Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.47%, afr) — too common for a highly-penetrant pathogenic allele
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 2.1 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 7.554 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.47%
African / African-American · 3,199/58,432 alleles
Filtering AF
5.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.25%
Overall
0.34%
3,608/1,060,758 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.47% | 18 |
| Admixed American | 0.713% | 140 |
| Middle Eastern | 0.478% | 209 |
| Remaining individualsnot grpmax-eligible | 0.455% | 220 |
| Ashkenazi Jewishnot grpmax-eligible | 0.207% | 483 |
| European (non-Finnish) | 0.0103% | 9,672 |
| South Asian | 0.00806% | 12,403 |
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.Ser37=
- Coding
- c.111C>T
- MANE Select
- NM_005225
- dbSNP
- rs3213143
- Type
- single nucleotide variant
- Location
- chr20:33686154 (GRCh38)
- Gene constraint
- LOEUF 0.399 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 63.40 · 8 PDB
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-ser37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown