E2F1 p.Ala78=
c.234G>C · rs984482701 · VCV734667
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.443%, 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 -0.6 | GERP 1.7, phastCons 0.049 |
| Overall | ||
| CADD | 7.105 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.443%
African / African-American · 269/60,666 alleles
Filtering AF
0.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.383%
Overall
0.0267%
303/1,133,460 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.443% | 226 |
| Middle Eastern | 0.222% | 451 |
| Admixed American | 0.0344% | 2,908 |
| Remaining individualsnot grpmax-eligible | 0.0284% | 3,524 |
| South Asian | 0.00427% | 23,446 |
| European (non-Finnish) | 0.000972% | 102,903 |
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.Ala78=
- Coding
- c.234G>C
- MANE Select
- NM_005225
- dbSNP
- rs984482701
- Type
- single nucleotide variant
- Location
- chr20:33686031 (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 78
- the 'disordered' region; the 'cyclin a:cdk2 binding' region
Similar variants
- E2F1 p.Ala78Ser Uncertain significance ★ ⚠ same residue
- RBP3 p.Val78Met Uncertain significance ★ ⚠ same residue
- 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
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-ala78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown