Is EED p.Met256Thr (c.767T>C) pathogenic?

EED p.Met256Thr (c.767T>C) is classified Likely pathogenic in EED (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-13). AlphaMissense: likely pathogenic (1); Absent from gnomAD v4.1; Associated with autism spectrum disorder.

What condition is associated with EED p.Met256Thr (c.767T>C)?

EED p.Met256Thr (c.767T>C) is associated with autism spectrum disorder (ClinVar).

How common is EED p.Met256Thr (c.767T>C) in the general population?

EED p.Met256Thr (c.767T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EED p.Met256Thr (c.767T>C)?

AlphaMissense predicts likely pathogenic (score 1) — an in-silico prediction, not a clinical call.

EED p.Met256Thr

c.767T>C · rs2495862536 · VCV2429866

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

1 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

autism spectrum disorder

Computational evidence

Protein change
AlphaMissense	1	likely pathogenic ✓ concordant with ClinVar · top 8% in EED
REVEL	0.62	indeterminate
SaProt	LLR -14.45	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>G here scores Δ0.22 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.8	GERP 2.4, phastCons 1
Regional constraint	o/e 0.45	unconstrained · MANE · 28 kb · p 8.5e-32 · regional, not allelic
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EED
Protein: p.Met256Thr
Coding: c.767T>C
MANE Select: NM_003797
dbSNP: rs2495862536
Type: single nucleotide variant
Location: chr11:86266123 (GRCh38)
Gene constraint: LOEUF 0.41 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 87.21 · 81 PDB
Residue 256: the 'interaction with ezh2' region; the 'required for interaction with the matrix protein ma of hiv-1' region; a β-strand

Full EED gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autism spectrum disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-met256thr (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown