EED p.Thr405=
c.1215T>G · rs765631955 · VCV730225
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0424%, eas)
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 1.5 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 10.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0424%
East Asian · 19/44,860 alleles
Filtering AF
0.0277%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.023%
Overall
0.0013%
19/1,461,054 alleles · ultra-rare
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.Thr405=
- Coding
- c.1215T>G
- MANE Select
- NM_003797
- dbSNP
- rs765631955
- Type
- single nucleotide variant
- Location
- chr11:86278414 (GRCh38)
- Gene constraint
- LOEUF 0.41 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.21 · 81 PDB
- Residue 405
- the 'interaction with ezh2' region; the 'required for interaction with the matrix protein ma of hiv-1' region
Similar variants
- EED p.Asn194Ser Pathogenic/Likely pathogenic ★★ same type
- EED p.Asp237Gly Likely pathogenic ★★ same type
- EED p.Ala17Val Uncertain significance ★★ ⚠ same type
- EED p.Arg4Met Uncertain significance ★★ ⚠ same type
- EED p.Lys83Ile Uncertain significance ★★ ⚠ same type
- EED c.267+20C>G Benign/Likely benign ★★ same type
- EED c.268-43G>A Benign ★★ same type
- EED c.361-19G>A Likely benign ★★ 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/eed-p-thr405 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown