Is EZH2 p.His158= (c.474C>T) pathogenic?

EZH2 p.His158= (c.474C>T) is classified Likely benign in EZH2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-08-31). Ultra-rare (popmax 0.0305%, amr); Associated with Weaver syndrome.

What condition is associated with EZH2 p.His158= (c.474C>T)?

EZH2 p.His158= (c.474C>T) is associated with Weaver syndrome (ClinVar).

How common is EZH2 p.His158= (c.474C>T) in the general population?

EZH2 p.His158= (c.474C>T) is ultra-rare (popmax 0.0305%, amr) (gnomAD).

EZH2 p.His158=

c.474C>T · rs147319809 · VCV416829

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0305%, amr)

Conditions

Weaver 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 -2.4	GERP -3.7
Overall
CADD	3.296	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0305% Admixed American · 18/59,084 alleles

Filtering AF 0.0197% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0162%

Overall 0.00752% 121/1,608,580 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0305%	3,282
Middle Eastern	0.0165%	6,050
Remaining individualsnot grpmax-eligible	0.0145%	6,920
African / African-American	0.00938%	10,659
European (non-Finnish)	0.00721%	13,861
East Asian	0.00224%	44,556

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: EZH2
Protein: p.His158=
Coding: c.474C>T
MANE Select: NM_004456
dbSNP: rs147319809
Type: single nucleotide variant
Location: chr7:148829738 (GRCh38)
Gene constraint: LOEUF 0.272 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.58 · 41 PDB
Residue 158: the 'interaction with dnmt1, dnmt3a and dnmt3b' region; a turn

Full EZH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Weaver syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EZH2 p.His158Tyr Likely pathogenic ★ ⚠ same residue
EZH2 p.Arg684Cys Pathogenic ★★ same condition
EZH2 p.Glu745Lys Pathogenic/Likely pathogenic ★★ same condition
EZH2 p.Ser695Leu Pathogenic/Likely pathogenic ★★ same condition
EZH2 p.Tyr133Cys Pathogenic/Likely pathogenic ★★ same condition
EZH2 p.Val626Met Pathogenic ★★ same condition
EZH2 p.Val679Leu Likely pathogenic ★★ same condition
EZH2 c.626-3T>C 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/ezh2-p-his158 (accessed [today's date]).

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