E2F1 p.Ala102Thr
c.304G>A · rs145741678 · VCV785835
Computational evidence
| Protein change | ||
| AlphaMissense | 0.1099 | likely benign |
|---|---|---|
| REVEL | 0.083 | moderately benign-leaning |
| SaProt | LLR -6.89 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 6, phastCons 1 |
| Regional constraint | o/e 0.58 | unconstrained · MANE · 6,229 bp · p 1.9e-06 · regional, not allelic |
| Overall | ||
| CADD | 24.2 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Amishnot grpmax-eligible | 3.29% | 30 |
| South Asiangrpmax | 0.748% | 134 |
| European (non-Finnish) | 0.645% | 155 |
| Remaining individualsnot grpmax-eligible | 0.491% | 204 |
| Middle Eastern | 0.396% | 253 |
| Admixed American | 0.225% | 445 |
| Ashkenazi Jewishnot grpmax-eligible | 0.196% | 510 |
| Finnishnot grpmax-eligible | 0.144% | 696 |
| African / African-American | 0.109% | 916 |
Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Ala102Thr
- Coding
- c.304G>A
- MANE Select
- NM_005225
- dbSNP
- rs145741678
- Type
- single nucleotide variant
- Location
- chr20:33680374 (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 102
- the 'cyclin a:cdk2 binding' region; the 'interaction with birc2/c-iap1' region; the 'disordered' region
Similar variants
- RBP3 p.Val102fs Pathogenic ★ 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
- RBP3 p.Tyr841Ter 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-ala102thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown