FXN
Chr 9ARfrataxin
Also known as: CyaY, FA, FARR, FRDA, X25
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]
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
This gene — mechanism propensity
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
148 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 7 | 5 | 4 | 0 | 16 |
Likely Pathogenic | 7 | 2 | 1 | 0 | 10 |
VUS | 1 | 50 | 3 | 3 | 57 |
Likely Benign | 0 | 7 | 3 | 9 | 19 |
Benign | 0 | 3 | 18 | 4 | 25 |
Conflicting | — | 9 | |||
| Total | 15 | 67 | 29 | 16 | 136 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →41 pathogenic / likely-pathogenic (of 57) ClinVar copy-number / structural variants overlap FXN — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →
Protein Context — Lollipop Plot
FXN · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
A Study of SGT-212 Gene Therapy in Friedreich's Ataxia
RECRUITINGA Natural History Study to TRACK Brain and Spinal Cord Changes in Individuals with Friedreich Ataxia (TRACK-FA)
ACTIVE NOT RECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
RECRUITINGCharacterisation of the Cognitive Profile of Patients Suffering From Friedreich's Ataxia
RECRUITINGBiomarkers in Friedreich's Ataxia
RECRUITINGA Randomized, Parallel-arm, Double Blind, Placebo-controlled Study to Assess the Efficacy of Fampridine for Patients With Spinocerebellar Ataxia SCA27B Caused by a GAA Expansion in the FGF14 Gene
RECRUITINGGene Therapy for Cardiomyopathy Associated With Friedreich's Ataxia
ACTIVE NOT RECRUITINGFriedreich Ataxia Nerve Ultrasund
RECRUITINGPhase IA and IB Study of AAVrh.10hFXN Gene Therapy for the Cardiomyopathy of Friedreich's Ataxia
RECRUITINGExternal Resources
Links to major genomics databases and tools