Is EZH2 p.Ser413Thr (c.1237T>A) pathogenic?

EZH2 p.Ser413Thr (c.1237T>A) is classified Uncertain significance in EZH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-05). AlphaMissense: ambiguous (0.4095); Absent from gnomAD v4.1; Associated with Weaver syndrome.

What condition is associated with EZH2 p.Ser413Thr (c.1237T>A)?

EZH2 p.Ser413Thr (c.1237T>A) is associated with Weaver syndrome (ClinVar).

How common is EZH2 p.Ser413Thr (c.1237T>A) in the general population?

EZH2 p.Ser413Thr (c.1237T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EZH2 p.Ser413Thr (c.1237T>A)?

AlphaMissense predicts ambiguous (score 0.4095) — an in-silico prediction, not a clinical call.

EZH2 p.Ser413Thr

c.1237T>A · VCV3666154

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4095 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Weaver syndrome

Computational evidence

Protein change
AlphaMissense	0.4095	ambiguous
REVEL	0.302	indeterminate
SaProt	LLR -7.58	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Regional constraint	o/e 0.63	unconstrained · MANE · 9,905 bp · p 5.7e-11 · regional, not allelic
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S408T vs ClinVar S413T) — verify the residue.

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: EZH2
Protein: p.Ser413Thr
Coding: c.1237T>A
MANE Select: NM_004456
Type: single nucleotide variant
Location: chr7:148817880 (GRCh38)
Gene constraint: LOEUF 0.272 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.58 · 41 PDB
Residue 408 UniProt numbering: the 'interaction with cdyl' region; the 'disordered' region

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.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
EZH2 p.Ala255Val 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-ser413thr (accessed [today's date]).

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