Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.61%, afr) — too common for a highly-penetrant pathogenic allele
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 -1.3 | GERP -3.2 |
| Overall | ||
| CADD | 5.632 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.61%
African / African-American · 4,959/74,992 alleles
Filtering AF
6.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.4%
Overall
0.336%
5,416/1,613,296 alleles · common
exomes 2,595/1,461,016 · genomes 2,821/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.61% | 15 |
| Remaining individualsnot grpmax-eligible | 0.374% | 267 |
| Admixed American | 0.258% | 387 |
| Middle Eastern | 0.0826% | 1,211 |
| South Asian | 0.00659% | 15,179 |
| European (non-Finnish) | 0.00483% | 20,689 |
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
- FNTA
- Protein
- p.Pro309=
- Coding
- c.927C>A
- MANE Select
- NM_002027
- dbSNP
- rs2230266
- Type
- single nucleotide variant
- Location
- chr8:43084791 (GRCh38)
- Gene constraint
- LOEUF 1.425 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.12 · 14 PDB
- Residue 309
- an α-helix
Similar variants
- FNTA p.Arg121Gln Uncertain significance ★ ⚠ same type
- FNTA p.Arg287Cys Uncertain significance ★ ⚠ same type
- FNTA p.Arg287Gly Uncertain significance ★ ⚠ same type
- FNTA p.Arg287Pro Uncertain significance ★ ⚠ same type
- FNTA p.Asn165Thr Uncertain significance ★ ⚠ same type
- FNTA p.Asn218Lys Uncertain significance ★ ⚠ same type
- FNTA p.Asn329Ser Uncertain significance ★ ⚠ same type
- FNTA p.Asp110Gly 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/fnta-p-pro309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown