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FANCA (Fanconi anemia, complementation group A)

Written2012-03Jose Antonio Casado, Juan Antonio Bueren
Hematopoiesis, Gene Therapy, Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas,, Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
This article is an update of :
2002-06Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France
2001-12Hans Joenje
Department of Clinical Genetics, Human Genetics VU University Medical Center Van der Boechorststraat 7, NL-1081 BT Amsterdam, The Netherlands
1998-04Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)


Alias (NCBI)FA
HGNC Alias symbFAA
HGNC Previous nameFACA
HGNC Previous nameFanconi anemia complementation group A
LocusID (NCBI) 2175
Atlas_Id 102
Location 16q24.3  [Link to chromosome band 16q24]
Location_base_pair Starts at 89798354 and ends at 89816647 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping FANCA.png]
  Figure 1. Genomic contex of FANCA gene in chromosome 16. Image adapted from NCBI.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ANKRD11 (16q24.3)::FANCA (16q24.3)FANCA (16q24.3)::CACNA2D4 (12p13.33)FANCA (16q24.3)::FANCA (16q24.3)
PAK1 (11q13.5)::FANCA (16q24.3)SPG7 (16q24.3)::FANCA (16q24.3)


Description 43 exons spanning 80 kb with 4365 bp open reading frame (Lo Ten Foe et al., 1996). The 5-prime region upstream of the putative transcription start site of FANCA has a GC-rich region instead of TATA or CAAT boxes, which is typical of housekeeping genes (Ianzano et al., 1997). Numerous Alu repeats are present in the FANCA gene, suggesting that Alu-mediated recombination may be an important mechanism for the generation of Fanconi anemia-producing mutations.
Transcription Multiple transcrips have been described and two types produces proteins; a 5,5 kb mRNA corresponding to NM_000135.2 (5460 bp) and NM_001018112 (1673 bp) by alternative splicing (no experimental confirmation available).
Pseudogene Not described.


Note Two isoforms with accession number in UniProt; the canonical sequence NP_000126.2 (1455 aa) and NP_001018122.1 (297 aa).
Description 1455 amino acids (163 kDa) conserved in lower vertebrates including zebrafish with 2 nuclear localisation signals (NLS) consensus sequences in N-terminus (Lightfoot et al., 1999), putative peroxidase domain (Ren and Youssoufian, 2001) and a partial leucine zipper in 1069-1090 (Lo Ten Foe et al., 1996), none proven to be functional as such. Despite FANCA protein lack of sequence homologies or motifs that can be assigned to a molecular function, many interactions with other proteins have been described. In this sense, FANCA has a FANCG-binding domain overlapping with NLS region (Waisfisz et al., 1999), a region of interaction with the protein FAAP20 between residues 1095 and 1200 (Ali et al., 2012) or for interaction with BRCA1 through the central part of FANCA protein (aa 740-1083) (Folias et al., 2002).
Through different complexes FANCA can interact with other proteins such as alpha spectrin II, SWI/SNF complex or BLM (DNA-helicase Bloom protein) and other proteins associated with this complex (McMahon et al., 1999; Otsuki et al, 2001; Meetei et al., 2003). FANCA is normally phosphorylated including phosphorylation by ATR-CHK1 on serine 1449 in a process that is required for the formation of the nuclear complex (Collins et al., 2009). FANCA has a consensus sequence for Akt kinase near serine 1149 and its phosphorylation can act as a negative regulator (Otsuki et al., 2002) (Figure 2).
  Figure 2. Scheme of FANCA protein. The sizes of the regions are only approximate.
Expression Wide: brain, liver, placenta, testis, tonsils (mRNA); in mice: protein expression predominant in lymphoid organs, testis, ovary (Van de Vrugt et al., 2000).
Localisation FANCA can be cytoplasmic and nuclear where it exerts its primary function.
Function FANCA is one of the15 known FA proteins that participate in the FA/BRCA pathway which participates in the repair of DNA interstrand cross-links, probably involving homologous recombination and the coordination for other DNA damage repair events, including nucleotide excision repair (NER) and translesion synthesis (Moldovan and D'Andrea, 2009). The FA/BRCA pathway may be divided in three parts; 1) FA core complex (FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL and FANCM) and six associated factors (FAAP100, FAAP24, FAAP20, HES1, MHF1 and MHF2), 2) ID complex (FANCD2 and FANCI) and 3) downstream FA proteins (FANCD1/BRCA2, FANCN/PALB2, FANCJ/BRIP1, FANCP/SLX4, FANCO/RAD51C) (Moldovan and D'Andrea, 2009; Ali et al., 2012) (Figure 3).
Several subcomplex are formed in the cytoplasm and from here FANCB-FANCL-FAAP100 are transported together to the nucleus (Ling et al., 2007). FANCA and FANCG form a complex in the cytoplasm, through an N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex and phosphorylation of FANCA would induce its translocation into the nucleus (Garcia-Higuera et al., 2000; Kruyt et al., 1999). The FA subcomplexes translocates into the nucleus, where FANCE and FANCF are present; and join to the complex (de Winter et al., 2000; kee and D'Andrea, 2010). A large FA core complex is generated with FANCM-FAAP24. Interstrand cross-links are recognized by the FANCM-FAAP24-MHF1/2 complex which recruits the rest of the FA core proteins by interaction between FANCM and FANCF. Because of the ubiquitin E3 ligase activity present in FANCL (Hodson et al., 2011) the heterodimer ID complex formed by FANCD2 and FANCI can be monoubiquitinated and then translocated to chromatin, interacting with downstream proteins in the FA pathway such as FANCD1/BRCA2, FANCN/PALB2, FANCJ/BRIP1, FANCP/SLX4, FANCO/RAD51C and with BRCA1 (Garcia-Higuera et al., 2001) and the nuclease FAN1 (Liu et al., 2010). These downstream FA proteins are involved in DNA repair by homologous recombination (Moldovan and D'Andrea, 2009). In addition to DNA damage, the FA pathway can be activated during S phase of cell cycle. After DNA repair, FANCD2 and FANCI return to the non-ubiquinated form by the action of a complex ubiquitin-specific protease USP1/UAF1 (Nijman et al., 2005) (Figure 3).
Biallelic mutations in FANCA (or in any other gene encoding proteins of the FA core complex) prevent the ubiquitin E3 ligase activity and the monoubiquinitation of FANCD2 and FANCI resulting in a defective FA/BRCA pathway.
  Figure 3. Overview of the FA/BRCA pathway. Fanconi proteins are shown in yellow. Other proteins in the FA core complex necessary for monoubiquitination of the ID complex are shown in blue (FAAP; fanconi anemia associated protein). Downstream proteins involved in the pathway are shown in pink. (ICL: interstrand cross-link). ATR-CHK1 phosphorylates multiple FA and FA-associated proteins including FANCA, FANCE, FANCD2, FANCI and BRCA1. Not all protein interactions are shown and proximity nor imply direct interaction (Adapted from Valeri et al., 2011).
Homology No known complete homology or functional motifs.


Note Epigenetics: Although hypermethylation of the promotor of different FA genes (FANCD1/BRCA2, FANCB, FANCC, FANCL, FANCN and especially in FANCF) has been described in several sporadic malignancies this effect has not been described so far in FANCA (Valeri et al., 2011).
Germinal The number of different pathogenic mutations in FANCA gene is very high. Mutations are heterogeneous; point mutations, splicing mutations, large intragene deletions probably Alu-mediated or insertions have been described (Morgan et al., 1999; Levran et al., 2005). Over 90% of the mutations are private, with about 30% being relatively large deletions. Founder mutations have been described in South Africa and Spanish Gypsies (Tipping et al., 2001; Callen et al., 2005). Unlike mutations in downstream FA genes such as FANCD1/BRCA2 (breast, ovarian, and solid childhood cancer), FANCN/PALB2 (breast cancer) or FANCO/RAD51C (breast and ovarian cancer), FANCJ/BRIP1 (breast cancer and solid childhood cancer), the carriers of monoallelic mutations in FANCA do not seem to have a significant risk of cancer (Garcia and Benitez, 2008). However, It has been recently described in Finnish breast cancer families that FANCA deletions might contribute to breast cancer susceptibility, potentially in combination with other germline mutations (Solyom et al., 2011).
Somatic In FA-A patients, the presence of wild type cells with a restored FANCA function, can be obtained via back mutation, intragenic crossover, compensating deletions/insertions, or gene conversion of either the paternal or maternal allele. This can lead to a selective advantage of corrected cells generating the so-called somatic mosaicism (Gregory et al., 2001; Gross et al., 2002). The clinical significance of this mosaicism is unclear but there are cases that show improvement of their hematological status when the correction involves hematopoietic stem cells. Somatic mutations and epigenetic silencing in some FA genes occur in a variety of cancers in the general population (non-FA patients) (Valeri et al., 2011). In relation to FANCA, deletions or point mutations were found in several sporadic AML (Tischkowitz et al., 2004; Condie et al., 2002).

Implicated in

Entity Fanconi anaemia (FA)
Note FANCA is implicated in the FA complementation group A (FA-A) that is the most frequent complementation group accounting for about 70% of FA cases, although geographical variations may alter the prevalence in some complementation groups (Casado et al., 2007).
Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia and squamous cell carcinoma), progressive bone marrow failure (pancytopenia), and several congenital abnormalities mainly: skin hiperpigmentation, skeletal malformation, small stature or urogenital abnormalities (Auerbach, 2009).
Prognosis Fanconi anaemia's prognosis is poor; mean survival is 20 years: patients die of bone marrow failure (infections, haemorrhages), leukaemia, or solid cancer specially squamous carcinomas (SCC) in adult patients. Hematopoietic stem cell transplantation with a suitable HLA-matched donor is currently the best treatment to cure the aplastic anemia or leukaemia (Gluckman and Wagner, 2008).
It has been shown that significant phenotypic differences were found between the various complementation groups. In FA group A, patients homozygous for null mutations had an earlier onset of anemia and a higher incidence of leukemia than those with mutations producing an altered protein. Patients homozygous for null mutations in FANCA are high-risk groups with a poor hematologic outcome and should be considered as candidates both for frequent monitoring and early therapeutic intervention (Faivre et al., 2000). However, in another recent study, no clinical differences in terms of onset of hematologic disease and number of congenital anomalies were found in patients with expression of a mutant form of FANCA protein compared with patients without expression of the protein (Castella et al., 2011).
Cytogenetics Compared to control cells, an increase of chromatid-type aberrations (breaks, gaps, interchanges; increased rate of breaks) is observed in FA cells when samples are treated with specific clastogens known as DNA inter-strand cross-linking agents (e.g. mitomycin C, diepoxybutane). Theses agents are widely used for FA diagnosis (Auerbach, 1993).


FAAP20: a novel ubiquitin-binding FA nuclear core-complex protein required for functional integrity of the FA-BRCA DNA repair pathway.
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PMID 21273304
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PMID 19109555
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Leuk Lymphoma. 2002 Sep;43(9):1849-53.
PMID 12685843
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PMID 11110674
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PMID 12354784
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PMID 18258506
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Mol Cell. 2001 Feb;7(2):249-62.
PMID 11239454
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PMID 18084332
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PMID 11226273
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PMID 11673408
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PMID 12697994
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J Biol Chem. 2011 Sep 16;286(37):32628-37. Epub 2011 Jul 20.
PMID 21775430
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PMID 9169126
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PMID 20713514
Resistance to mitomycin C requires direct interaction between the Fanconi anemia proteins FANCA and FANCG in the nucleus through an arginine-rich domain.
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J Biol Chem. 1999 Nov 26;274(48):34212-8.
PMID 10567393
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Hum Mutat. 2005 Feb;25(2):142-9.
PMID 15643609
Characterization of regions functional in the nuclear localization of the Fanconi anemia group A protein.
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Hum Mol Genet. 1999 Jun;8(6):1007-15.
PMID 10332032
FAAP100 is essential for activation of the Fanconi anemia-associated DNA damage response pathway.
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EMBO J. 2007 Apr 18;26(8):2104-14. Epub 2007 Mar 29.
PMID 17396147
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Science. 2010 Aug 6;329(5992):693-6. Epub 2010 Jul 29.
PMID 20671156
Expression cloning of a cDNA for the major Fanconi anaemia gene, FAA.
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Nat Genet. 1996 Nov;14(3):320-3.
PMID 8896563
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McMahon LW, Walsh CE, Lambert MW.
J Biol Chem. 1999 Nov 12;274(46):32904-8.
PMID 10551855
A multiprotein nuclear complex connects Fanconi anemia and Bloom syndrome.
Meetei AR, Sechi S, Wallisch M, Yang D, Young MK, Joenje H, Hoatlin ME, Wang W.
Mol Cell Biol. 2003 May;23(10):3417-26.
PMID 12724401
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Annu Rev Genet. 2009;43:223-49.
PMID 19686080
High frequency of large intragenic deletions in the Fanconi anemia group A gene.
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Am J Hum Genet. 1999 Nov;65(5):1330-41.
PMID 10521298
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PMID 15694335
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Hum Mol Genet. 2001 Nov 1;10(23):2651-60.
PMID 11726552
Phosphorylation of Fanconi anemia protein, FANCA, is regulated by Akt kinase.
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PMID 11161829
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Cancer Lett. 2011 Mar 28;302(2):113-8. Epub 2011 Jan 13.
PMID 21236561
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Proc Natl Acad Sci U S A. 2001 May 8;98(10):5734-9.
PMID 11344308
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PMID 14749703
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Clin Transl Oncol. 2011 Apr;13(4):215-21. (REVIEW)
PMID 21493181
A physical complex of the Fanconi anemia proteins FANCG/XRCC9 and FANCA.
Waisfisz Q, de Winter JP, Kruyt FA, de Groot J, van der Weel L, Dijkmans LM, Zhi Y, Arwert F, Scheper RJ, Youssoufian H, Hoatlin ME, Joenje H.
Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10320-5.
PMID 10468606
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de Winter JP, van der Weel L, de Groot J, Stone S, Waisfisz Q, Arwert F, Scheper RJ, Kruyt FA, Hoatlin ME, Joenje H.
Hum Mol Genet. 2000 Nov 1;9(18):2665-74.
PMID 11063725
Cloning and characterization of murine fanconi anemia group A gene: Fanca protein is expressed in lymphoid tissues, testis, and ovary.
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Mamm Genome. 2000 Apr;11(4):326-31.
PMID 10754110


This paper should be referenced as such :
Casado, JA ; Bueren, JA
FANCA (Fanconi anemia, complementation group A)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(9):620-625.
Free journal version : [ pdf ]   [ DOI ]
History of this paper:
Huret, JL. FA1 (Fanconi anaemia 1). Atlas Genet Cytogenet Oncol Haematol. 1998;2(3):81-82.
Joenje, H. FANCA (Fanconi anaemia A). Atlas Genet Cytogenet Oncol Haematol. 2002;6(2):84-86.
Huret, JL. FANCA (Fanconi anaemia complementation group A). Atlas Genet Cytogenet Oncol Haematol. 2002;6(4):272-274.

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

External links

HGNC (Hugo)FANCA   3582
LRG (Locus Reference Genomic)LRG_495
Atlas Explorer : (Salamanque)FANCA
Entrez_Gene (NCBI)FANCA    FA complementation group A
AliasesFA; FA-H; FA1; FAA; 
GeneCards (Weizmann)FANCA
Ensembl hg19 (Hinxton)ENSG00000187741 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000187741 [Gene_View]  ENSG00000187741 [Sequence]  chr16:89798354-89816647 [Contig_View]  FANCA [Vega]
ICGC DataPortalENSG00000187741
Genatlas (Paris)FANCA
Genetics Home Reference (NIH)FANCA
Genomic and cartography
GoldenPath hg38 (UCSC)FANCA  -     chr16:89798354-89816647 -  16q24.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)FANCA  -     16q24.3   [Description]    (hg19-Feb_2009)
GoldenPathFANCA - 16q24.3 [CytoView hg19]  FANCA - 16q24.3 [CytoView hg38]
Genome Data Viewer NCBIFANCA [Mapview hg19]  
OMIM227650   607139   
Gene and transcription
Genbank (Entrez)AK299282 AK301168 AY339878 AY339879 AY339880
RefSeq transcript (Entrez)NM_000135 NM_001018112 NM_001286167 NM_001351830
Consensus coding sequences : CCDS (NCBI)FANCA
Gene Expression Viewer (FireBrowse)FANCA [ Firebrowse - Broad ]
GenevisibleExpression of FANCA in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)2175
GTEX Portal (Tissue expression)FANCA
Human Protein AtlasENSG00000187741-FANCA [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)FANCA
Human Protein Atlas [tissue]ENSG00000187741-FANCA [tissue]
Protein Interaction databases
Ontologies - Pathways
PubMed214 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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