EED p.Ala242=
c.726T>C · rs372966988 · VCV2854403
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
Conditions
1
Cohen-Gibson syndrome
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 1.9 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 15.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,074 alleles
Filtering AF
0.00581%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00273%
44/1,611,808 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,037 |
| Admixed American | 0.0117% | 8,570 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,801 |
| European (non-Finnish) | 0.00272% | 36,813 |
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
- EED
- Protein
- p.Ala242=
- Coding
- c.726T>C
- MANE Select
- NM_003797
- dbSNP
- rs372966988
- Type
- single nucleotide variant
- Location
- chr11:86264263 (GRCh38)
- Gene constraint
- LOEUF 0.41 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.21 · 81 PDB
- Residue 242
- the 'interaction with ezh2' region; the 'required for interaction with the matrix protein ma of hiv-1' region; a β-strand
Similar variants
- EED p.Ala242Ser Uncertain significance ★ ⚠ same residue
- EED p.Asn194Ser Pathogenic/Likely pathogenic ★★ same condition
- EED p.Asp237Gly Likely pathogenic ★★ same condition
- EED p.Ala17Val Uncertain significance ★★ ⚠ same condition
- EED p.Arg4Met Uncertain significance ★★ ⚠ same condition
- EED p.Lys83Ile Uncertain significance ★★ ⚠ same condition
- EED c.267+20C>G Benign/Likely benign ★★ same condition
- EED c.361-19G>A Likely benign ★★ same condition
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/eed-p-ala242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown