Human Gene FANCA (uc002fow.1) Description and Page Index
  Description: Homo sapiens Fanconi anemia, complementation group A (FANCA), transcript variant 2, mRNA.
RefSeq Summary (NM_001018112): The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group A. Alternative splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are the most common cause of Fanconi anemia. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr16:89,864,767-89,883,065 Size: 18,299 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr16:89,865,487-89,883,023 Size: 17,537 Coding Exon Count: 11 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:89,864,767-89,883,065)mRNA (may differ from genome)Protein (297 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
Stanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FANCA
CDC HuGE Published Literature: FANCA
Positive Disease Associations: Caffeine , cervical intraepithelial neoplasia grade 3 , Hair Color , Melanosis
Related Studies:
  1. Caffeine
    Marilyn C Cornelis et al. PLoS genetics 2011, Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption., PLoS genetics. [PubMed 21490707]
  2. cervical intraepithelial neoplasia grade 3
    Sophia S Wang , et al. The Journal of infectious diseases 2009 199(1):20-30, Common variants in immune and DNA repair genes and risk for human papillomavirus persistence and progression to cervical cancer., The Journal of infectious diseases 2009 199(1):20-30. [PubMed 19012493]
    Our results require replication but support the role of FANCA variants in cervical cancer susceptibility and of IRF3 in HPV persistence.
  3. Hair Color
    Nicholas Eriksson et al. PLoS genetics 2010, Web-based, participant-driven studies yield novel genetic associations for common traits., PLoS genetics. [PubMed 20585627]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: FANCA
Diseases sorted by gene-association score: fanconi anemia, complementation group a* (1639), fanca-related fanconi anemia* (100), maternal uniparental disomy of chromosome 16 (18), fanconi anemia, complementation group e (10), congenital hypoplastic anemia (10), fanconi anemia, complementation group b (9), fanconi anemia, complementation group f (7), pancytopenia (7), tracheoesophageal fistula (5), seckel syndrome (4), deficiency anemia (3), squamous cell carcinoma, head and neck (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.84 RPKM in Testis
Total median expression: 51.90 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.5042-0.488 Picture PostScript Text
3' UTR -257.12720-0.357 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF15865 - Fanconi anaemia group A protein N terminus

ModBase Predicted Comparative 3D Structure on O15360-2
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  Descriptions from all associated GenBank mRNAs
  X99226 - H.sapiens mRNA for FAA protein.
AK299282 - Homo sapiens cDNA FLJ61351 complete cds, highly similar to Fanconi anemia group A protein.
BC156522 - Synthetic construct Homo sapiens clone IMAGE:100063088, MGC:190686 Fanconi anemia, complementation group A (FANCA) mRNA, encodes complete protein.
BC172515 - Synthetic construct Homo sapiens clone IMAGE:100069209, MGC:199220 Fanconi anemia, complementation group A (FANCA) mRNA, encodes complete protein.
AY339878 - Homo sapiens nonfunctional Fanconi anemia complementation group A variant mRNA; alternatively spliced.
BC022498 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:4800187), with apparent retained intron.
BC008979 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:3456104), complete cds.
BC064540 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:5725803), complete cds.
BC120979 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:40115594), complete cds.
BC127633 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:40115596), complete cds.
BC120978 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:40115593), complete cds.
BC141971 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:40115598), complete cds.
BC141972 - Homo sapiens Fanconi anemia, complementation group A, mRNA (cDNA clone IMAGE:40115599), complete cds.
BT007366 - Homo sapiens Fanconi anemia, complementation group A mRNA, complete cds.
JD485193 - Sequence 466217 from Patent EP1572962.
JD458559 - Sequence 439583 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_bard1Pathway - BRCA1-dependent Ub-ligase activity
h_atrbrcaPathway - Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility

Reactome (by CSHL, EBI, and GO)

Protein O15360 (Reactome details) participates in the following event(s):

R-HSA-6785126 FA core complex assembles at DNA interstrand crosslinks (ICLs)
R-HSA-6786155 POLN binds ICL-DNA
R-HSA-6785342 FANCD2:FANCI complex and UBE2T bind ICL-DNA associated with the FA core complex
R-HSA-6786171 FANCD2 deubiquitination by USP1:WDR48
R-HSA-6788385 The complex of ATR and ATRIP is recruited to ICL-DNA
R-HSA-6785732 DNA nucleases bind monoubiquitinated ID2 complex
R-HSA-6785361 Monoubiquitination of FANCD2:FANCI
R-HSA-6788392 ATR phosphorylates RPA2, FANCI, FANCD2 and FANCM at ICL-DNA
R-HSA-6783310 Fanconi Anemia Pathway
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: FAA, FACA, FANCH, NM_001018112, NP_001018122, O15360-2, uc002fov.1
UCSC ID: uc002fow.1
RefSeq Accession: NM_001018112
Protein: O15360-2, splice isoform of O15360 CCDS: CCDS42221.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene FANCA:
fa (Fanconi Anemia)
tef-ov (Esophageal Atresia/Tracheoesophageal Fistula Overview)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001018112.1
exon count: 11CDS single in 3' UTR: no RNA size: 1673
ORF size: 894CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1094.00frame shift in genome: no % Coverage: 98.98
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.