Gene Gene information from NCBI Gene database.
Entrez ID 2395
Gene name Frataxin
Gene symbol FXN
Synonyms (NCBI Gene)
CyaYFAFARRFRDAX25
Chromosome 9
Chromosome location 9q21.11
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 r
SNPs SNP information provided by dbSNP.
18
SNP ID Visualize variation Clinical significance Consequence
rs56214919 T>G Likely-pathogenic Synonymous variant, missense variant, coding sequence variant
rs104894105 T>C,G Pathogenic Coding sequence variant, stop gained, missense variant
rs104894106 A>G,T Pathogenic Coding sequence variant, missense variant
rs104894107 G>C,T Pathogenic Coding sequence variant, missense variant
rs104894108 G>A,T Pathogenic Initiator codon variant, missense variant
miRNA miRNA information provided by mirtarbase database.
625
miRTarBase ID miRNA Experiments Reference
MIRT007228 hsa-miR-559 Luciferase reporter assay 23382970
MIRT007229 hsa-miR-589-5p Luciferase reporter assay 23382970
MIRT007230 hsa-miR-1270 Luciferase reporter assay 23382970
MIRT007231 hsa-miR-620 Luciferase reporter assay 23382970
MIRT007232 hsa-miR-522-3p Luciferase reporter assay 23382970
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
SRF Unknown 20808827
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
69
GO ID Ontology Definition Evidence Reference
GO:0004322 Function Ferroxidase activity IDA 15641778
GO:0004322 Function Ferroxidase activity IEA
GO:0005515 Function Protein binding IPI 15123683, 15961414, 26702583, 31101807, 32296183, 32814053
GO:0005737 Component Cytoplasm IEA
GO:0005739 Component Mitochondrion HTP 34800366
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606829 3951 ENSG00000165060
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q16595
Protein name Frataxin, mitochondrial (EC 1.16.3.1) (Friedreich ataxia protein) (Fxn) [Cleaved into: Frataxin intermediate form (i-FXN); Frataxin(56-210) (m56-FXN); Frataxin(78-210) (d-FXN) (m78-FXN); Frataxin mature form (Frataxin(81-210)) (m81-FXN); Extramitochondria
Protein function [Frataxin mature form]: 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 (PubMed:12785837, PubMe
PDB 1EKG , 1LY7 , 3S4M , 3S5D , 3S5E , 3S5F , 3T3J , 3T3K , 3T3L , 3T3T , 3T3X , 5KZ5 , 6NZU , 8PK8 , 8PK9 , 8RME
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01491 Frataxin_Cyay 90 198 Frataxin-like domain Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in the heart, peripheral blood lymphocytes and dermal fibroblasts. {ECO:0000269|PubMed:17468497}.
Sequence
MWTLGRRAVAGLLASPSPAQAQTLTRVPRPAELAPLCGRRGLRTDIDATCTPRRASSNQR
GLNQIWNVKKQSVYLMNLRKSGTLGHPGSLDETTYERLAEETLDSLAEFFEDLADKPYTF
EDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGV
SLHELLAAELTKALKTKL
DLSSLAYSGKDA
Sequence length 210
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Porphyrin metabolism   Mitochondrial protein import
Mitochondrial iron-sulfur cluster biogenesis
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
40
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Friedreich ataxia Pathogenic; Likely pathogenic rs104894105, rs140987490, rs104894106, rs104894108, rs56214919, rs141935559 RCV000004186
RCV000004187
RCV000004188
RCV000004190
RCV000004191
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Friedreich ataxia 1 Likely pathogenic; Pathogenic rs2133102338, rs193922938, rs104894106, rs104894108, rs143232208, rs2539217018, rs886037630, rs146818694 RCV001726502
RCV001726540
RCV004689408
RCV004017228
RCV003999024
View all (3 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
BILIARY TRACT CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cardiovascular phenotype Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adamantinous Craniopharyngioma Adamantinous Craniopharyngioma BEFREE 30031876
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of colon Adenocarcinoma Of Colon BEFREE 16091420
★☆☆☆☆
Found in Text Mining only
Adult Oligodendroglioma Oligodendroglioma BEFREE 17499976
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 17191135, 24613765, 31456211
★☆☆☆☆
Found in Text Mining only
Ataxia Ataxia Pubtator 17110750, 19485941, 20001966, 23242090, 33348670, 34747814, 38396238 Associate
★☆☆☆☆
Found in Text Mining only
Ataxia Telangiectasia Ataxia Telangiectasia BEFREE 14653406, 15279807, 16700949, 19440741, 21496573, 2722185, 9708552
★☆☆☆☆
Found in Text Mining only
Ataxia with vitamin E deficiency Friedreich Ataxia BEFREE 26068213, 29891058, 7726167, 8602747, 9463307
★☆☆☆☆
Found in Text Mining only
ATAXIA, EARLY-ONSET, WITH OCULOMOTOR APRAXIA AND HYPOALBUMINEMIA Ataxia-oculomotor apraxia BEFREE 17572444, 17917453, 30599859
★☆☆☆☆
Found in Text Mining only
Ataxia, Spinocerebellar Spinocerebellar Ataxia BEFREE 11844730, 11960886, 16500684, 16644517, 18267270, 18725397, 20393313, 24840976, 28716278, 29440566, 29891061, 30786918, 31838195, 9339708, 9429138
View all (1 more)
★☆☆☆☆
Found in Text Mining only
Ataxias, Hereditary Ataxia BEFREE 25765228, 29509186, 30786918, 31494282, 31575456, 7231446
★☆☆☆☆
Found in Text Mining only