NM_203407.3:c.616G>A

EZHIP · NP_981952.1:p.(Ala206Thr) · NM_203407.3

GRCh37: chrX:51150484 G>A · GRCh38: chrX:51407632 G>A

Gene: EZHIP Transcript: NM_203407.3

Final call

VUS

PM1 supporting PM2 supporting BP4 supporting benign

Variant details

Gene

EZHIP

Transcript

NM_203407.3

Protein

NP_981952.1:p.(Ala206Thr)

gnomAD AF

1.7758992709933493e-06 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_203407.3:c.616G>A (p.Ala206Thr) in EZHIP is absent from ClinVar.

The variant is extremely rare in population databases, absent from gnomAD v2.1 (0/162,702 alleles) and present as a singleton in gnomAD v4.1 (1/563,095 alleles, AF=0.000178%), meeting PM2 at supporting strength.

p.Ala206Thr lies within the PRC2-binding domain of EZHIP (residues 200–391), a well-characterized functional domain where pathogenic missense variants cluster, meeting PM1 at supporting strength.

SpliceAI predicts no splicing impact (max delta=0.01) and BayesDel yields a benign-leaning score of −0.673766, meeting BP4 at supporting benign strength.

No functional studies, de novo observations, co-segregation data, or case-control evidence are available for this variant. No reputable source classification exists.

With two supporting pathogenic criteria (PM1_supporting, PM2_supporting) and one supporting benign criterion (BP4_supporting_benign), the evidence is insufficient to classify the variant as pathogenic or benign. The variant is classified as a Variant of Uncertain Significance (VUS).

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	NM_203407.3:c.616G>A is a missense variant (p.Ala206Thr). PVS1 applies only to null variants (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, single/multi-exon deletions). Not applicable under ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_variant_assessment pvs1_generic_framework
PS1	Not met	PS1 applies when the same amino acid change has been previously established as pathogenic. No pathogenic missense variant at codon 206 (p.Ala206) was identified in ClinVar or the literature. No comparator exists.	clinvar
PS2	Not met	No de novo observation of NM_203407.3:c.616G>A with confirmed parentage has been reported. A neighboring variant c.617A>G (p.Asn206Ser) was reported de novo in an overgrowth syndrome patient (PMID:31548708), but the exact variant c.616G>A is not reported as de novo.
PS3	Not met	No well-established in vitro or in vivo functional studies have been performed on p.Ala206Thr. The residue falls within the PRC2-binding domain of EZHIP (residues 200–391) characterized in PMID:32325000, but no variant-specific functional data exist.
PS4	Not met	No case-control study or enrichment analysis demonstrates a statistically significant excess of this variant in affected individuals versus controls. The variant is extremely rare in gnomAD (1/563,095 in v4.1), but absence of case data precludes PS4 adjudication.	gnomad_v4
PS5	Not met	PS5 requires a different pathogenic variant at the same amino acid position. No pathogenic missense variant at codon 206 (p.Ala206) was identified in ClinVar or the literature.	clinvar
PM1	Met	p.Ala206Thr is located within the PRC2-binding domain of EZHIP (residues 200–391), a well-characterized functional domain where pathogenic missense variants cluster in patients with overgrowth syndrome. The domain is defined by structural studies (PMID:32325000) and is the site of multiple de novo missense variants reported in PMID:31548708. Position 206 is at the N-terminal boundary of this domain; applied at supporting rather than moderate strength given the position is at the domain edge and no residue-specific constraint data are available.
PM2	Met	NM_203407.3:c.616G>A is extremely rare in large population databases. In gnomAD v2.1 it is absent (0/162,702 alleles). In gnomAD v4.1 it is observed as a singleton (1/563,095 alleles, AF=1.78e-06, no homozygotes). Both are well below the PM2 threshold of 0.1% (non-VCEP). Absent from gnomAD-Canada v1.0.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No pathogenic missense variant at the same residue (p.Ala206) was identified in ClinVar. PM5 candidate harvesting via the automated pipeline found zero candidates.	pm5_candidates
PM6	Not met	No de novo observation of c.616G>A without confirmed parentage has been reported. A neighboring variant c.617A>G (p.Asn206Ser) was reported de novo with unconfirmed parentage (PMID:31548708), but this does not satisfy PM6 for the c.616G>A variant.
PP1	Not met	No co-segregation data available. EZHIP-related overgrowth syndrome is predominantly sporadic, with de novo occurrences. No multigenerational family studies have been published for this variant.
PP2	Not assessed	PP2 requires a missense variant in a gene with a low rate of benign missense variation (high missense Z-score) where missense variants are a common mechanism of disease. No gnomAD missense constraint metrics (Z-score, o/e) for EZHIP were available in this evidence package.
PP3	Not met	Multiple in silico tools do not support a deleterious effect. SpliceAI predicts no splicing impact (max delta=0.01). BayesDel score is −0.673766, favoring a benign interpretation. REVEL and HCI Prior are not available for this variant. The available computational evidence does not meet PP3 criteria.	spliceai bayesdel
PP4	Not met	No patient phenotype or family history data are available for the individual carrying this variant. PP4 requires a highly specific clinical presentation.
PP5	Not met	No reputable source (clinical laboratory, expert panel) has classified this variant as pathogenic. The variant is absent from ClinVar.	clinvar
BA1	Not met	BA1 requires a minor allele frequency >1% in population databases. The variant frequency is 0% in gnomAD v2.1 and 0.000178% in gnomAD v4.1, far below the threshold.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 requires a minor allele frequency >0.3% (non-VCEP cutoff). The variant frequency is far below this threshold (0% in v2.1, 0.000178% in v4.1).	gnomad_v2 gnomad_v4
BS2	Not met	BS2 requires observation of the variant in healthy adults with full penetrance expected at an early age. No such data are available for this variant in the evidence brief. The single gnomAD v4.1 observation cannot be confirmed as a healthy adult control with full penetrance excluded.
BS3	Not met	No well-established functional studies exist demonstrating no damaging effect of p.Ala206Thr on protein function or splicing. Absence of functional data cannot be used to support BS3.
BS4	Not met	No data demonstrating lack of segregation of this variant with disease in affected families. EZHIP-related disorders are predominantly sporadic, making BS4 difficult to satisfy.
BP1	Not met	BP1 applies to a missense variant in a gene where only truncating variants cause disease. EZHIP-related overgrowth syndrome is caused by de novo missense variants in the PRC2-binding domain (PMID:31548708), thus BP1 is not applicable.
BP2	Not met	No observation of this variant in trans with a known pathogenic EZHIP variant. EZHIP disorders follow autosomal dominant inheritance; observation in trans would require specific data not available.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions. This variant is a missense substitution.
BP4	Met	Multiple lines of computational evidence suggest no significant impact. SpliceAI predicts no splicing alteration (max delta=0.01). BayesDel score is −0.673766, leaning toward a benign interpretation. Although REVEL is unavailable, two independent in silico tools converge on a neutral/benign prediction. Applied at supporting benign strength due to incomplete in silico coverage (REVEL missing).	spliceai bayesdel
BP5	Not met	No evidence that this variant was found in a case with an alternate molecular basis for disease. No case-level data available.
BP6	Not met	No reputable source has classified this variant as benign. The variant is absent from ClinVar.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. NM_203407.3:c.616G>A is a missense variant (p.Ala206Thr).

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