Variant classification summary

NM_004456.5:c.1936T>A

EZH2 · NP_004447.2:p.(Tyr646Asn) · NM_004456.5

GRCh37: chr7:148508728 A>T · GRCh38: chr7:148811636 A>T

Gene: EZH2 Transcript: NM_004456.5

Final call

Likely Pathogenic

PS3 strong PM1 moderate PM2 supporting PP3 moderate

Variant details

Gene

EZH2

Transcript

NM_004456.5

Protein

NP_004447.2:p.(Tyr646Asn)

gnomAD AF

ClinVar

Oncogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

Likely Pathogenic: PS3 strong reflects reproducible altered EZH2/PRC2 function in biochemical, cellular, and in vivo studies.

2

Likely Pathogenic: PM1 moderate reflects the recurrent Tyr646 catalytic-domain hotspot without identified benign variation.

3

Likely Pathogenic: PM2 supporting reflects absence from gnomAD v2.1 and v4.1.

4

Likely Pathogenic: PP3 moderate reflects REVEL 0.895, above the generic missense threshold of 0.773.

Final determination: Under the generic ACMG/AMP 2015 fallback, one strong pathogenic criterion plus one or two moderate pathogenic criteria supports Likely Pathogenic; PM2 supporting and PP3 moderate provide additional pathogenic evidence, with no benign rule satisfied.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	Not applicable: PVS1 requires a null variant (nonsense, frameshift, canonical splice, start-loss or stop-loss), and this is a missense variant.	pvs1_generic_framework generic_acmg_combination_rules
PS1	Not assessed	Not assessed: the same Tyr-to-Asn substitution is reported, but no established pathogenic comparator under generic germline ACMG/AMP criteria is available.	PMID:21078963 PMID:21190999 PMID:23680150 clinvar
PS2	Not assessed	Not assessed: no proband-level de novo observation with confirmed maternity and paternity is documented for NM_004456.5:c.1936T>A.
PS3	Met	Met (strong): recombinant PRC2 Y641N showed 9.01 versus 4.90 units/ng/min on dimethylated H3K27, with altered H3K27me3 in heterozygous cells.	PMID:21190999 PMID:21078963 PMID:23680150
PS4	Not assessed	Not assessed: no verified affected-versus-control counts, odds ratio/relative risk, or 95% confidence interval were reported for EZH2 p.Tyr646Asn.	PMID:20081860 PMID:21190999
PM1	Met	Met at moderate strength: Tyr646 is a statistically significant recurrent EZH2 hotspot with documented altered PRC2 activity and the variant is absent from gnomAD v2.1 and v4.1.	hotspots PMID:21078963 PMID:21190999 gnomad_v2 gnomad_v4
PM2	Met	Met at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, meeting the PM2 supporting threshold of <=0.0001.	gnomad_v2 gnomad_v4
PM3	N/A	Not applicable: PM3 is restricted to recessive disorders, whereas the available EZH2 context is dominant-negative Weaver syndrome.
PM4	N/A	Not applicable: PM4 requires a protein-length change, and this is a missense variant.	pvs1_generic_framework generic_acmg_combination_rules
PM5	Not assessed	Not assessed: alternate missense substitutions occur at Tyr646, but none is established as pathogenic under the generic ACMG/AMP evidence available here.	PMID:21078963 PMID:20081860 PMID:21190999 clinvar
PM6	Not assessed	Not assessed: no germline de novo observation without confirmed maternity and paternity is documented for NM_004456.5:c.1936T>A.
PP1	Not assessed	Not assessed: no affected relatives, informative meioses, or variant co-segregation results are documented for this family.
PP2	Not assessed	Not assessed: a validated low benign-missense rate and the required generic gene-level missense-mechanism evidence are not available.
PP3	Met	Met at moderate strength: REVEL 0.895 meets the generic PP3 moderate threshold of >=0.773 for this missense variant.	revel
PP4	Not assessed	Not assessed: the case materials do not provide a patient phenotype or family history sufficiently specific for a single-genetic-etiology disease.
PP5	Not met	Not met: ClinVar has one single-submitter Oncogenic record and no exact-variant expert-panel Pathogenic or Likely pathogenic classification.	clinvar oncokb
BA1	Not met	Not met: the variant is absent from gnomAD v2.1 and v4.1, providing no allele frequency at or above the 0.05 BA1 threshold.	gnomad_v2 gnomad_v4 clinvar
BS1	Not met	Not met: gnomAD v2.1 and v4.1 report absence, so the filtering allele frequency cannot exceed the generic BS1 default of 0.01.	gnomad_v2 gnomad_v4
BS2	Not assessed	Not assessed: no healthy adult carrying the variant, zygosity, or age-appropriate unaffected status is documented.	gnomad_v2 gnomad_v4 clinvar
BS3	Not met	Not met: Y641N PRC2 activity increased to 9.01 versus 4.90 units/ng/min on dimethylated H3K27, contradicting a no-damaging-effect result.	PMID:21190999 PMID:21078963 PMID:23680150
BS4	Not assessed	Not assessed: no affected family members with negative variant testing are documented to demonstrate lack of segregation.
BP1	Not met	Not met: EZH2 disease context emphasizes heterozygous missense variants and reports no early truncating mutations as the primary mechanism.	pvs1_gene_context
BP2	Not assessed	Not assessed: no pathogenic variant in trans or cis, parental or offspring phase testing, or affected-proband allelic observation is documented.
BP3	N/A	Not applicable: BP3 requires an in-frame indel in a repeat region, and this is a missense variant.	pvs1_generic_framework generic_acmg_combination_rules
BP4	Not met	Not met: REVEL 0.895 exceeds the generic BP4 supporting threshold of <=0.29 for this missense variant.	revel
BP5	Not assessed	Not assessed: no case documents EZH2 p.Tyr646Asn alongside an independently established alternate molecular basis for disease.
BP6	Not met	Not met: no exact-variant ClinVar expert-panel Benign or Likely benign classification is present; the available submission is single-submitter Oncogenic.	clinvar
BP7	N/A	Not applicable: BP7 requires a synonymous variant, and this is a missense variant.	generic_acmg_combination_rules

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