E2F1 p.Ser392=
c.1176C>T · rs142009843 · VCV3033085
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0772%, 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 -0.33 | GERP -1.5 |
| Overall | ||
| CADD | 5.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0772%
European (non-Finnish) · 898/1,163,164 alleles
Filtering AF
0.073%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0713%
Overall
0.0607%
960/1,582,378 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0772% | 1,295 |
| Remaining individualsnot grpmax-eligible | 0.036% | 2,780 |
| Admixed American | 0.0337% | 2,964 |
| Finnishnot grpmax-eligible | 0.0244% | 4,106 |
| Middle Eastern | 0.0166% | 6,018 |
| African / African-American | 0.0054% | 18,524 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00345% | 29,014 |
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
- E2F1
- Protein
- p.Ser392=
- Coding
- c.1176C>T
- MANE Select
- NM_005225
- dbSNP
- rs142009843
- Type
- single nucleotide variant
- Location
- chr20:33676870 (GRCh38)
- Gene constraint
- LOEUF 0.399 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 63.40 · 8 PDB
- Residue 392
- the 'transactivation' region
Similar variants
- RBP3 p.Arg388Ter Pathogenic ★★ same type
- RBP3 p.Gln141Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 p.Gln54Ter Pathogenic ★★ same type
- RBP3 p.Glu149Ter Pathogenic ★★ same type
- RBP3 p.Glu692Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 p.Tyr784Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 p.Tyr841Ter Pathogenic/Likely pathogenic ★★ same type
- RBP3 c.3388+4C>G 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/e2f1-p-ser392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown