FXN frataxin [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 9q21.11

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (69035752..69079076)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (81209298..81252406)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (71650668..71693992)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Frataxin Loss Promotes Angiotensin II-Induced Endothelial-to-Mesenchymal Transition.
Title: Frataxin Loss Promotes Angiotensin II-Induced Endothelial-to-Mesenchymal Transition.
An In Silico Analysis of Genetic Variants and Structural Modeling of the Human Frataxin Protein in Friedreich's Ataxia.
Title: An In Silico Analysis of Genetic Variants and Structural Modeling of the Human Frataxin Protein in Friedreich's Ataxia.
Phenotypic variation of FXN compound heterozygotes in a Friedreich ataxia cohort.
Title: Phenotypic variation of FXN compound heterozygotes in a Friedreich ataxia cohort.
The Regulation of the Disease-Causing Gene FXN.
Title: The Regulation of the Disease-Causing Gene FXN.
The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue - Broad Energy Barriers and the General Properties of the Transition State.
Title: The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue - Broad Energy Barriers and the General Properties of the Transition State.
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.
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.
FXN gene methylation determines carrier status in Friedreich ataxia.
Title: FXN gene methylation determines carrier status in Friedreich ataxia.
Astrocytic mitochondrial frataxin-A promising target for ischemic brain injury.
Title: Astrocytic mitochondrial frataxin-A promising target for ischemic brain injury.
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.

Submit: New GeneRIF Correction See all GeneRIFs (176)

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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D8S2282 (e-PCR)
- UniSTS:473910

D11S3663 (e-PCR)
- UniSTS:152897

WI-17089 (e-PCR)
- UniSTS:78439

D1S1425 (e-PCR)
- UniSTS:149621

G35510 (e-PCR)
- UniSTS:44150

D11S3114 (e-PCR)
- UniSTS:152207

L17971 (e-PCR)
- UniSTS:43966

RH93216 (e-PCR)
- UniSTS:91898

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 iron chaperone activity	TAS Traceable Author Statement more info
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	IMP Inferred from Mutant Phenotype more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor 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 mitochondrial respiratory chain complex III assembly	TAS Traceable Author Statement 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
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 [2Fe-2S] assembly complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in mitochondrial matrix	IC Inferred by Curator 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
located_in mitochondrion	HTP more info	PubMed
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

EC 1.16.3.1

NP_852090.1

EC 1.16.3.1

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

NG_008845.2 RefSeqGene

Range

5190..48514

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GenBank, FASTA, Sequence Viewer (Graphics), LRG_339

mRNA and Protein(s)

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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

69035752..69079076

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

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.