FXN

gene
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Also known as FAFARRX25CyaY

Summary

FXN (frataxin, HGNC:3951) is a protein-coding gene on chromosome 9q21.11, encoding Frataxin, mitochondrial (Q16595). Functions as an activator of persulfide transfer to the scaffoding protein ISCU as component of the core iron-sulfur cluster (ISC) assembly complex and participates to the [2Fe-2S] cluster assembly. It is a selective cancer dependency (DepMap: 64.6% of cell lines).

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.

Source: NCBI Gene 2395 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Friedreich ataxia (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 6
  • Clinical variants (ClinVar): 151 total — 16 pathogenic, 9 likely-pathogenic
  • Phenotypes (HPO): 78
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 64.6% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_000144

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3951
Approved symbolFXN
Namefrataxin
Location9q21.11
Locus typegene with protein product
StatusApproved
AliasesFA, FARR, X25, CyaY
Ensembl geneENSG00000165060
Ensembl biotypeprotein_coding
OMIM606829
Entrez2395

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 nonsense_mediated_decay

ENST00000377270, ENST00000396366, ENST00000484259, ENST00000498653, ENST00000644653, ENST00000863456, ENST00000863457, ENST00000915363

RefSeq mRNA: 2 — MANE Select: NM_000144 NM_000144, NM_181425

CCDS: CCDS43834, CCDS6626

Canonical transcript exons

ENST00000484259 — 5 exons

ExonStartEnd
ENSE000010898586906493869065035
ENSE000018837156904638569046482
ENSE000018874046907261269079076
ENSE000038232776903575269035947
ENSE000038284416905314069053260

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 90.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.2595 / max 127.6879, expressed in 1806 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
9681020.25951806

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111490.16gold quality
apex of heartUBERON:000209889.07gold quality
heart left ventricleUBERON:000208488.96gold quality
cardiac ventricleUBERON:000208288.60gold quality
right adrenal glandUBERON:000123388.53gold quality
right adrenal gland cortexUBERON:003582788.21gold quality
hindlimb stylopod muscleUBERON:000425288.17gold quality
left adrenal glandUBERON:000123487.95gold quality
left adrenal gland cortexUBERON:003582587.35gold quality
gastrocnemiusUBERON:000138886.91gold quality
right atrium auricular regionUBERON:000663186.90gold quality
liverUBERON:000210786.66gold quality
mucosa of transverse colonUBERON:000499186.64gold quality
muscle of legUBERON:000138386.44gold quality
adrenal cortexUBERON:000123586.37gold quality
adrenal glandUBERON:000236986.16gold quality
heartUBERON:000094885.94gold quality
cardiac atriumUBERON:000208185.04gold quality
body of pancreasUBERON:000115084.75gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.49gold quality
right ovaryUBERON:000211884.33gold quality
left ovaryUBERON:000211984.14gold quality
muscle organUBERON:000163084.13gold quality
granulocyteCL:000009483.95gold quality
rectumUBERON:000105283.27gold quality
monocyteCL:000057683.24gold quality
leukocyteCL:000073883.22gold quality
smooth muscle tissueUBERON:000113583.01gold quality
mononuclear cellCL:000084282.92gold quality
pancreasUBERON:000126482.29gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-HCAD-6yes46.35
E-CURD-112yes8.96
E-ANND-3yes8.23

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF, DNMT1, EGR3, GLI3, MYC, PPARG, SRF, TFAP2A, TP53

miRNA regulators (miRDB)

181 targeting FXN, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-5692A100.0074.406850
HSA-MIR-574-5P100.0066.01989
HSA-MIR-5193100.0067.261744
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-366299.9973.825684
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-590-3P99.9674.346478
HSA-MIR-302E99.9670.742669
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-570-3P99.9672.414910
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-205-3P99.9269.923165
HSA-MIR-129799.9173.413162
HSA-MIR-61399.9171.501710
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-4731-5P99.8967.232537

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 64.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • trinucleotide repeat in friedreich ataxia (PMID:11810294)
  • findings suggest that Friedreich ataxia results from decreased mitochondrial iron storage due to frataxin deficiency which may impair iron metabolism, promote oxidative damage and lead to progressive iron accumulation (PMID:11823441)
  • Frataxin and cardiac troponin T gene mutations co-exist in a child with Friedreich ataxia and familial hypertrophic cardiomyopathy. (PMID:11857753)
  • association of polymorphic trinucleotide repeat (GAA)n with diabetes mellitus type 2 in the Moscow population (PMID:11862710)
  • frataxin protein is concluded to have a protective role for the nucleus as well as the mitochondria (PMID:12019217)
  • molecular structure and iron-binding properties (PMID:12140189)
  • Expansion of GAA repeats in the intron of this gene is involved in the autosomal recessive Friedreich ataxia. (PMID:12354077)
  • The extended X-ray absorption fine structure (EXAFS) analysis agrees with previous electron microscopy data showing that frataxin cores are composed of very small ferrihydrite crystallites. (PMID:12755598)
  • Frataxin functions as an iron donor for assembly of [2Fe-2S] clusters in ISU-type proteins. (PMID:12785837)
  • Friedreich ataxia is caused by expansion of a GAA triplet repeat (GAA-TR) in the FRDA gene. (PMID:14962663)
  • analysis of frataxin-mediated iron delivery to ferrochelatase in the final step of heme biosynthesis (PMID:15123683)
  • We found one novel haplotype, ACCT, among the expanded alleles as well as among normal individuals, though at low frequency; this haplotype may be characteristic of Indian populations (PMID:15180699)
  • mouse model of FRDA GAA repeat instability (PMID:15233994)
  • frataxin is an iron chaperone protein that protects the aconitase [4Fe-4S]2+ cluster from disassembly and promotes enzyme reactivation (PMID:15247478)
  • Transgenic mice show an altered response during hematopoietic differentiation, suggesting that frataxin may directly affect heme synthesis. (PMID:15304363)
  • results demonstrate (i) that frataxin is a component of the human Fe/S cluster assembly machinery and (ii) that it plays a role in the maturation of both mitochondrial and cytosolic Fe/S proteins (PMID:15509595)
  • The FRDA GAA repeat mutation in Friedreich ataxia is destabilized, frequently undergoing large contractions, during DNA replication. (PMID:15534367)
  • frataxin is a modular protein that depends on self-assembly to accomplish its diverse functions (PMID:15581888)
  • Analysis of stable monomeric and assembled forms of human frataxin reveals that the assembled protein has ferroxidase activity and detoxifies redox-active iron by sequestering it in a protein-protected compartment. (PMID:15641778)
  • Data suggest that frataxin may be involved in the biosynthesis of iron-sulphur proteins such as IscU1 not only within the mitochondria, but also in the extramitochondrial compartment. (PMID:16091420)
  • Deficiency of transgenic frataxin protein in Drosophila embryos results in diminished activities of numerous heme- and iron-sulfur-containing enzymes, loss of intracellular iron homeostasis and increased susceptibility to iron toxicity (PMID:16203742)
  • an increase in oxidative metabolism induced by mitochondrial frataxin may inhibit cancer growth in mammals (PMID:16263703)
  • Human mature frataxin is distributed between two distinct subcellular compartments; both mitochondrial and extramitochondrial forms can suppress apoptosis. (PMID:16608849)
  • extramitochondrial frataxin can fully replace mitochondrial frataxin in promoting survival of FA cells (PMID:16608849)
  • Frataxin, iron-sulfur clusters, heme and reactive oxygen species have roles in aging (PMID:16677095)
  • A comparison the comformational properties of wild-type and mutant frataxins under physiological conditions and under adverse conditions are reported. (PMID:16787388)
  • Data suggest that DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats and reduced levels of frataxin in Friedreich’s ataxia.( (PMID:16857735)
  • Earliest consequences of frataxin deficiency occur in ISC proteins of the cytoplasm, resulting in oxidative damage and stress and activation of the unfolded protein response which has been associated with neurological disease. (PMID:17098208)
  • Progressive GAA expansions of FXN protein in dorsal root ganglia of Friedreich’s ataxia patients. (PMID:17262846)
  • N-terminus of Mitochondrial processing peptidase-processed frataxin shows a unique high-affinity iron site and that this iron center appears to mediate a self-cleavage reaction (PMID:17285345)
  • Frataxin interacts with ISD11 and multiple mitochondrial chaperones. (PMID:17331979)
  • In living cells, the main form of mature frataxin is generated by a proteolytic cleavage between Lys80 and Ser81, yielding a 130 aa protein (frataxin 81-210). (PMID:17468497)
  • analysis of frataxin and its maturation in human cells (PMID:17468497)
  • Identification of a region that is important for maximal FXN gene expression and show that repeat expansion leads to changes in DNA methylation and chromatin organization in this region. (PMID:17478498)
  • In heterozygosity for a null allele, a strong correlation was observed between the size of GAA expansion and the age at onset, supporting the hypothesis that the residual function of frataxin in patients’ cells derive exclusively from the expanded allele. (PMID:17703324)
  • The FXN GAA repeat expansion mutation induces comparable epigenetic changes in human and transgenic mouse brain and heart tissues. (PMID:18045775)
  • The effect of DNA double-strand break repair on instability of the (GAA*TTC)n sequence of the FXN gene. (PMID:18045804)
  • Frataxin has some roles in controlling the balance between different mitochondrial iron pools that are partially in common with those of mitochondrial ferritin. (PMID:18160053)
  • Friedrich’s disease presents a typical mutation, an expansion of trinucleotide GAA-repeats, in the FRDA gene. (PMID:18379460)
  • Frataxin expression is regulated by iron; frataxin mRNA levels decrease significantly in multiple human cell lines treated with the iron chelator, desferal. (PMID:18424449)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriofxnENSDARG00000074356
mus_musculusFxnENSMUSG00000059363
rattus_norvegicusFxnENSRNOG00000015213
drosophila_melanogasterfhFBGN0030092
caenorhabditis_elegansWBGENE00001486

Protein

Protein identifiers

Frataxin, mitochondrialQ16595 (reviewed: Q16595)

Alternative names: Friedreich ataxia protein

All UniProt accessions (4): A0A0S2Z3G4, A0A0S2Z3Q8, C9JAX1, Q16595

UniProt curated annotations — full annotation on UniProt →

Function. Functions as an activator of persulfide transfer to the scaffoding protein ISCU as component of the core iron-sulfur cluster (ISC) assembly complex and participates to the [2Fe-2S] cluster assembly. Accelerates sulfur transfer from NFS1 persulfide intermediate to ISCU and to small thiols such as L-cysteine and glutathione leading to persulfuration of these thiols and ultimately sulfide release. Binds ferrous ion and is released from FXN upon the addition of both L-cysteine and reduced FDX2 during [2Fe-2S] cluster assembly. The core iron-sulfur cluster (ISC) assembly complex is involved in the de novo synthesis of a [2Fe-2S] cluster, the first step of the mitochondrial iron-sulfur protein biogenesis. This process is initiated by the cysteine desulfurase complex (NFS1:LYRM4:NDUFAB1) that produces persulfide which is delivered on the scaffold protein ISCU in a FXN-dependent manner. Then this complex is stabilized by FDX2 which provides reducing equivalents to accomplish the [2Fe-2S] cluster assembly. Finally, the [2Fe-2S] cluster is transferred from ISCU to chaperone proteins, including HSCB, HSPA9 and GLRX5. 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. May function as an iron chaperone protein that protects the aconitase [4Fe-4S]2+ cluster from disassembly and promotes enzyme reactivation. May play a role as a high affinity iron binding partner for FECH that is capable of both delivering iron to ferrochelatase and mediating the terminal step in mitochondrial heme biosynthesis. Modulates the RNA-binding activity of ACO1. May be involved in the cytoplasmic iron-sulfur protein biogenesis. May contribute to oxidative stress resistance and overall cell survival.

Subunit / interactions. Component of the mitochondrial core iron-sulfur cluster (ISC) complex composed of NFS1, LYRM4, NDUFAB1, ISCU, FXN, and FDX2; this complex is a heterohexamer containing two copies of each monomer. Homodimer. 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 weight aggregates that incorporate iron. Interacts with LYRM4. Interacts (via ferrous form) with ISCU; the interaction is possible when both are bound to the dimeric form of the cysteine desulfurase complex (NFS1:LYRM4) and the interaction enhances FXN interaction to the dimeric form of the cysteine desulfurase complex (NFS1:LYRM4). 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. Interacts with HSPA9. Interacts with ACO1. Interacts with ISCU (cytoplasmic form).

Subcellular location. Mitochondrion Cytoplasm. Cytosol.

Tissue specificity. Expressed in the heart, peripheral blood lymphocytes and dermal fibroblasts.

Post-translational modifications. 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.

Disease relevance. 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. The disease is caused by variants affecting the gene represented in this entry.

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. Not highly expressed and may be artifactual.

Similarity. Belongs to the frataxin family.

Isoforms (3)

UniProt IDNamesCanonical?
Q16595-11yes
Q16595-22
Q16595-33

RefSeq proteins (2): NP_000135, NP_852090 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002908Frataxin/CyaYFamily
IPR017789FrataxinFamily
IPR020895Frataxin_CSConserved_site
IPR036524Frataxin/CyaY_sfHomologous_superfamily

Pfam: PF01491

Catalyzed reactions (Rhea), 1 shown:

  • 4 Fe(2+) + O2 + 4 H(+) = 4 Fe(3+) + 2 H2O (RHEA:11148)

UniProt features (45 total): mutagenesis site 12, strand 10, sequence variant 9, chain 5, sequence conflict 2, helix 2, turn 2, splice variant 2, transit peptide 1

Structure

Experimental structures (PDB)

19 structures.

PDBMethodResolution (Å)
3T3LX-RAY DIFFRACTION1.15
3T3KX-RAY DIFFRACTION1.24
3S4MX-RAY DIFFRACTION1.3
3S5EX-RAY DIFFRACTION1.31
3T3TX-RAY DIFFRACTION1.38
3S5DX-RAY DIFFRACTION1.5
3S5FX-RAY DIFFRACTION1.5
9HO5X-RAY DIFFRACTION1.5
3T3XX-RAY DIFFRACTION1.57
3T3JX-RAY DIFFRACTION1.7
9HO4X-RAY DIFFRACTION1.76
1EKGX-RAY DIFFRACTION1.8
9HO6X-RAY DIFFRACTION2
8PK8ELECTRON MICROSCOPY2.49
8RMEELECTRON MICROSCOPY2.49
8PK9ELECTRON MICROSCOPY2.58
6NZUELECTRON MICROSCOPY3.2
5KZ5ELECTRON MICROSCOPY14.3
1LY7SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16595-F175.930.53

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (12):

PositionPhenotype
39–40abolishes cleavage to yield frataxin intermediate form and allows accumulation of frataxin(56-210) and frataxin(78-210).
53–54no effect on processing of wild-type fxn.
78–79abolishes cleavage to yield frataxin mature form and allows accumulation of frataxin(56-210) and frataxin(78-210).
79–80abolishes cleavage to yield frataxin mature form and allows the accumulation of frataxin(56-210).
96does not affect interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial localizati
104does not affect interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial localizati
108significantly reduces interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial loca
111significantly reduces interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial loca
115does not affect interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial localizati
124drasticly reduces interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial localiza
146does not affect interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial localizati
173loss of interaction with the core iron-sulfur cluster assembly complex. does not affect mitochondrial localization. does

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-1268020Mitochondrial protein import
R-HSA-1362409Mitochondrial iron-sulfur cluster biogenesis
R-HSA-9854311Maturation of TCA enzymes and regulation of TCA cycle
R-HSA-9865881Complex III assembly

MSigDB gene sets: 416 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_BEHAVIOR, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, GOBP_TRANSITION_METAL_ION_TRANSPORT, GOBP_ADULT_BEHAVIOR, HOEGERKORP_CD44_TARGETS_TEMPORAL_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_INTRACELLULAR_IRON_ION_HOMEOSTASIS, GOBP_GROWTH, GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_LYASE_ACTIVITY, GOBP_TETRAPYRROLE_BIOSYNTHETIC_PROCESS, GOBP_ADULT_LOCOMOTORY_BEHAVIOR, GOBP_IRON_ION_TRANSPORT

GO Biological Process (29): oxidative phosphorylation (GO:0006119), heme biosynthetic process (GO:0006783), iron ion transport (GO:0006826), intracellular iron ion homeostasis (GO:0006879), adult walking behavior (GO:0007628), embryo development ending in birth or egg hatching (GO:0009792), response to iron ion (GO:0010039), iron-sulfur cluster assembly (GO:0016226), protein autoprocessing (GO:0016540), proprioception (GO:0019230), mitochondrial respiratory chain complex III assembly (GO:0034551), organ growth (GO:0035265), negative regulation of multicellular organism growth (GO:0040015), negative regulation of apoptotic process (GO:0043066), [2Fe-2S] cluster assembly (GO:0044571), [4Fe-4S] cluster assembly (GO:0044572), negative regulation of organ growth (GO:0046621), muscle cell cellular homeostasis (GO:0046716), positive regulation of lyase activity (GO:0051349), protein maturation (GO:0051604), cellular response to hydrogen peroxide (GO:0070301), negative regulation of release of cytochrome c from mitochondria (GO:0090201), monoatomic ion transport (GO:0006811), mitochondrion organization (GO:0007005), aerobic respiration (GO:0009060), iron incorporation into metallo-sulfur cluster (GO:0018283), intracellular monoatomic cation homeostasis (GO:0030003), regulation of growth (GO:0040008), inorganic ion homeostasis (GO:0098771)

GO Molecular Function (9): ferroxidase activity (GO:0004322), enzyme activator activity (GO:0008047), ferrous iron binding (GO:0008198), ferric iron binding (GO:0008199), iron chaperone activity (GO:0034986), 2 iron, 2 sulfur cluster binding (GO:0051537), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), metal ion binding (GO:0046872)

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), cytosol (GO:0005829), mitochondrial [2Fe-2S] assembly complex (GO:0099128), iron-sulfur cluster assembly complex (GO:1990229), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Protein localization1
Metabolism1
Citric acid cycle (TCA cycle)1
Respiratory electron transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
iron ion binding3
cytoplasm3
mitochondrion2
negative regulation of developmental growth2
negative regulation of multicellular organismal process2
iron-sulfur cluster assembly2
catalytic activity2
cellular anatomical structure2
aerobic respiration1
proton motive force-driven ATP synthesis1
porphyrin-containing compound biosynthetic process1
heme metabolic process1
pigment biosynthetic process1
transition metal ion transport1
intracellular monoatomic cation homeostasis1
inorganic ion homeostasis1
adult locomotory behavior1
walking behavior1
embryo development1
response to metal ion1
metallo-sulfur cluster assembly1
protein processing1
sensory perception1
neuromuscular process controlling posture1
respiratory chain complex III assembly1
mitochondrial respiratory chain complex assembly1
multicellular organismal process1
developmental growth1
multicellular organism growth1
regulation of multicellular organism growth1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
organ growth1
regulation of organ growth1
cellular homeostasis1
lyase activity1
positive regulation of catalytic activity1
gene expression1
protein metabolic process1

Protein interactions and networks

STRING

2172 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FXNLYRM4Q9HD34999
FXNNFS1Q9Y697998
FXNISCUQ9H1K1997
FXNACO2Q99798964
FXNACO1P21399963
FXNFECHP22830935
FXNHSPA9P30036901
FXNSETXQ7Z333863
FXNFTMTQ8N4E7848
FXNAPTXQ7Z2E3840
FXNNFU1Q9UMS0834
FXNFDX1P10109824
FXNPIP5K1BP78518815
FXNIREB2P48200813
FXNISCA2Q86U28787

IntAct

54 interactions, top by confidence:

ABTypeScore
FXNDAPP1psi-mi:“MI:0915”(physical association)0.720
LYRM4NDUFAB1psi-mi:“MI:0914”(association)0.640
ISCUacpPpsi-mi:“MI:0915”(physical association)0.570
GOLGA6L9FXNpsi-mi:“MI:0915”(physical association)0.560
FXNCORO2Apsi-mi:“MI:0915”(physical association)0.560
FXNPIAS1psi-mi:“MI:0915”(physical association)0.560
FXNCAPN10psi-mi:“MI:0915”(physical association)0.560
FXNRASSF1psi-mi:“MI:0915”(physical association)0.560
FXNRNF138psi-mi:“MI:0915”(physical association)0.560
FXNSKIC8psi-mi:“MI:0915”(physical association)0.560
FXNRNF183psi-mi:“MI:0915”(physical association)0.560
FXNSAMD3psi-mi:“MI:0915”(physical association)0.560
FXNARL17psi-mi:“MI:0915”(physical association)0.560

BioGRID (65): FXN (Affinity Capture-MS), RNF126 (Affinity Capture-Western), FXN (Affinity Capture-Western), FXN (Biochemical Activity), GLRX5 (Co-fractionation), FXN (Co-fractionation), FXN (Co-fractionation), FXN (Co-fractionation), FXN (Co-fractionation), FXN (Co-fractionation), CLIC4 (Co-fractionation), LACTB2 (Co-fractionation), FXN (Co-fractionation), FXN (Co-fractionation), FXN (Co-fractionation)

ESM2 similar proteins: A1L1P7, A6ZND9, A6ZSH0, B0BN56, B3LIY9, B3LPE4, B5VQB0, C5DKM2, D3ZYW7, F4I9Q5, O14320, O35658, O35796, O35943, O49196, P37841, P42797, P42844, P49727, P51132, P51133, P51135, P82928, Q01607, Q04907, Q05B87, Q07021, Q08230, Q09759, Q0IH40, Q16595, Q1JPN0, Q2KI49, Q3T0B6, Q5REH5, Q84WZ8, Q8HXX9, Q8N5N7, Q8VZE7, Q94JS0

Diamond homologs: A4G9P9, A7MQK4, A8G850, A8GN05, A8GRM5, B0BX32, B0YLW8, B5BIV3, B7VMD7, B8GQ85, C3PN35, C4K1X9, I7HD01, O35943, O74831, P40128, Q05B87, Q07540, Q16595, Q1RIC4, Q47JL4, Q4UM50, Q54C45, Q5PKM9, Q68X49, Q6CZG6, Q6LLN3, Q8HXX9, Q8SWI3, Q92IH7, Q9TY03, Q9W385, Q9ZDK5, Q9ZR07, A1AHX3, A4WG10, A6T3G3, A6TGJ0, A7ZU09, A8A6R1

SIGNOR signaling

3 interactions.

AEffectBMechanism
SRC“down-regulates quantity by destabilization”FXNphosphorylation
RNF126“down-regulates quantity by destabilization”FXNubiquitination
FXN“form complex”“Mitochondrial Fe-S Cluster Assembly Complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 28 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Maturation of TCA enzymes and regulation of TCA cycle5150.3×9e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

151 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic16
Likely pathogenic9
Uncertain significance60
Likely benign16
Benign25

Top pathogenic / likely-pathogenic (25)

Variant IDHGVSClassification
1065563NM_000144.5(FXN):c.165+1338AAG[180]Pathogenic
1807205NM_000144.5(FXN):c.169del (p.Ser57fs)Pathogenic
3384335NM_000144.5(FXN):c.2del (p.Met1fs)Pathogenic
35514NM_000144.5(FXN):c.371_376delinsTACACCTTGAGGACA (p.Asp124_Ser126delinsValHisLeuGluAspThr)Pathogenic
3571552NM_000144.5(FXN):c.165+5G>CPathogenic
3979NM_000144.5(FXN):c.317T>G (p.Leu106Ter)Pathogenic
3980NM_000144.5(FXN):c.385-2A>GPathogenic
3981NM_000144.5(FXN):c.460A>T (p.Ile154Phe)Pathogenic
3983NM_000144.5(FXN):c.3G>T (p.Met1Ile)Pathogenic
3985NM_000144.5(FXN):c.157del (p.Arg53fs)Pathogenic
4072409NC_000009.12:g.69037287_69037304GAA[120]Pathogenic
4685500NM_000144.5(FXN):c.211del (p.Gln71fs)Pathogenic
549677NM_000144.5(FXN):c.438C>G (p.Asn146Lys)Pathogenic
561195NG_008845.2:g.6725GAA[(200_900)]Pathogenic
585889NM_000144.5(FXN):c.285T>A (p.Tyr95Ter)Pathogenic
585891NM_000144.5(FXN):c.317T>C (p.Leu106Ser)Pathogenic
1064596NM_000144.5(FXN):c.166-5T>GLikely pathogenic
3233904NM_000144.5(FXN):c.483-12_483delLikely pathogenic
3340519NM_000144.5(FXN):c.482+1G>TLikely pathogenic
3902437NM_000144.5(FXN):c.410G>T (p.Gly137Val)Likely pathogenic
3984NM_000144.5(FXN):c.517T>G (p.Trp173Gly)Likely pathogenic
447362NM_000144.5(FXN):c.385-1G>CLikely pathogenic
447363NM_000144.5(FXN):c.483-2A>GLikely pathogenic
585887NM_000144.5(FXN):c.165+2_165+3insTTLikely pathogenic
804823NM_000144.5(FXN):c.498T>G (p.Tyr166Ter)Likely pathogenic

SpliceAI

559 predictions. Top by Δscore:

VariantEffectΔscore
9:69035943:GCGCA:Gdonor_gain1.0000
9:69035945:GCA:Gdonor_gain1.0000
9:69035948:G:GGdonor_gain1.0000
9:69046481:GG:Gdonor_gain1.0000
9:69046482:GG:Gdonor_gain1.0000
9:69053138:A:AGacceptor_gain1.0000
9:69053139:G:GTacceptor_gain1.0000
9:69053139:GC:Gacceptor_gain1.0000
9:69053139:GCT:Gacceptor_gain1.0000
9:69053139:GCTCT:Gacceptor_gain1.0000
9:69053240:G:GTdonor_gain1.0000
9:69064928:A:AGacceptor_gain1.0000
9:69064936:AGAGT:Aacceptor_gain1.0000
9:69064937:GA:Gacceptor_gain1.0000
9:69064937:GAGTG:Gacceptor_gain1.0000
9:69035944:CGCA:Cdonor_gain0.9900
9:69035945:GCAG:Gdonor_gain0.9900
9:69035946:CA:Cdonor_gain0.9900
9:69035946:CAG:Cdonor_loss0.9900
9:69035947:AGT:Adonor_loss0.9900
9:69035949:T:Adonor_loss0.9900
9:69035950:AAGTA:Adonor_loss0.9900
9:69035951:AGTA:Adonor_loss0.9900
9:69046379:TTTCA:Tacceptor_loss0.9900
9:69046380:TTCA:Tacceptor_loss0.9900
9:69046382:CAGAG:Cacceptor_loss0.9900
9:69046383:A:AGacceptor_gain0.9900
9:69046383:A:Gacceptor_loss0.9900
9:69046384:G:GGacceptor_gain0.9900
9:69046384:GA:Gacceptor_gain0.9900

AlphaMissense

1339 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:69065016:T:AW155R0.998
9:69065016:T:CW155R0.998
9:69065018:G:CW155C0.997
9:69065018:G:TW155C0.997
9:69064994:G:CK147N0.996
9:69064994:G:TK147N0.996
9:69065014:T:CI154T0.996
9:69065020:T:CL156P0.996
9:69072646:T:AW173R0.996
9:69072646:T:CW173R0.996
9:69064987:T:AI145N0.995
9:69064991:C:AN146K0.995
9:69064991:C:GN146K0.995
9:69072648:G:CW173C0.995
9:69072648:G:TW173C0.995
9:69065012:A:CQ153H0.994
9:69065012:A:TQ153H0.994
9:69065014:T:GI154S0.994
9:69072625:T:GY166D0.994
9:69064948:T:CL132S0.993
9:69064997:G:CQ148H0.993
9:69064997:G:TQ148H0.993
9:69065011:A:CQ153P0.993
9:69072622:C:AR165S0.993
9:69064980:T:GY143D0.992
9:69072614:G:AG162E0.992
9:69064987:T:GI145S0.991
9:69064989:A:GN146D0.991
9:69064984:T:AV144E0.990
9:69065014:T:AI154N0.990

dbSNP variants (sampled 300 via entrez): RS1000003747 (9:69066438 A>C,G), RS1000026936 (9:69063351 A>C), RS1000059908 (9:69063687 T>A,G), RS1000216546 (9:69041046 T>A,G), RS1000217473 (9:69058980 A>G), RS1000301834 (9:69057318 C>T), RS1000317313 (9:69034143 CT>C), RS1000389384 (9:69051090 T>TTTTTA), RS1000390367 (9:69047303 G>A), RS1000481324 (9:69069849 A>C,G), RS1000517863 (9:69042406 T>C,G), RS1000723664 (9:69052709 A>AT), RS1000798135 (9:69048903 T>C), RS1000934505 (9:69066090 A>G), RS1000941987 (9:69045971 A>G)

Disease associations

OMIM: gene MIM:606829 | disease phenotypes: MIM:229300

GenCC curated gene-disease

DiseaseClassificationInheritance
Friedreich ataxia 1DefinitiveAutosomal recessive
Friedreich ataxiaStrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Friedreich ataxiaDefinitiveAR

Mondo (5): Friedreich ataxia 1 (MONDO:0100340), hypertrophic cardiomyopathy (MONDO:0005045), Friedreich ataxia (MONDO:0100339), Friedreich ataxia with retained reflexes (MONDO:0800301), (MONDO:0009245)

Orphanet (2): Friedreich ataxia (Orphanet:95), Rare hypertrophic cardiomyopathy (Orphanet:217569)

HPO phenotypes

78 total (30 of 78 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000012Urinary urgency
HP:0000365Hearing impairment
HP:0000505Visual impairment
HP:0000570Abnormal saccadic eye movements
HP:0000639Nystagmus
HP:0000648Optic atrophy
HP:0000649Abnormality of visual evoked potentials
HP:0000716Depression
HP:0000739Anxiety
HP:0000763Sensory neuropathy
HP:0000819Diabetes mellitus
HP:0001063Acrocyanosis
HP:0001123Visual field defect
HP:0001251Ataxia
HP:0001257Spasticity
HP:0001260Dysarthria
HP:0001272Cerebellar atrophy
HP:0001310Dysmetria
HP:0001315Reduced tendon reflexes
HP:0001324Muscle weakness
HP:0001332Dystonia
HP:0001618Dysphonia
HP:0001626Abnormality of the cardiovascular system
HP:0001635Congestive heart failure
HP:0001638Cardiomyopathy
HP:0001639Hypertrophic cardiomyopathy
HP:0001691Muscular subvalvular aortic stenosis
HP:0001760Abnormal foot morphology
HP:0001761Pes cavus

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002719_8Seasonality9.000000e-06
GCST003542_111Night sleep phenotypes1.000000e-06
GCST003997_29Myopia7.000000e-21
GCST005337_26Headache2.000000e-08
GCST007930_140Medication use (agents acting on the renin-angiotensin system)5.000000e-11
GCST010002_320Refractive error3.000000e-39

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0006876seasonality measurement
EFO:0009931Agents acting on the renin-angiotensin system use measurement

MeSH disease descriptors (3)

DescriptorNameTree numbers
D002312Cardiomyopathy, HypertrophicC14.280.238.100; C14.280.484.048.750.070.160
D005621Friedreich AtaxiaC10.228.140.252.700.150; C10.228.854.787.200; C10.574.500.825.200; C16.320.400.780.200; C18.452.660.300
C565561Friedreich Ataxia 1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2321640 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

57 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases expression, decreases expression3
Ironincreases abundance, increases metabolic processing, affects binding3
Acetaminophenaffects cotreatment, decreases expression2
Cisplatinincreases expression2
Tretinoinaffects cotreatment, increases expression, decreases expression2
Valproic Acidaffects expression, increases expression2
GSK-J4decreases expression1
RG2833increases expression1
bisphenol Fincreases expression, affects cotreatment1
A-196 compoundincreases expression, increases response to substance1
alpha phellandrenedecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
trichostatin Aaffects expression1
beta-lapachonedecreases expression1
arseniteaffects binding, increases reaction1
cobaltous chloridedecreases expression1
potassium chromate(VI)decreases expression, affects cotreatment1
4-hydroxy-2-nonenalaffects expression, affects reaction1
epigallocatechin gallateaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
benzyloxycarbonylvalyl-alanyl-aspartyl fluoromethyl ketoneaffects reaction, affects response to substance1
2-palmitoylglycerolincreases expression1
nutlin 3affects cotreatment, increases secretion1
abrinedecreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidinedecreases expression, increases response to substance1
bisphenol Saffects cotreatment, increases expression1
ferrostatin-1affects reaction, affects response to substance1
Resveratrolincreases expression1
Deferiproneincreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL2329912BindingBinding affinity to recombinant His-tagged frataxin (unknown origin) at 1 uM at 37 degC by UF-LC/MS analysis relative to controlDiscovery of a novel small molecule inhibitor targeting the frataxin/ubiquitin interaction via structure-based virtual screening and bioassays. — J Med Chem

Cellosaurus cell lines

102 cell lines: 51 transformed cell line, 35 finite cell line, 16 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_0U91GM14519Transformed cell lineFemale
CVCL_0U92GM15847Transformed cell lineFemale
CVCL_0U93GM15848Transformed cell lineMale
CVCL_0U94GM15849Transformed cell lineMale
CVCL_0U95GM16201Transformed cell lineFemale
CVCL_0U97GM16204Transformed cell lineFemale
CVCL_0U98GM16205Transformed cell lineMale
CVCL_0U99GM16218Transformed cell lineMale
CVCL_0V00GM16219Transformed cell lineFemale
CVCL_0V01GM16222Transformed cell lineFemale

Clinical trials (associated diseases)

328 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT01716221PHASE4COMPLETEDAn Objective Double-blind Evaluation of Bupropion and Citalopram in an Individual With Friedreich Ataxia
NCT04801303PHASE4COMPLETEDEvaluation of the Effects of Calcitriol’s in the Neurological Symptoms of Friedreich’s Ataxia Patients
NCT00879060PHASE4COMPLETEDClinical and Therapeutic Implications of Fibrosis in Hypertrophic Cardiomyopathy
NCT01721967PHASE4COMPLETEDRanolazine for the Treatment of Chest Pain in HCM Patients
NCT02948998PHASE4UNKNOWNEvaluating the Effect of Spironolactone on Hypertrophic Cardiomyopathy
NCT03249272PHASE4TERMINATEDMicrovascular Dysfunction in Nonischemic Cardiomyopathy: Insights From CMR Assessment of Coronary Flow Reserve
NCT04133532PHASE4COMPLETEDEffect of Metoprolol in Post Alcohol Septal Ablation Patients With Hypertrophic Cardiomyopathy
NCT06401343PHASE4RECRUITINGUse of SGLT2i in noHCM With HFpEF
NCT07103655PHASE4NOT_YET_RECRUITINGThe Therapeutic Value of Mavacamten in Hypertrophic Cardiomyopathy With Mid-to-Apical Left Ventricular Obstruction
NCT07600177PHASE4RECRUITINGMavacamten to Aficamten Transition in Patients With Obstructive Hypertrophic Cardiomyopathy
NCT05515536PHASE3ACTIVE_NOT_RECRUITINGA Study to Assess the Safety and Efficacy of Vatiquinone in Participants With Friedreich Ataxia
NCT06953583PHASE3RECRUITINGA Study to Learn More About the Effects and Long-Term Safety of BIIB141 (Omaveloxolone) in Participants With Friedreich’s Ataxia Aged 2 to 15 Years Old (BRAVE)
NCT00537680PHASE3COMPLETEDStudy to Assess the Efficacy, Safety and Tolerability of Idebenone in the Treatment of Friedreich’s Ataxia
NCT00697073PHASE3COMPLETEDStudy to Assess the Safety and Tolerability of Idebenone in the Treatment of Friedreich’s Ataxia Patients
NCT00811681PHASE3COMPLETEDEffect of Pioglitazone Administered to Patients With Friedreich’s Ataxia: Proof of Concept
NCT00905268PHASE3COMPLETEDA Study of Efficacy, Safety and Tolerability of Idebenone in the Treatment of Friedreich’s Ataxia (FRDA) Patients
NCT01303406PHASE3COMPLETEDPatient Reported Outcomes in Friedreich’s Ataxia Patients After Withdrawal From Treatment With Idebenone (PROTI)
NCT02415127PHASE3COMPLETEDSafety, Tolerability and Efficacy of ACTIMMUNE® Dose Escalation in Friedreich’s Ataxia
NCT02593773PHASE3COMPLETEDSafety, Tolerability and Efficacy of ACTIMMUNE® Dose Escalation in Friedreich’s Ataxia Study
NCT02797080PHASE3COMPLETEDLong-Term Safety Extension Study of ACTIMMUNE® (Interferon γ-1b) in Children and Young Adults With Friedreich’s Ataxia
NCT04102501PHASE3COMPLETEDA Study to Assess Efficacy, Long Term Safety and Tolerability of RT001 in Subjects With Friedreich’s Ataxia
NCT00317967PHASE3COMPLETEDStudy to Determine if Atorvastatin Reduces Size and Stiffness of Muscle in the Left Ventricle of the Heart
NCT00698074PHASE3UNKNOWNDiastolic Ventricular Interaction and the Effects of Biventricular Pacing in Hypertrophic Cardiomyopathy
NCT00821353PHASE3COMPLETEDAntiarrhythmic Therapy Versus Catheter Ablation for Atrial Fibrillation in Hypertrophic Cardiomyopathy
NCT02431221PHASE3WITHDRAWNEfficacy, Safety, and Tolerability of Perhexiline in Subjects With Hypertrophic Cardiomyopathy and Heart Failure
NCT03470545PHASE3COMPLETEDClinical Study to Evaluate Mavacamten (MYK-461) in Adults With Symptomatic Obstructive Hypertrophic Cardiomyopathy
NCT05174416PHASE3COMPLETEDA Study to Evaluate the Efficacy and Safety of Mavacamten in Chinese Adults With Symptomatic Obstructive HCM
NCT05182658PHASE3ACTIVE_NOT_RECRUITINGEmpagliflozin in Hypertrophic Cardiomyopathy
NCT05186818PHASE3COMPLETEDPhase 3 Trial to Evaluate the Efficacy and Safety of Aficamten Compared to Placebo in Adults With Symptomatic oHCM
NCT05767346PHASE3COMPLETEDPhase 3 Trial to Evaluate the Efficacy and Safety of Aficamten Compared to Metoprolol Succinate in Adults With Symptomatic oHCM
NCT06116968PHASE3COMPLETEDAn Open-Label Study of Aficamten for Chinese Patients With Symptomatic oHCM
NCT06873828PHASE3NOT_YET_RECRUITINGEvaluation of the Efficacy and Safety of Wearable ECG (AT-Patch) in Patients With Hypertrophic Cardiomyopathy Requiring 48-Hour Holter MonitoringEvaluation of the Efficacy and Safety of Wearable ECG (AT-Patch) in Patients With Hypertrophic Cardiomyopathy Requiring 48-Hour Holter Monitoring
NCT07021976PHASE3RECRUITINGA Phase III Trial of HRS-1893 in Patients With Obstructive Hypertrophic Cardiomyopathy
NCT07023341PHASE3ACTIVE_NOT_RECRUITINGA Study to Learn More About How Well Aficamten Works in Japanese Participants With Symptomatic Obstructive Hypertrophic Cardiomyopathy
NCT07202897PHASE3NOT_YET_RECRUITINGLA-HCM Study : Rivaroxaban for Antithrombotic Prevention in Hypertrophic Cardiomyopathy Patients With Abnormal Left Atrial Strain.
NCT00229632PHASE2COMPLETEDIdebenone to Treat Friedreich’s Ataxia
NCT00824512PHASE2COMPLETEDEfficacy of EGb761 in Patients Suffering From Friedreich Ataxia
NCT01493973PHASE2COMPLETEDEfficacy Study of Epoetin Alfa in Friedreich Ataxia
NCT01965327PHASE2COMPLETEDInterferon Gamma-1b in Friedreich Ataxia (FRDA)
NCT02035020PHASE2COMPLETEDA Phase IIa Trial to Test Safety and Efficacy Interferon Gamma Treatment in Elevating Frataxin Levels in FRDA Patients