NM_004456.4:c.1966G>A

EZH2 · NP_004447.2:p.(Ala656Thr) · NM_004456.4

GRCh37: chr7:148507488 C>T · GRCh38: chr7:148810396 C>T

Gene: EZH2 Transcript: NM_004456.4

Final call

VUS

PM2 supporting

Variant details

Gene

EZH2

Transcript

NM_004456.4

Protein

NP_004447.2:p.(Ala656Thr)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_004456.4:c.1966G>A (p.Ala656Thr) is a missense variant in EZH2 that is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).

No additional pathogenic or benign criteria are met. The variant has not been reported in ClinVar, has no functional studies, no segregation data, no de novo observations, and in silico predictors are discordant (REVEL 0.753 damaging; BayesDel 0.311 benign).

With a single supporting criterion (PM2) and no conflicting benign evidence, the variant is classified as a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines (PMID:25741868).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	This is a missense variant (p.Ala656Thr) and does not fall into any PVS1 null-variant category (nonsense, frameshift, or canonical ±1,2 splice consensus). The generic PVS1 decision framework (PMC6185798) confirms this variant is not eligible for PVS1.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No prior report of a different nucleotide change at codon 656 resulting in the same p.Ala656Thr missense alteration with a pathogenic classification. The variant is absent from ClinVar.	clinvar
PS2	Not met	No de novo observation has been reported for this variant. No publications identified through the literature pipeline.
PS3	Not met	No well-established functional studies demonstrating a damaging effect have been reported for this variant. OncoKB lists the variant as Unknown Oncogenic Effect and no PMIDs with functional data were identified.	oncokb
PS4	Not met	No case-control studies or statistical evidence of enrichment in affected individuals versus controls. The variant is absent from ClinVar, so no disease association data exist.	clinvar
PS5	Not met	No pathogenic missense variants have been reported at codon 656 (Ala656) in ClinVar. No comparators exist to satisfy the PS5 requirement of a different pathogenic missense at the same residue.	clinvar pm5_candidates
PM1	Not met	The variant does not lie in a statistically significant mutational hotspot as assessed by Cancer Hotspots. No domain-specific enrichment data are available. Codon 656 is in the C-terminal region of EZH2 but has not been established as a critical functional domain for germline disease.
PM2	Met	The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with an allele frequency of 0. This meets the PM2 threshold for absence from population databases (allele frequency <0.1% for non-VCEP).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No pathogenic missense variants have been identified at the same residue (Ala656) to enable PM5 comparison. Automated ClinVar candidate harvesting for codon 656 returned zero candidates.	pm5_candidates
PM6	Not met	No de novo observation has been reported for this variant. No publications describing de novo occurrence were identified.
PP1	Not met	No co-segregation data are available for this variant. No family studies have been reported.
PP2	Not assessed	HCI prior score is unavailable for EZH2 (gene not supported by the HCI prior database). Without quantitative data on the gene's benign missense variation rate, PP2 cannot be reliably assessed. Note that EZH2 Weaver syndrome is primarily driven by missense variants (dominant-negative mechanism), but the rate of benign missense variation cannot be determined without HCI prior.
PP3	Not met	Insufficient consensus among multiple in silico predictors. REVEL score of 0.753 is above the pathogenicity threshold (≥0.5), but BayesDel score of 0.311 is below the damaging threshold (<0.5), and SpliceAI predicts no splicing impact (max delta score 0.02). PP3 requires multiple lines of computational support, which are not met here.	revel bayesdel spliceai
PP4	Not met	No clinical phenotype or family history data are available to assess whether the patient's presentation is highly specific for EZH2-associated Weaver syndrome.
PP5	Not met	No reputable source has classified this variant as pathogenic. The variant is absent from ClinVar with zero submissions.	clinvar
BA1	Not met	The variant is absent from gnomAD (allele frequency = 0). Does not meet the BA1 threshold of >1% population frequency.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from gnomAD (allele frequency = 0). Does not meet the BS1 threshold of >0.3% for rare disease (non-VCEP cutoff).	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	The variant has not been observed in any healthy adult individuals in population databases. No evidence of occurrence with full penetrance expected but absent disease.
BS3	Not met	No well-established functional studies demonstrating no deleterious effect have been reported for this variant.
BS4	Not met	No segregation data are available to assess lack of segregation with disease in affected families.
BP1	Not met	EZH2 Weaver syndrome is primarily caused by missense variants through a dominant-negative mechanism, not by truncating mutations. The literature (PMID:40846643) explicitly notes the lack of early truncating mutations in EZH2 and supports a dominant-negative mechanism for missense variants. BP1 requires that the gene's primary disease mechanism is truncating, which does not apply to EZH2.
BP2	Not met	No observation of this variant in trans with a known pathogenic dominant variant in EZH2. No data available.
BP4	Not met	Insufficient consensus among multiple in silico predictors for a benign effect. REVEL score of 0.753 indicates a damaging prediction, contradicting the requirement for multiple lines of benign computational evidence. Only BayesDel (0.311) supports a benign interpretation, and SpliceAI (max delta 0.02) is neutral.	revel bayesdel spliceai
BP5	Not met	No case has been reported in which this variant is found in an individual with an alternate molecular basis for disease.
BP6	Not met	No reputable source has classified this variant as benign. The variant is absent from ClinVar.	clinvar
BP7	N/A	This is a missense variant (p.Ala656Thr), not a synonymous or intronic variant. BP7 applies only to synonymous variants with no predicted splice impact. SpliceAI predicts no splicing impact (max delta 0.02), but the criterion is fundamentally inapplicable to missense variants.

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