E4F1 p.Thr93=
c.279C>G · rs146632512 · VCV2646056
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.238%, 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 -1 | GERP -3.6 |
| Overall | ||
| CADD | 2.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.238%
European (non-Finnish) · 2,803/1,179,784 alleles
Filtering AF
0.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.227%
Overall
0.186%
3,002/1,612,926 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.238% | 421 |
| Remaining individualsnot grpmax-eligible | 0.128% | 781 |
| Finnishnot grpmax-eligible | 0.0793% | 1,262 |
| Admixed American | 0.0567% | 1,765 |
| African / African-American | 0.0253% | 3,951 |
| Middle Eastern | 0.0165% | 6,050 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,400 |
| South Asian | 0.0121% | 8,280 |
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
- E4F1
- Protein
- p.Thr93=
- Coding
- c.279C>G
- MANE Select
- NM_004424
- dbSNP
- rs146632512
- Type
- single nucleotide variant
- Location
- chr16:2228493 (GRCh38)
- Gene constraint
- LOEUF 0.638 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.68
Similar variants
- E4F1 p.Arg490His Uncertain significance ★★ ⚠ same type
- E4F1 p.Lys144Gln Likely pathogenic ★ ⚠ same type
- E4F1 p.Ala124Val Uncertain significance ★ ⚠ same type
- E4F1 p.Ala152Val Uncertain significance ★ ⚠ same type
- E4F1 p.Ala15Thr Uncertain significance ★ ⚠ same type
- E4F1 p.Ala21Asp Uncertain significance ★ ⚠ same type
- E4F1 p.Ala21Ser Uncertain significance ★ ⚠ same type
- E4F1 p.Ala292Thr 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/e4f1-p-thr93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown