EIF3F p.Pro75=
c.225C>A · rs375415343 · VCV3039652
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.432%, afr)
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 0.39 | GERP -2.1, phastCons 0.02 |
| Overall | ||
| CADD | 6.111 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.432%
African / African-American · 320/74,148 alleles
Filtering AF
0.393%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.377%
Overall
0.023%
367/1,597,102 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.432% | 232 |
| Remaining individualsnot grpmax-eligible | 0.0472% | 2,118 |
| Admixed American | 0.0276% | 3,618 |
| South Asian | 0.00112% | 88,940 |
| European (non-Finnish) | 8.52e-05% | 1,173,202 |
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.Pro75=
- Coding
- c.225C>A
- MANE Select
- NM_003754
- dbSNP
- rs375415343
- Type
- single nucleotide variant
- Location
- chr11:7987577 (GRCh38)
- Gene constraint
- LOEUF 0.46 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.97 · 29 PDB
- Residue 75
- the 'disordered' region
Similar variants
- 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
- EIF3F c.*24C>T Benign ★★ 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-pro75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown