EIF3F p.Pro39=
c.117C>T · VCV3910858
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0246%, eas)
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 -5.8 | GERP -2.3 |
| Overall | ||
| CADD | 2.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0246%
East Asian · 11/44,790 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00106%
17/1,605,128 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0246% | 4,072 |
| European (non-Finnish) | 0.000509% | 196,472 |
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
- EIF3F
- Protein
- p.Pro39=
- Coding
- c.117C>T
- MANE Select
- NM_003754
- Type
- single nucleotide variant
- Location
- chr11:7987469 (GRCh38)
- Gene constraint
- LOEUF 0.46 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.97 · 29 PDB
- Residue 39
- a UniProt-annotated variant site (in); the 'disordered' region
Similar variants
- EIF3F p.Pro39Leu Benign ⚠ same residue
- EIF3F p.Phe232Val Pathogenic/Likely pathogenic ★★ same type
- EIF3F p.Arg306Cys Uncertain significance ★★ ⚠ same type
- EIF3F p.Asn260Ser Uncertain significance ★★ same type
- EIF3F p.Asp292Glu Uncertain significance ★★ ⚠ same type
- EIF3F p.Ser267Gly Uncertain significance ★★ ⚠ same type
- EIF3F p.Thr14Met Uncertain significance ★★ ⚠ same type
- EIF3F p.Thr303Ile 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/eif3f-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown