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Aliases for FXN Gene

Aliases for FXN Gene

  • Frataxin 2 3 5
  • Friedreich Ataxia Protein 3 4
  • FRDA 3 4
  • X25 3 4
  • Frataxin, Mitochondrial 3
  • Friedreich Ataxia 2
  • EC 1.16.3.1 4
  • CyaY 3
  • FARR 3
  • Fxn 4
  • FA 3

External Ids for FXN Gene

Previous HGNC Symbols for FXN Gene

  • FRDA

Previous GeneCards Identifiers for FXN Gene

  • GC09P068879
  • GC09P070840
  • GC09P071650
  • GC09P041495

Summaries for FXN Gene

Entrez Gene Summary for FXN Gene

  • This nuclear gene encodes a mitochondrial protein which belongs to the FRATAXIN family. The protein functions in regulating mitochondrial iron transport and respiration. The expansion of intronic trinucleotide repeat GAA from 8-33 repeats to >90 repeats results in Friedreich ataxia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

GeneCards Summary for FXN Gene

FXN (Frataxin) is a Protein Coding gene. Diseases associated with FXN include Friedreich Ataxia and Hereditary Ataxia. Among its related pathways are Metabolism and Mitochondrial iron-sulfur cluster biogenesis. GO annotations related to this gene include iron-sulfur cluster binding and ferrous iron binding.

UniProtKB/Swiss-Prot for FXN Gene

  • Promotes the biosynthesis of heme and assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. May play a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+); the oligomeric form but not the monomeric form has in vitro ferroxidase activity. May be able to store large amounts of iron in the form of a ferrihydrite mineral by oligomerization; however, the physiological relevance is unsure as reports are conflicting and the function has only been shown using heterologous overexpression systems. Modulates the RNA-binding activity of ACO1.

Gene Wiki entry for FXN Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FXN Gene

Genomics for FXN Gene

Regulatory Elements for FXN Gene

Enhancers for FXN Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09F069089 0.2 ENCODE 15.2 +55.0 55049 2.3 CTCF FOXP2 RAD21 SP7 TJP2 FXN FAM189A2 PIR63068 ENSG00000270236
GH09F068997 1 Ensembl ENCODE 11.8 -36.4 -36412 2.1 PKNOX1 CBX3 ARID4B ZNF48 RAD21 RARA ZNF143 MIXL1 THAP11 ZNF654 FXN PIP5K1B FAM122A LOC105376073 GC09P069001 LOC101927069
GH09F068995 1.3 Ensembl ENCODE 11.5 -38.6 -38619 1.7 PIP5K1B FXN RNU6-820P FAM122A LOC105376073 ENSG00000226337 TMEM252 GC09P069001 LOC101927069
GH09F069191 1.2 Ensembl ENCODE 11.5 +157.4 157410 1.5 ELF3 CTCF RAD21 YY1 GATA3 ZNF143 SMC3 DEK MIXL1 GATAD2A TJP2 FXN GC09P069204 ENSG00000283143
GH09F069128 0.8 Ensembl ENCODE 11.2 +95.7 95673 5.2 HDAC1 PKNOX1 ARID4B SIN3A ZSCAN9 FOS MIXL1 HMG20B SP5 JUNB TJP2 FXN PGM5 ENSG00000283143
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around FXN on UCSC Golden Path with GeneCards custom track

Promoters for FXN Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001305050 1041 1801 HDGF ATF1 MLX ARID4B SIN3A DMAP1 ZNF48 YY1 SLC30A9 CBX5

Genomic Location for FXN Gene

Chromosome:
9
Start:
69,035,259 bp from pter
End:
69,100,178 bp from pter
Size:
64,920 bases
Orientation:
Plus strand

Genomic View for FXN Gene

Genes around FXN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FXN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FXN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FXN Gene

Proteins for FXN Gene

  • Protein details for FXN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16595-FRDA_HUMAN
    Recommended name:
    Frataxin, mitochondrial
    Protein Accession:
    Q16595
    Secondary Accessions:
    • A8MXJ6
    • C9JJ89
    • O15545
    • O95656
    • Q15294
    • Q5VZ01

    Protein attributes for FXN Gene

    Size:
    210 amino acids
    Molecular mass:
    23135 Da
    Quaternary structure:
    • Monomer (probable predominant form). Oligomer. Monomers and polymeric aggregates of >1 MDa have been isolated from mitochondria. A small fraction of heterologous overexpressed recombinant frataxin forms high-molecular wight aggregates that incoroprate iron. Interacts with LYRM4 AND HSPA9. Interacts with ACO1. Interacts with ISCU isoform 1 and isoform 2. Interacts with FECH; one iron-bound FXN monomer seems to interact with a FECH homodimer. Interacts with SDHA and SDHB. Interacts with ACO2; the interaction is dependent on citrate (By similarity).
    Miscellaneous:
    • The unusual migration profile of mature frataxin on SDS-PAGE due to its acidic N-terminus most likely contributed to conflicting reports for the N-terminus of the mature protein. Unlike prokaryotic and yeast frataxin homologs, which self-assemble at high iron concentrations, oligomerization of human frataxin is not induced by iron. The existence of a specialized mitochondrial ferritin in mammalia (FTMT) is suggesting that iron storage would be redundant function, at least in mammalian mitochondria.

    Three dimensional structures from OCA and Proteopedia for FXN Gene

    Alternative splice isoforms for FXN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FXN Gene

Post-translational modifications for FXN Gene

  • Processed in two steps by mitochondrial processing peptidase (MPP). MPP first cleaves the precursor to intermediate form and subsequently converts the intermediate to yield frataxin mature form (frataxin(81-210)) which is the predominant form. The additional forms, frataxin(56-210) and frataxin(78-210), seem to be produced when the normal maturation process is impaired; their physiological relevance is unsure.
  • Ubiquitination at Lys 197
  • Modification sites at PhosphoSitePlus

Other Protein References for FXN Gene

No data available for DME Specific Peptides for FXN Gene

Domains & Families for FXN Gene

Protein Domains for FXN Gene

Suggested Antigen Peptide Sequences for FXN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q16595

UniProtKB/Swiss-Prot:

FRDA_HUMAN :
  • Belongs to the frataxin family.
Family:
  • Belongs to the frataxin family.
genes like me logo Genes that share domains with FXN: view

No data available for Gene Families for FXN Gene

Function for FXN Gene

Molecular function for FXN Gene

UniProtKB/Swiss-Prot CatalyticActivity:
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O.
UniProtKB/Swiss-Prot Function:
Promotes the biosynthesis of heme and assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. May play a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+); the oligomeric form but not the monomeric form has in vitro ferroxidase activity. May be able to store large amounts of iron in the form of a ferrihydrite mineral by oligomerization; however, the physiological relevance is unsure as reports are conflicting and the function has only been shown using heterologous overexpression systems. Modulates the RNA-binding activity of ACO1.

Enzyme Numbers (IUBMB) for FXN Gene

Gene Ontology (GO) - Molecular Function for FXN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004322 ferroxidase activity IDA 15641778
GO:0005515 protein binding IPI 15123683
GO:0008198 ferrous iron binding IDA 12785837
GO:0008199 ferric iron binding IDA 12785837
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with FXN: view
genes like me logo Genes that share phenotypes with FXN: view

Human Phenotype Ontology for FXN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FXN Gene

MGI Knock Outs for FXN:

Animal Model Products

miRNA for FXN Gene

miRTarBase miRNAs that target FXN

Inhibitory RNA Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for FXN Gene

Localization for FXN Gene

Subcellular locations from UniProtKB/Swiss-Prot for FXN Gene

Mitochondrion. Cytoplasm, cytosol. Note=PubMed:18725397 reports localization exclusively in mitochondria. {ECO:0000305 PubMed:18725397}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for FXN Gene COMPARTMENTS Subcellular localization image for FXN gene
Compartment Confidence
cytosol 5
mitochondrion 5
nucleus 2
extracellular 1

Gene Ontology (GO) - Cellular Components for FXN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA 17468497
GO:0005759 mitochondrial matrix TAS --
GO:0005829 cytosol IDA 17468497
genes like me logo Genes that share ontologies with FXN: view

Pathways & Interactions for FXN Gene

genes like me logo Genes that share pathways with FXN: view

Pathways by source for FXN Gene

Gene Ontology (GO) - Biological Process for FXN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006119 oxidative phosphorylation IEA --
GO:0006783 heme biosynthetic process NAS 15123683
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006879 cellular iron ion homeostasis IMP 18160053
genes like me logo Genes that share ontologies with FXN: view

No data available for SIGNOR curated interactions for FXN Gene

Drugs & Compounds for FXN Gene

(12) Drugs for FXN Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Oxygen Approved, Vet_approved Pharma 0
Water Approved Pharma 0
heme Pharma Agonist 0

(13) Additional Compounds for FXN Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Fe2+
  • Armco iron
  • Carbonyl iron
  • FE
  • Ferrovac e
  • Hematite
15438-31-0
Fe3+
  • Fe(III)
  • Ferric ion
  • Iron(3+)
7439-89-6
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
genes like me logo Genes that share compounds with FXN: view

Transcripts for FXN Gene

Unigene Clusters for FXN Gene

Frataxin:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for FXN Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6
SP1: - -
SP2: -
SP3: -
SP4: -

Relevant External Links for FXN Gene

GeneLoc Exon Structure for
FXN
ECgene alternative splicing isoforms for
FXN

Expression for FXN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for FXN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FXN Gene

This gene is overexpressed in Liver, secretome (18.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for FXN Gene



Protein tissue co-expression partners for FXN Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of FXN Gene:

FXN

SOURCE GeneReport for Unigene cluster for FXN Gene:

Hs.20685

mRNA Expression by UniProt/SwissProt for FXN Gene:

Q16595-FRDA_HUMAN
Tissue specificity: Expressed in the heart, peripheral blood lymphocytes and dermal fibroblasts.
genes like me logo Genes that share expression patterns with FXN: view

Primer Products

No data available for mRNA differential expression in normal tissues for FXN Gene

Orthologs for FXN Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for FXN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FXN 34
  • 96.19 (n)
cow
(Bos Taurus)
Mammalia FXN 34 35
  • 79.59 (n)
dog
(Canis familiaris)
Mammalia FXN 34 35
  • 79.33 (n)
mouse
(Mus musculus)
Mammalia Fxn 34 16 35
  • 74.96 (n)
rat
(Rattus norvegicus)
Mammalia Fxn 34
  • 73.86 (n)
oppossum
(Monodelphis domestica)
Mammalia FXN 35
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves FXN 34 35
  • 71.36 (n)
lizard
(Anolis carolinensis)
Reptilia FXN 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497789 34
  • 69.44 (n)
zebrafish
(Danio rerio)
Actinopterygii fxn 34 35
  • 62.82 (n)
fruit fly
(Drosophila melanogaster)
Insecta fh 35
  • 40 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea frh-1 35
  • 43 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YFH1 35 37
  • 32 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons FH 34
  • 45.31 (n)
rice
(Oryza sativa)
Liliopsida Os01g0783600 34
  • 53.09 (n)
Species where no ortholog for FXN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for FXN Gene

ENSEMBL:
Gene Tree for FXN (if available)
TreeFam:
Gene Tree for FXN (if available)

Paralogs for FXN Gene

(1) SIMAP similar genes for FXN Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for FXN Gene

genes like me logo Genes that share paralogs with FXN: view

No data available for Paralogs for FXN Gene

Variants for FXN Gene

Sequence variations from dbSNP and Humsavar for FXN Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs104894105 Friedreich ataxia (FRDA) [MIM:229300], Pathogenic 69,053,193(+) CTCTT(C/G/T)AGCAG reference, missense, stop-gained
rs104894106 Friedreich ataxia (FRDA) [MIM:229300], Pathogenic 69,065,013(+) AGCAA(A/T)TCTGG reference, missense
rs104894107 Friedreich ataxia (FRDA) [MIM:229300], Pathogenic 69,064,942(+) GAGTG(C/G/T)TGTCT reference, missense
rs138034837 Friedreich ataxia (FRDA) [MIM:229300] 69,072,622(+) CTAAG(C/T)GTTAT intron-variant, reference, synonymous-codon, missense
rs138471431 Friedreich ataxia (FRDA) [MIM:229300] 69,065,016(+) AAATC(C/T)GGCTA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for FXN Gene

Variant ID Type Subtype PubMed ID
dgv4062n106 CNV deletion 24896259
dgv4063n106 CNV deletion 24896259
dgv45e194 CNV deletion 18987734
dgv7665n100 CNV gain 25217958
dgv7666n100 CNV gain 25217958
dgv7667n100 CNV gain 25217958
esv1673718 CNV deletion 17803354
esv2422258 CNV duplication 17116639
esv2624430 CNV deletion 19546169
esv2659849 CNV deletion 23128226
esv2738527 CNV deletion 23290073
esv2738528 CNV deletion 23290073
esv2738530 CNV deletion 23290073
esv2738531 CNV deletion 23290073
esv2761531 CNV gain 21179565
esv3093 CNV loss 18987735
esv3544873 CNV deletion 23714750
esv3544874 CNV deletion 23714750
esv3544875 CNV deletion 23714750
esv3576657 CNV gain 25503493
esv3620551 CNV loss 21293372
esv3891678 CNV gain 25118596
esv3891679 CNV gain 25118596
esv6324 CNV loss 19470904
nsv1035268 CNV loss 25217958
nsv1075245 CNV deletion 25765185
nsv1075651 CNV deletion 25765185
nsv1151955 CNV deletion 26484159
nsv466393 CNV gain 19166990
nsv466397 CNV gain 19166990
nsv508550 CNV deletion 20534489
nsv614547 CNV gain 21841781
nsv614548 CNV gain 21841781
nsv614549 CNV gain 21841781
nsv614550 CNV gain 21841781
nsv614551 CNV loss 21841781
nsv6549 CNV deletion 18451855
nsv6550 CNV deletion 18451855
nsv824939 CNV loss 20364138
nsv957708 CNV deletion 24416366
nsv957715 CNV deletion 24416366
nsv968705 CNV duplication 23825009

Variation tolerance for FXN Gene

Residual Variation Intolerance Score: 66.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.90; 18.80% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FXN Gene

Human Gene Mutation Database (HGMD)
FXN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FXN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FXN Gene

Disorders for FXN Gene

MalaCards: The human disease database

(18) MalaCards diseases for FXN Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
friedreich ataxia
  • friedreich ataxia with retained reflexes
hereditary ataxia
  • hereditary ataxias
ataxia
ataxia with isolated vitamin e deficiency
  • vitamin e, familial isolated deficiency of
anemia, sideroblastic, with ataxia
  • anemia, sideroblastic, and spinocerebellar ataxia
- elite association - COSMIC cancer census association via MalaCards
Search FXN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FRDA_HUMAN
  • Friedreich ataxia (FRDA) [MIM:229300]: Autosomal recessive, progressive degenerative disease characterized by neurodegeneration and cardiomyopathy it is the most common inherited ataxia. The disorder is usually manifest before adolescence and is generally characterized by incoordination of limb movements, dysarthria, nystagmus, diminished or absent tendon reflexes, Babinski sign, impairment of position and vibratory senses, scoliosis, pes cavus, and hammer toe. In most patients, FRDA is due to GAA triplet repeat expansions in the first intron of the frataxin gene. But in some cases the disease is due to mutations in the coding region. {ECO:0000269 PubMed:10732799, ECO:0000269 PubMed:10874325, ECO:0000269 PubMed:9150176, ECO:0000269 PubMed:9779809, ECO:0000269 PubMed:9989622, ECO:0000269 Ref.35, ECO:0000269 Ref.7, ECO:0000269 Ref.8}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for FXN

Genetic Association Database (GAD)
FXN
Human Genome Epidemiology (HuGE) Navigator
FXN
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
FXN
genes like me logo Genes that share disorders with FXN: view

No data available for Genatlas for FXN Gene

Publications for FXN Gene

  1. Molecular control of the cytosolic aconitase/IRP1 switch by extramitochondrial frataxin. (PMID: 20053667) Condo I. … Testi R. (Hum. Mol. Genet. 2010) 3 4 22 64
  2. The in vivo mitochondrial two-step maturation of human frataxin. (PMID: 18725397) Schmucker S. … Puccio H. (Hum. Mol. Genet. 2008) 3 4 22 64
  3. Mitochondrial frataxin interacts with ISD11 of the NFS1/ISCU complex and multiple mitochondrial chaperones. (PMID: 17331979) Shan Y. … Cortopassi G. (Hum. Mol. Genet. 2007) 3 4 22 64
  4. In vivo maturation of human frataxin. (PMID: 17468497) Condo I. … Testi R. (Hum. Mol. Genet. 2007) 3 4 22 64
  5. A pool of extramitochondrial frataxin that promotes cell survival. (PMID: 16608849) Condo I. … Testi R. (J. Biol. Chem. 2006) 3 4 22 64

Products for FXN Gene

  • Addgene plasmids for FXN

Sources for FXN Gene

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