FXN p.Arg29=
c.87G>A · VCV4903200
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0775%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.6 | GERP -0.19 |
| Overall | ||
| CADD | 5.778 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0775%
South Asian · 62/80,038 alleles
Filtering AF
0.062%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0564%
Overall
0.00621%
93/1,496,620 alleles · ultra-rare
exomes 91/1,344,496 · genomes 2/152,124 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0775% | 1,291 |
| Middle Eastern | 0.0233% | 4,288 |
| Remaining individualsnot grpmax-eligible | 0.00861% | 11,610 |
| Finnishnot grpmax-eligible | 0.00228% | 43,774 |
| European (non-Finnish) | 0.00212% | 47,077 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- FXN
- Protein
- p.Arg29=
- Coding
- c.87G>A
- MANE Select
- NM_000144
- Type
- single nucleotide variant
- Location
- chr9:69035869 (GRCh38)
- Gene constraint
- LOEUF 0.809 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 75.93 · 19 PDB
Similar variants
- FXN p.Leu106Ser Pathogenic ★★ same type
- FXN p.Met1Ile Pathogenic ★★ same type
- FXN p.Arg43His Uncertain significance ★★ ⚠ same type
- FXN p.Gly138Arg Uncertain significance ★★ ⚠ same type
- FXN p.Leu24Phe Uncertain significance ★★ ⚠ same type
- FXN p.Leu33Val Uncertain significance ★★ ⚠ same type
- FXN p.Pro30Thr Uncertain significance ★★ ⚠ same type
- FXN p.Ser158Phe Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/fxn-p-arg29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown