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FANCF (Fanconi anemia, complementation group F)

Written2002-06Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)FAF
Other alias
HGNC (Hugo) FANCF
LocusID (NCBI) 2188
Atlas_Id 294
Location 11p14.3  [Link to chromosome band 11p14]
Location_base_pair Starts at 22622533 and ends at 22625841 bp from pter ( according to hg19-Feb_2009)  [Mapping FANCF.png]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2016)		CC2D2A (4p15.32) / FANCF (11p14.3)

DNA/RNA

Description 1 exon; 1124 bp open reading frame

Protein

Description 374 amino acids ; 42 kDa
Expression weak;
Localisation predominantly nuclear
Function part of the FA complex with FANCA, FANCC, FANCE, and FANCG; this complex is only found in the nucleus.
  • FANCA and FANCG form a complex in the cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated ) FANCD2, downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the non-ubiquinated form.
    • Homology ROM (prokaryote)

    Implicated in

    Note
      
    Entity Fanconi anaemia (FA); FANCF is implicated in the FA complementation group F; it represents about 2-3% of FA cases
    Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia and squamous cell carcinoma)
    Prognosis Fanconi anaemia's prognosis is poor; mean survival is 20 years: patients die of bone marrow failure (infections, haemorrhages), leukaemia, or solid cancer.
  • It has recently been shown that significant phenotypic differences were found between the various complementation groups. Patients from the rare groups FA-D, FA-E, and FA-F had somatic abnormalities more frequently.
    • Cytogenetics Spontaneously enhanced chromatid-type aberrations (breaks, gaps, interchanges; increased rate of breaks compared to control, when induced by specific clastogens known as DNA cross-linking agents (e.g. mitomycin C, diepoxybutane).
      

    Bibliography

    Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia.
    Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J
    Human molecular genetics. 2002 ; 11 (4) : 439-444.
    PMID 11854176
     
    Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group.
    Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG
    Blood. 2000 ; 96 (13) : 4064-4070.
    PMID 11110674
     
    Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway.
    Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD
    Molecular cell. 2001 ; 7 (2) : 249-262.
    PMID 11239454
     
    Fanconi anemia and DNA repair.
    Grompe M, D'Andrea A
    Human molecular genetics. 2001 ; 10 (20) : 2253-2259.
    PMID 11673408
     
    Correction of cross-linker sensitivity of Fanconi anemia group F cells by CD33-mediated protein transfer.
    Holmes RK, Harutyunyan K, Shah M, Joenje H, Youssoufian H
    Blood. 2001 ; 98 (13) : 3817-3822.
    PMID 11739191
     
    Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway.
    Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG
    Human molecular genetics. 2001 ; 10 (4) : 423-429.
    PMID 11157805
     
    Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner.
    Qiao F, Moss A, Kupfer GM
    The Journal of biological chemistry. 2001 ; 276 (26) : 23391-23396.
    PMID 11297559
     
    Function of the Fanconi anemia pathway in Fanconi anemia complementation group F and D1 cells.
    Siddique MA, Nakanishi K, Taniguchi T, Grompe M, D'Andrea AD
    Experimental hematology. 2001 ; 29 (12) : 1448-1455.
    PMID 11750104
     
    Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes.
    Yamashita T, Nakahata T
    International journal of hematology. 2001 ; 74 (1) : 33-41.
    PMID 11530803
     
    The Fanconi anemia protein FANCF forms a nuclear complex with FANCA, FANCC and FANCG.
    de Winter JP, van der Weel L, de Groot J, Stone S, Waisfisz Q, Arwert F, Scheper RJ, Kruyt FA, Hoatlin ME, Joenje H
    Human molecular genetics. 2000 ; 9 (18) : 2665-2674.
    PMID 11063725
     

    Citation

    This paper should be referenced as such :
    Huret, JL
    FANCF (Fanconi anemia, complementation group F)
    Atlas Genet Cytogenet Oncol Haematol. 2002;6(4):281-282.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/FANCFID294.html

    Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 2 ]
      Fanconi anemia Familial Myeloproliferative Disorders

    External links

    Nomenclature
    HGNC (Hugo)FANCF   3587
    LRG (Locus Reference Genomic)LRG_527
    Cards
    AtlasFANCFID294
    Entrez_Gene (NCBI)FANCF  2188  Fanconi anemia complementation group F
    AliasesFAF
    GeneCards (Weizmann)FANCF
    Ensembl hg19 (Hinxton)ENSG00000183161 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000183161 [Gene_View]  chr11:22622533-22625841 [Contig_View]  FANCF [Vega]
    ICGC DataPortalENSG00000183161
    TCGA cBioPortalFANCF
    AceView (NCBI)FANCF
    Genatlas (Paris)FANCF
    WikiGenes2188
    SOURCE (Princeton)FANCF
    Genetics Home Reference (NIH)FANCF
    Genomic and cartography
    GoldenPath hg38 (UCSC)FANCF  -     chr11:22622533-22625841 -  11p14.3   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)FANCF  -     11p14.3   [Description]    (hg19-Feb_2009)
    EnsemblFANCF - 11p14.3 [CytoView hg19]  FANCF - 11p14.3 [CytoView hg38]
    Mapping of homologs : NCBIFANCF [Mapview hg19]  FANCF [Mapview hg38]
    OMIM189960   603467   613897   
    Gene and transcription
    Genbank (Entrez)AF181994 AF181995 AK001716 AK023153 AK223277
    RefSeq transcript (Entrez)NM_022725
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)FANCF
    Cluster EST : UnigeneHs.632151 [ NCBI ]
    CGAP (NCI)Hs.632151
    Alternative Splicing GalleryENSG00000183161
    Gene ExpressionFANCF [ NCBI-GEO ]   FANCF [ EBI - ARRAY_EXPRESS ]   FANCF [ SEEK ]   FANCF [ MEM ]
    Gene Expression Viewer (FireBrowse)FANCF [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)2188
    GTEX Portal (Tissue expression)FANCF
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtQ9NPI8   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtQ9NPI8  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProQ9NPI8
    Splice isoforms : SwissVarQ9NPI8
    PhosPhoSitePlusQ9NPI8
    Domains : Interpro (EBI)FANCF   
    Domain families : Pfam (Sanger)
    Domain families : Pfam (NCBI)
    Domain structure : Prodom (Prabi Lyon)PD321645 (PD321645)   
    Conserved Domain (NCBI)FANCF
    DMDM Disease mutations2188
    Blocks (Seattle)FANCF
    PDB (SRS)2IQC   
    PDB (PDBSum)2IQC   
    PDB (IMB)2IQC   
    PDB (RSDB)2IQC   
    Structural Biology KnowledgeBase2IQC   
    SCOP (Structural Classification of Proteins)2IQC   
    CATH (Classification of proteins structures)2IQC   
    SuperfamilyQ9NPI8
    Human Protein AtlasENSG00000183161
    Peptide AtlasQ9NPI8
    HPRD04589
    IPIIPI00009290   IPI00816297   
    Protein Interaction databases
    DIP (DOE-UCLA)Q9NPI8
    IntAct (EBI)Q9NPI8
    FunCoupENSG00000183161
    BioGRIDFANCF
    STRING (EMBL)FANCF
    ZODIACFANCF
    Ontologies - Pathways
    QuickGOQ9NPI8
    Ontology : AmiGOovarian follicle development  molecular_function  protein binding  nucleoplasm  spermatogenesis  biological_process  protein ubiquitination  interstrand cross-link repair  Fanconi anaemia nuclear complex  ubiquitin protein ligase activity  
    Ontology : EGO-EBIovarian follicle development  molecular_function  protein binding  nucleoplasm  spermatogenesis  biological_process  protein ubiquitination  interstrand cross-link repair  Fanconi anaemia nuclear complex  ubiquitin protein ligase activity  
    Pathways : BIOCARTABRCA1-dependent Ub-ligase activity [Genes]    Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility [Genes]   
    Pathways : KEGGFanconi anemia pathway   
    REACTOMEQ9NPI8 [protein]
    REACTOME PathwaysR-HSA-6783310 [pathway]   
    NDEx NetworkFANCF
    Atlas of Cancer Signalling NetworkFANCF
    Wikipedia pathwaysFANCF
    Orthology - Evolution
    OrthoDB2188
    GeneTree (enSembl)ENSG00000183161
    Phylogenetic Trees/Animal Genes : TreeFamFANCF
    HOVERGENQ9NPI8
    HOGENOMQ9NPI8
    Homologs : HomoloGeneFANCF
    Homology/Alignments : Family Browser (UCSC)FANCF
    Gene fusions - Rearrangements
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerFANCF [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)FANCF
    dbVarFANCF
    ClinVarFANCF
    1000_GenomesFANCF 
    Exome Variant ServerFANCF
    ExAC (Exome Aggregation Consortium)FANCF (select the gene name)
    Genetic variants : HAPMAP2188
    Genomic Variants (DGV)FANCF [DGVbeta]
    DECIPHERFANCF [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisFANCF 
    Mutations
    ICGC Data PortalFANCF 
    TCGA Data PortalFANCF 
    Broad Tumor PortalFANCF
    OASIS PortalFANCF [ Somatic mutations - Copy number]
    Cancer Gene: CensusFANCF 
    Somatic Mutations in Cancer : COSMICFANCF  [overview]  [genome browser]  [tissue]  [distribution]  
    Mutations and Diseases : HGMDFANCF
    LOVD (Leiden Open Variation Database)Whole genome datasets
    LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
    LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
    LOVD (Leiden Open Variation Database)Fanconi anemia database
    BioMutasearch FANCF
    DgiDB (Drug Gene Interaction Database)FANCF
    DoCM (Curated mutations)FANCF (select the gene name)
    CIViC (Clinical Interpretations of Variants in Cancer)FANCF (select a term)
    intoGenFANCF
    NCG5 (London)FANCF
    Cancer3DFANCF(select the gene name)
    Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    Diseases
    OMIM189960    603467    613897   
    Orphanet634   
    MedgenFANCF
    Genetic Testing Registry FANCF
    NextProtQ9NPI8 [Medical]
    TSGene2188
    GENETestsFANCF
    Target ValidationFANCF
    Huge Navigator FANCF [HugePedia]
    snp3D : Map Gene to Disease2188
    BioCentury BCIQFANCF
    ClinGenFANCF
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD2188
    Chemical/Pharm GKB GenePA28001
    Clinical trialFANCF
    Miscellaneous
    canSAR (ICR)FANCF (select the gene name)
    Other databaseFanconi anemia mutation database
    Probes
    Litterature
    PubMed61 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineFANCF
    EVEXFANCF
    GoPubMedFANCF
    iHOPFANCF
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

    © Atlas of Genetics and Cytogenetics in Oncology and Haematology
    indexed on : Fri Jun 30 11:06:34 CEST 2017
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    For comments and suggestions or contributions, please contact us

    jlhuret@AtlasGeneticsOncology.org.