EIF3F p.Thr175=
c.525G>A · rs147597507 · VCV2672458
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, sas)
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 0.081 | GERP -3.2, phastCons 0.055 |
| Overall | ||
| CADD | 10.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
South Asian · 30/91,080 alleles
Filtering AF
0.0237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0205%
Overall
0.00874%
141/1,613,944 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0329% | 3,036 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,926 |
| European (non-Finnish) | 0.00847% | 11,800 |
| African / African-American | 0.00534% | 18,724 |
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.Thr175=
- Coding
- c.525G>A
- MANE Select
- NM_003754
- dbSNP
- rs147597507
- Type
- single nucleotide variant
- Location
- chr11:7992896 (GRCh38)
- Gene constraint
- LOEUF 0.46 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.97 · 29 PDB
- Residue 175
- the mpn domain; a β-strand
Similar variants
- EIF3F p.Thr175fs Uncertain significance ★ 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-thr175 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown