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FXN frataxin [ Homo sapiens (human) ]

Gene ID: 2395, updated on 5-Mar-2024

Summary

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Official Symbol
FXNprovided by HGNC
Official Full Name
frataxinprovided by HGNC
Primary source
HGNC:HGNC:3951
See related
Ensembl:ENSG00000165060 MIM:606829; AllianceGenome:HGNC:3951
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
FA; X25; CyaY; FARR; FRDA
Summary
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]
Expression
Ubiquitous expression in liver (RPKM 1.7), adrenal (RPKM 1.7) and 25 other tissues See more
Orthologs
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Genomic context

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See FXN in Genome Data Viewer
Location:
9q21.11
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (69035752..69079076)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (81209298..81252406)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (71650668..71693992)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 beta Neighboring gene uncharacterized LOC101927069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28443 Neighboring gene Sharpr-MPRA regulatory region 10428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28444 Neighboring gene CRISPRi-validated cis-regulatory element chr9.764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19931 Neighboring gene Sharpr-MPRA regulatory region 187 Neighboring gene Friedreich ataxia repeat instability region Neighboring gene Sharpr-MPRA regulatory region 4997 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:71660286-71661281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71669749-71670250 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71670251-71670750 Neighboring gene protein kinase cAMP-activated catalytic subunit gamma Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71681521-71682120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:71683371-71683870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:71703383-71703883 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71705161-71706130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71731558-71732058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71732059-71732559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71735458-71736416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71745576-71746105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28446 Neighboring gene uncharacterized LOC124902175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28447 Neighboring gene tight junction protein 2 Neighboring gene Sharpr-MPRA regulatory region 4978 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71856696-71857196 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71857197-71857697 Neighboring gene uncharacterized LOC124902176 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:71897736-71898504 Neighboring gene NANOG hESC enhancer GRCh37_chr9:71898508-71899009 Neighboring gene BRAF-activated non-protein coding RNA

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Astrocytic mitochondrial frataxin-A promising target for ischemic brain injury. Hazra R, et al. CNS Neurosci Ther, 2023 Mar. PMID 36550598, Free PMC Article
  2. G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects. Wang F, et al. Nucleic Acids Res, 2022 Dec 9. PMID 36511872, Free PMC Article
  3. Frataxin deficiency alters gene expression in Friedreich ataxia derived IPSC-neurons and cardiomyocytes. Angulo MB, et al. Mol Genet Genomic Med, 2023 Jan. PMID 36369844, Free PMC Article
  4. Generation of transgene-free iPSC lines from three patients with Friedreich's ataxia (FRDA) carrying GAA triplet expansions in the first intron of FXN gene. Kelekçi S, et al. Stem Cell Res, 2021 Jul. PMID 34214898
  5. Molecular Details of the Frataxin-Scaffold Interaction during Mitochondrial Fe-S Cluster Assembly. Campbell CJ, et al. Int J Mol Sci, 2021 Jun 2. PMID 34199378, Free PMC Article

See all (219) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Protective effect of FXN overexpression on ferroptosis in L-Glu-induced SH-SY5Y cells.
    Title: Protective effect of FXN overexpression on ferroptosis in L-Glu-induced SH-SY5Y cells.
  2. Human frataxin, the Friedreich ataxia deficient protein, interacts with mitochondrial respiratory chain.
    Title: Human frataxin, the Friedreich ataxia deficient protein, interacts with mitochondrial respiratory chain.
  3. FXN gene methylation determines carrier status in Friedreich ataxia.
    Title: FXN gene methylation determines carrier status in Friedreich ataxia.
  4. Astrocytic mitochondrial frataxin-A promising target for ischemic brain injury.
    Title: Astrocytic mitochondrial frataxin-A promising target for ischemic brain injury.
  5. G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects.
    Title: G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects.
  6. Frataxin deficiency alters gene expression in Friedreich ataxia derived IPSC-neurons and cardiomyocytes.
    Title: Frataxin deficiency alters gene expression in Friedreich ataxia derived IPSC-neurons and cardiomyocytes.
  7. Mitochondrial iron and calcium homeostasis in Friedreich ataxia.
    Title: Mitochondrial iron and calcium homeostasis in Friedreich ataxia.
  8. Frataxin deficiency promotes endothelial senescence in pulmonary hypertension.
    Title: Frataxin deficiency promotes endothelial senescence in pulmonary hypertension.
  9. Generation of transgene-free iPSC lines from three patients with Friedreich's ataxia (FRDA) carrying GAA triplet expansions in the first intron of FXN gene.
    Title: Generation of transgene-free iPSC lines from three patients with Friedreich's ataxia (FRDA) carrying GAA triplet expansions in the first intron of FXN gene.
  10. A Drosophila model of Friedreich ataxia with CRISPR/Cas9 insertion of GAA repeats in the frataxin gene reveals in vivo protection by N-acetyl cysteine.
    Title: A Drosophila model of Friedreich ataxia with CRISPR/Cas9 insertion of GAA repeats in the frataxin gene reveals in vivo protection by N-acetyl cysteine.
Submit: New GeneRIF Correction See all GeneRIFs (171)

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
Friedreich ataxia 1
MedGen: C1856689 OMIM: 229300 GeneReviews: Hereditary Ataxia Overview, Friedreich Ataxia
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

  • MGC57199

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2 iron, 2 sulfur cluster binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 2 iron, 2 sulfur cluster binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ferric iron binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ferric iron binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ferrous iron binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ferrous iron binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ferroxidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ferroxidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables iron chaperone activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables iron chaperone activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in [2Fe-2S] cluster assembly IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of [4Fe-4S] cluster assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in [4Fe-4S] cluster assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in adult walking behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to hydrogen peroxide IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in embryo development ending in birth or egg hatching IEA
Inferred from Electronic Annotation
more info
  
involved_in heme biosynthetic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in intracellular iron ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular iron ion homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in iron incorporation into metallo-sulfur cluster IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in iron incorporation into metallo-sulfur cluster IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in iron ion transport IEA
Inferred from Electronic Annotation
more info
  
involved_in iron-sulfur cluster assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in iron-sulfur cluster assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mitochondrion organization IEA
Inferred from Electronic Annotation
more info
  
involved_in muscle cell cellular homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of multicellular organism growth IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of organ growth IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of release of cytochrome c from mitochondria IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in organ growth IEA
Inferred from Electronic Annotation
more info
  
involved_in oxidative phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of aconitate hydratase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of catalytic activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of lyase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of lyase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of succinate dehydrogenase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in proprioception IEA
Inferred from Electronic Annotation
more info
  
involved_in protein autoprocessing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of ferrochelatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to iron ion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of L-cysteine desulfurase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
part_of iron-sulfur cluster assembly complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of mitochondrial iron-sulfur cluster assembly complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial matrix ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in mitochondrial matrix NAS
Non-traceable Author Statement
more info
 PubMed 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
frataxin, mitochondrial
Names
Friedreich ataxia protein
NP_000135.2
NP_852090.1

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_008845.2 RefSeqGene

    Range
    5190..48514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_339

mRNA and Protein(s)

  1. NM_000144.5 → NP_000135.2  frataxin, mitochondrial isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_000135.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL162730, BC023633, U43747
    Consensus CDS
    CCDS6626.1
    UniProtKB/Swiss-Prot
    A8MXJ6, C9JJ89, O15545, O95656, Q15294, Q16595, Q5VZ01
    UniProtKB/TrEMBL
    A0A0S2Z3G4
    Related
    ENSP00000419243.2, ENST00000484259.3
    Conserved Domains (1) summary
    TIGR03422
    Location:94 → 192
    mito_frataxin; frataxin

  2. NM_181425.3 → NP_852090.1  frataxin, mitochondrial isoform 2 preproprotein

    See identical proteins and their annotated locations for NP_852090.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AA232366, AL162730, BC023633, BF058880
    Consensus CDS
    CCDS43834.1
    UniProtKB/TrEMBL
    A0A2R8Y5A1
    Related
    ENSP00000379652.2, ENST00000396366.6
    Conserved Domains (1) summary
    cl00238
    Location:94 → 162
    Frataxin; Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    69035752..69079076
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    81209298..81252406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001161706.1: Suppressed sequence

    Description
    NM_001161706.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16595.2 GenPept UniProtKB/Swiss-Prot:Q16595

Gene LinkOut

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