nephritis
β˜…β˜†β˜†β˜†2024β†’ Residue 708
NM_014967.5(FAN1):c.871G>T (p.Glu291Ter)Likely pathogenic
Karyomegalic interstitial nephritis
β˜…β˜†β˜†β˜†2024β†’ Residue 291
NM_014967.5(FAN1):c.31_34del (p.Lys11fs)Likely pathogenic
Karyomegalic interstitial nephritis
β˜…β˜†β˜†β˜†2024β†’ Residue 11
View on ClinVar β†—
Related Genes
MUS81Protein interaction100%SLX1AProtein interaction99%MTMR10Protein interaction95%EME1Protein interaction93%TRPM1Protein interaction85%FAAP24Protein interaction83%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
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FAN1MUS81SLX1AMTMR10EME1TRPM1FAAP24
PROTEIN STRUCTURE
Preparing viewer…
PDB4REC Β· 2.20 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.01LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.85 [0.71–1.01]
RankingsWhere FAN1 stands among ~20K protein-coding genes
  • #7,453of 20,598
    Most Researched62
  • #1,172of 5,498
    Most Pathogenic Variants60 Β· top quartile
  • #9,914of 17,882
    Most Constrained (LOEUF)1.01
Genes detectedFAN1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Potential disease-modifying therapies for Huntington's disease: lessons learned and future opportunities.
PMID: 35716694
Lancet Neurol Β· 2022
1.00
2
Antisense oligonucleotide-mediated MSH3 suppression reduces somatic CAG repeat expansion in Huntington's disease iPSC-derived striatal neurons.
PMID: 39937881
Sci Transl Med Β· 2025
0.90
3
Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability.
PMID: 37827155
Cell Β· 2023
0.80
4
Huntington's Disease Clinical Trials Corner: March 2024.
PMID: 38489195
J Huntingtons Dis Β· 2024
0.70
5
FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism.
PMID: 37549289
Proc Natl Acad Sci U S A Β· 2023
0.60