Is EED p.Ile352Val (c.1054A>G) pathogenic?

EED p.Ile352Val (c.1054A>G) is classified Uncertain significance in EED (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-08). AlphaMissense: likely benign (0.1039); Very rare (popmax 0.00227%, sas); Associated with Inborn genetic diseases.

What condition is associated with EED p.Ile352Val (c.1054A>G)?

EED p.Ile352Val (c.1054A>G) is associated with Inborn genetic diseases (ClinVar).

How common is EED p.Ile352Val (c.1054A>G) in the general population?

EED p.Ile352Val (c.1054A>G) is very rare (popmax 0.00227%, sas) (gnomAD).

What do computational predictors say about EED p.Ile352Val (c.1054A>G)?

AlphaMissense predicts likely benign (score 0.1039) — an in-silico prediction, not a clinical call.

EED p.Ile352Val

c.1054A>G · rs760494356 · VCV3087233

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1039 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00227%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1039	likely benign
REVEL	0.042	moderately benign-leaning
SaProt	LLR -7.06	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 11	GERP 2.4, phastCons 1
Regional constraint	o/e 0.45	unconstrained · MANE · 28 kb · p 8.5e-32 · regional, not allelic
Overall
CADD	20.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00227% South Asian · 2/88,086 alleles

Filtering AF 0.000377% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000141%

Overall 0.000188% 3/1,594,876 alleles · very rare exomes 3/1,442,562 · genomes 0/152,314 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00227%	44,043
European (non-Finnish)	8.57e-05%	1,167,018

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.Ile352Val
Coding: c.1054A>G
MANE Select: NM_003797
dbSNP: rs760494356
Type: single nucleotide variant
Location: chr11:86277067 (GRCh38)
Gene constraint: LOEUF 0.41 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 87.21 · 81 PDB
Residue 352: 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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EED c.268-3T>C Conflicting classifications of pathogenicity ★ same condition
EED p.Ala327Ser Uncertain significance ★ ⚠ same condition
EED p.Ala41Thr Uncertain significance ★ ⚠ same condition
EED p.Arg4Ser Uncertain significance ★ ⚠ same condition
EED p.Asn102Asp Uncertain significance ★ ⚠ same condition
EED p.Asn266Thr Uncertain significance ★ ⚠ same condition
EED p.Asn272Ser Uncertain significance ★ ⚠ same condition
EED p.Asn38Thr Uncertain significance ★ ⚠ 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-ile352val (accessed [today's date]).

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