F2R p.Val139=
c.417G>A · VCV3910467
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0261%, nfe)
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 -0.7 | GERP -3.3 |
| Overall | ||
| CADD | 6.361 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0261%
European (non-Finnish) · 308/1,180,034 alleles
Filtering AF
0.0237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0228%
Overall
0.0198%
319/1,614,164 alleles · ultra-rare
exomes 281/1,461,892 · genomes 38/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0261% | 3,831 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| Finnishnot grpmax-eligible | 0.00781% | 12,807 |
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
- F2R
- Protein
- p.Val139=
- Coding
- c.417G>A
- MANE Select
- NM_001992
- Type
- single nucleotide variant
- Location
- chr5:76732642 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.50 · 13 PDB
- Residue 139
- an α-helix
Similar variants
- F2R p.Leu38= Benign ★★ same type
- F2R p.Ser172= Benign ★★ same type
- F2R p.Tyr381Cys Benign ★★ same type
- F2R p.Val246= Benign ★★ same type
- F2R p.Ala10Val Uncertain significance ★ ⚠ same type
- F2R p.Ala203Thr Uncertain significance ★ ⚠ same type
- F2R p.Ala268Ser Uncertain significance ★ ⚠ same type
- F2R p.Arg214Ser 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/f2r-p-val139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown