EZH2 p.Cys565=
c.1695C>T · rs753286051 · VCV2658140
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,613,290)
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 5.1 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 11.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,613,290). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- EZH2
- Protein
- p.Cys565=
- Coding
- c.1695C>T
- MANE Select
- NM_004456
- dbSNP
- rs753286051
- Type
- single nucleotide variant
- Location
- chr7:148814115 (GRCh38)
- Gene constraint
- LOEUF 0.272 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.58 · 41 PDB
- Residue 565
- the cxc domain; a β-strand
Similar variants
- EZH2 p.Arg684Cys Pathogenic ★★ same type
- EZH2 p.Glu745Lys Pathogenic/Likely pathogenic ★★ same type
- EZH2 p.Ser695Leu Pathogenic/Likely pathogenic ★★ same type
- EZH2 p.Tyr133Cys Pathogenic/Likely pathogenic ★★ same type
- EZH2 p.Tyr741His Likely pathogenic ★★ same type
- EZH2 p.Val626Met Pathogenic ★★ same type
- EZH2 p.Val679Leu Likely pathogenic ★★ same type
- EZH2 c.626-3T>C Uncertain significance ★★ 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/ezh2-p-cys565 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown