FXN p.Asp115=
c.345C>T · rs756215781 · VCV1731615
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00551%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.88 | GERP -1.2, phastCons 0.003 |
| Overall | ||
| CADD | 8.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00551%
European (non-Finnish) · 65/1,179,922 alleles
Filtering AF
0.00443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00403%
Overall
0.00409%
66/1,613,778 alleles · very rare
exomes 65/1,461,690 · genomes 1/152,088 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00551% | 18,153 |
| South Asian | 0.0011% | 91,080 |
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.Asp115=
- Coding
- c.345C>T
- MANE Select
- NM_000144
- dbSNP
- rs756215781
- Type
- single nucleotide variant
- Location
- chr9:69053221 (GRCh38)
- Gene constraint
- LOEUF 0.809 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 75.93 · 19 PDB
Similar variants
- FXN p.Arg43His Uncertain significance ★★ ⚠ same condition
- FXN p.Gly138Arg Uncertain significance ★★ ⚠ same condition
- FXN p.Leu24Phe Uncertain significance ★★ ⚠ same condition
- FXN p.Pro30Thr Uncertain significance ★★ ⚠ same condition
- FXN p.Thr49Asn Uncertain significance ★★ ⚠ same condition
- FXN p.Arg54= Benign/Likely benign ★★ same condition
- FXN p.Asp178= Benign/Likely benign ★★ same condition
- FXN p.Asp209Gly Benign/Likely benign ★★ same condition
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-asp115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown