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    FAN1 FANCD2 and FANCI associated nuclease 1 [ Homo sapiens (human) ]

    Gene ID: 22909, updated on 4-Jan-2025

    Summary

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    Official Symbol
    FAN1provided by HGNC
    Official Full Name
    FANCD2 and FANCI associated nuclease 1provided by HGNC
    Primary source
    HGNC:HGNC:29170
    See related
    Ensembl:ENSG00000198690 MIM:613534; AllianceGenome:HGNC:29170
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KMIN; hFAN1; MTMR15; KIAA1018
    Summary
    This gene plays a role in DNA interstrand cross-link repair and encodes a protein with 5' flap endonuclease and 5'-3' exonuclease activity. Mutations in this gene cause karyomegalic interstitial nephritis. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in skin (RPKM 6.7), brain (RPKM 6.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FAN1 in Genome Data Viewer
    Location:
    15q13.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (30903852..30943108)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (28697834..28737186)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (31196055..31235311)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene endonuclease domain containing 1 pseudogene Neighboring gene HERC2 pseudogene 10 Neighboring gene MPRA-validated peak2284 silencer Neighboring gene MPRA-validated peak2285 silencer Neighboring gene TMEM183A pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31195700-31196697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31201877-31202376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31209335-31209834 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31214641-31215582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31215583-31216523 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31219875-31220375 Neighboring gene myotubularin related protein 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31246205-31246731 Neighboring gene RNA, U6 small nuclear 466, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:31283406-31283928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:31283929-31284450 Neighboring gene Sharpr-MPRA regulatory region 8183 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:31318084-31319283 Neighboring gene uncharacterized LOC105370752 Neighboring gene transient receptor potential cation channel subfamily M member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Common variants in FAN1, located in 15q13.3, confer risk for schizophrenia and bipolar disorder in Han Chinese. Jian X, et al. Prog Neuropsychopharmacol Biol Psychiatry, 2020 Dec 20. PMID 32450113
    2. Phenotypic and Genotypic Features of the FAN1 Mutation-Related Disease in a Large Hungarian Family. Császár I, et al. Int J Mol Sci, 2024 May 29. PMID 38892095, Free PMC Article
    3. Germline Mutations in FAN1 Cause Hereditary Colorectal Cancer by Impairing DNA Repair. Seguí N, et al. Gastroenterology, 2015 Sep. PMID 26052075
    4. Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer. Zhao Q, et al. Nat Commun, 2014 Dec 11. PMID 25500724, Free PMC Article
    5. Structural and functional relationships of FAN1. Jin H, et al. DNA Repair (Amst), 2017 Aug. PMID 28623094

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. New familial cases of karyomegalic interstitial nephritis with mutations in the FAN1 gene.
      Title: New familial cases of karyomegalic interstitial nephritis with mutations in the FAN1 gene.
    2. Phenotypic and Genotypic Features of the FAN1 Mutation-Related Disease in a Large Hungarian Family.
      Title: Phenotypic and Genotypic Features of the FAN1 Mutation-Related Disease in a Large Hungarian Family.
    3. Posttranscriptional regulation of FAN1 by miR-124-3p at rs3512 underlies onset-delaying genetic modification in Huntington's disease.
      Title: Posttranscriptional regulation of FAN1 by miR-124-3p at rs3512 underlies onset-delaying genetic modification in Huntington's disease.
    4. FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism.
      Title: FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism.
    5. Persistent DNA damage underlies tubular cell polyploidization and progression to chronic kidney disease in kidneys deficient in the DNA repair protein FAN1.
      Title: Persistent DNA damage underlies tubular cell polyploidization and progression to chronic kidney disease in kidneys deficient in the DNA repair protein FAN1.
    6. Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset.
      Title: Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset.
    7. New insights on familial colorectal cancer type X syndrome.
      Title: New insights on familial colorectal cancer type X syndrome.
    8. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.
      Title: FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.
    9. FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability.
      Title: FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability.
    10. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders.
      Title: FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders.
    Submit: New GeneRIF Correction See all GeneRIFs (37)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Karyomegalic interstitial nephritis
    MedGen: C3553774 OMIM: 614817 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp451H236, DKFZp686K16147

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-3' exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-3' exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5'-flap endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-flap endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables flap-structured DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables flap-structured DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables phosphodiesterase I activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin-modified protein reader activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in double-strand break repair via homologous recombination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in interstrand cross-link repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in interstrand cross-link repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nucleotide-excision repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nucleotide-excision repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    fanconi-associated nuclease 1
    Names
    FANCD2/FANCI-associated nuclease 1
    coiled-coil domain-containing protein MTMR15
    fanconi anemia associated nuclease 1
    myotubularin-related protein 15
    NP_001139566.1
    NP_001139567.1
    NP_001139568.1
    NP_055782.3
    XP_011519672.1
    XP_011519674.1
    XP_016877502.1
    XP_024305642.1
    XP_047288206.1
    XP_054185977.1
    XP_054185978.1
    XP_054185979.1
    XP_054185980.1
    XP_054185981.1
    XP_054187714.1
    XP_054187715.1
    XP_054187716.1
    XP_054187717.1
    XP_054187718.1
    XP_054233499.1
    XP_054233500.1
    XP_054233501.1
    XP_054233502.1
    XP_054233503.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_032946.2 RefSeqGene

      Range
      5064..44257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001146094.2 → NP_001139566.1  fanconi-associated nuclease 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (b) has a distinct C-terminus and is shorter than isoform a. Variants 2, 3 and 4 encode the same isoform (b).
      Source sequence(s)
      AK290987, BC044890, BX647391
      Consensus CDS
      CCDS58344.1
      UniProtKB/TrEMBL
      X5D9F0
      Related
      ENSP00000454544.1, ENST00000565466.5
      Conserved Domains (1) summary
      smart00734
      Location:41 → 62
      ZnF_Rad18; Rad18-like CCHC zinc finger

    2. NM_001146095.1 → NP_001139567.1  fanconi-associated nuclease 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR, and 3' coding region, compared to variant 1. The resulting isoform (b) has a distinct C-terminus and is shorter than isoform a. Variants 2, 3 and 4 encode the same isoform (b).
      Source sequence(s)
      BC044890, BC047882
      Consensus CDS
      CCDS58344.1
      UniProtKB/TrEMBL
      X5D9F0
      Related
      ENSP00000455983.1, ENST00000561594.5
      Conserved Domains (1) summary
      smart00734
      Location:41 → 62
      ZnF_Rad18; Rad18-like CCHC zinc finger

    3. NM_001146096.2 → NP_001139568.1  fanconi-associated nuclease 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, 3' UTR, and 3' coding region, compared to variant 1. The resulting isoform (b) has a distinct C-terminus and is shorter than isoform a. Variants 2, 3 and 4 encode the same isoform (b).
      Source sequence(s)
      BC044890, BP310263, BX647391
      Consensus CDS
      CCDS58344.1
      UniProtKB/TrEMBL
      X5D9F0
      Related
      ENSP00000454223.1, ENST00000561607.6
      Conserved Domains (1) summary
      smart00734
      Location:41 → 62
      ZnF_Rad18; Rad18-like CCHC zinc finger

    4. NM_014967.5 → NP_055782.3  fanconi-associated nuclease 1 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AB023235, BC044890, CR936727, CR936734, DA841207
      Consensus CDS
      CCDS32186.1
      UniProtKB/Swiss-Prot
      A8K4M2, Q86WU8, Q9Y2M0
      UniProtKB/TrEMBL
      D9MXF4
      Related
      ENSP00000354497.4, ENST00000362065.9
      Conserved Domains (2) summary
      smart00734
      Location:41 → 62
      ZnF_Rad18; Rad18-like CCHC zinc finger
      pfam08774
      Location:894 → 1008
      VRR_NUC; VRR-NUC domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      30903852..30943108
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521370.3 → XP_011519672.1  fanconi-associated nuclease 1 isoform X2

      UniProtKB/TrEMBL
      A0A590UKC0
      Related
      ENSP00000499780.1, ENST00000664837.1
      Conserved Domains (1) summary
      pfam08774
      Location:500 → 614
      VRR_NUC; VRR-NUC domain

    2. XM_047432250.1 → XP_047288206.1  fanconi-associated nuclease 1 isoform X1

      UniProtKB/TrEMBL
      D9MXF4
      Related
      ENST00000602886.2

    3. XM_011521372.3 → XP_011519674.1  fanconi-associated nuclease 1 isoform X4

      UniProtKB/TrEMBL
      X5D9F0
      Conserved Domains (1) summary
      smart00734
      Location:41 → 62
      ZnF_Rad18; Rad18-like CCHC zinc finger

    4. XM_024449874.2 → XP_024305642.1  fanconi-associated nuclease 1 isoform X3

      UniProtKB/TrEMBL
      A0A590UKC0
      Conserved Domains (1) summary
      pfam08774
      Location:499 → 613
      VRR_NUC; VRR-NUC domain

    5. XM_017022013.2 → XP_016877502.1  fanconi-associated nuclease 1 isoform X5

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_011332701.1 Reference GRCh38.p14 PATCHES

      Range
      3077132..3116385
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331740.1 → XP_054187715.1  fanconi-associated nuclease 1 isoform X2

      UniProtKB/TrEMBL
      A0A590UKC0

    2. XM_054331739.1 → XP_054187714.1  fanconi-associated nuclease 1 isoform X1

      UniProtKB/TrEMBL
      D9MXF4

    3. XM_054331742.1 → XP_054187717.1  fanconi-associated nuclease 1 isoform X4

      UniProtKB/TrEMBL
      X5D9F0

    4. XM_054331741.1 → XP_054187716.1  fanconi-associated nuclease 1 isoform X3

      UniProtKB/TrEMBL
      A0A590UKC0

    5. XM_054331743.1 → XP_054187718.1  fanconi-associated nuclease 1 isoform X5

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      3189584..3228837
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330003.1 → XP_054185978.1  fanconi-associated nuclease 1 isoform X2

      UniProtKB/TrEMBL
      A0A590UKC0

    2. XM_054330002.1 → XP_054185977.1  fanconi-associated nuclease 1 isoform X1

      UniProtKB/TrEMBL
      D9MXF4

    3. XM_054330005.1 → XP_054185980.1  fanconi-associated nuclease 1 isoform X4

      UniProtKB/TrEMBL
      X5D9F0

    4. XM_054330004.1 → XP_054185979.1  fanconi-associated nuclease 1 isoform X3

      UniProtKB/TrEMBL
      A0A590UKC0

    5. XM_054330006.1 → XP_054185981.1  fanconi-associated nuclease 1 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      28697834..28737186
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377525.1 → XP_054233500.1  fanconi-associated nuclease 1 isoform X2

      UniProtKB/TrEMBL
      A0A590UKC0

    2. XM_054377524.1 → XP_054233499.1  fanconi-associated nuclease 1 isoform X1

      UniProtKB/TrEMBL
      D9MXF4

    3. XM_054377527.1 → XP_054233502.1  fanconi-associated nuclease 1 isoform X4

      UniProtKB/TrEMBL
      X5D9F0

    4. XM_054377526.1 → XP_054233501.1  fanconi-associated nuclease 1 isoform X3

      UniProtKB/TrEMBL
      A0A590UKC0

    5. XM_054377528.1 → XP_054233503.1  fanconi-associated nuclease 1 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2M0.4 GenPept UniProtKB/Swiss-Prot:Q9Y2M0

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