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EZHIP
Final classification
VUS
EZHIP c.551A>G · p.Tyr184Cys
EZHIP

NM_203407.3:c.551A>G (p.Tyr184Cys) is a missense variant in EZHIP, a gene encoding a PRC2 inhibitory protein with a described role in posterior fossa group A ependymomas.

Gene
EZHIP
Transcript
NM_203407.3
HGVS · transcript:coding
NM_203407.3:c.551A>G
Consequence
N/A
GRCh38
chrX:51407567 A>G
GRCh37
chrX:51150419 A>G
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 supporting, PM2 supporting, BP4 supporting; combination = 2 supporting + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 supporting, PM2 supporting, BP4 supporting; combination = 2 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PS3PM2 BP4 VUS
EZHIP c.551A>G

NM_203407.3:c.551A>G (p.Tyr184Cys) is a missense variant in EZHIP, a gene encoding a PRC2 inhibitory protein with a described role in posterior fossa group A ependymomas.1 This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF = 6.60×10⁻⁶ (1/151,595 alleles) and gnomAD v4.1 AF = 5.40×10⁻⁶ (3/555,183 alleles), with no homozygotes observed (PM2_Supporting).2 In a functional study of EZHIP/CXorf67 in PFA ependymomas (PMID 29909548), lentiviral expression of the p.Tyr184Cys mutant in neural stem cells and HEK293 cells produced reduction in H3K27me3 levels comparable to wildtype, demonstrating that the variant retains PRC2 inhibitory activity. This constitutes PS3_Supporting in a somatic cancer context; relevance to germline disease is uncertain.3 Multiple lines of computational evidence predict a benign effect: BayesDel score of −0.923011 strongly predicts benign, and SpliceAI predicts no splicing impact (max delta = 0.01) (BP4_Supporting).4 The variant is absent from ClinVar and has not been classified by any clinical laboratory or expert panel.5 The p.Tyr184Cys substitution lies outside the characterized mutational hotspot region of EZHIP (codons 71–122) and is not located at a statistically significant cancer hotspot residue.6 Overall, the variant has one pathogenic supporting criterion (PS3_Supporting), one benign supporting criterion (BP4_Supporting), and one population-based supporting criterion (PM2_Supporting). The evidence is insufficient to classify the variant as pathogenic, likely pathogenic, benign, or likely benign; it remains a variant of uncertain significance.7

PS3 + PM2 + BP4 VUS
Gene diagram · NM_203407.3 · variants mapped to exon structure
EZHIP NM_203407.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 21 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PS3 supporting review Pathogenic
The p.Tyr184Cys variant was directly tested in lentiviral expression assays in NSCs and HEK293 cells and was shown to reduce H3K27me3 levels, consistent with retained EZHIP-mediated PRC2 inhibition. This is a single study in a somatic cancer biology context (PFA ependymoma); the functional effect is clear but the study does not constitute systematic range characterization, and the relevance to germline disease is uncertain.
PMID 29909548: Y184C was one of three CXorf67/EZHIP mutant variants (T73SI88FY184C) tested by lentiviral expression in NSCs and HEK293 cells. All three mutants produced H3K27me3 reduction similar to wildtype CXorf67 overexpression.
PM2 supporting Pathogenic
This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF = 6.60×10⁻⁶ (1/151,595 alleles), gnomAD v4.1 AF = 5.40×10⁻⁶ (3/555,183 alleles), and absent from gnomAD-Canada. These frequencies are well below the 0.1% PM2 threshold for a rare variant absent from controls.
gnomAD v2.1: 1 allele in 151595 (AF = 6.60×10⁻⁶)highest in South Asian (AF = 6.40×10⁻⁵)
BP4 supporting Benign
Multiple lines of computational evidence suggest no deleterious impact. BayesDel score of −0.923011 strongly predicts a benign effect, and SpliceAI predicts no splicing alteration (max delta score = 0.01). REVEL and HCI prior scores are unavailable.
BayesDel: −0.923011 (strongly benign prediction).SpliceAI: max delta = 0.01 (no splicing impact).
Assessed · not applied
Pathogenic
PVS1 NM_203407.3:c.551A>G (p.Tyr184Cys) is a missense variant and does not fall into the null-variant categories (nonsense, frameshift, canonical ±1,2 splice consensus variants) required for PVS1 application under the ClinGen SVI PVS1 decision framework.
PS1 No established pathogenic variant with the same amino acid change (p.Tyr184Cys) is reported in ClinVar or the published literature.
PS2 No de novo occurrence data are available for this variant; no parental testing has been reported.
PS4 No case-control studies or systematic case series reporting this variant in affected individuals with a germline phenotype are available.
PM1 The p.Tyr184Cys variant lies outside the characterized mutational hotspot region of EZHIP/CXorf67 (codons 71–122) and is not located in a statistically significant hotspot per cancerhotspots.org.
PM5 No pathogenic missense variant at the same amino acid residue (Tyr184) has been identified in ClinVar.
PM6 No de novo occurrence has been reported for this variant; parental confirmation is absent.
PP1 No segregation data are available for this variant in affected families.
PP2 EZHIP is not established as a gene in which missense variants are a common mechanism of disease with a low rate of benign missense variation.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No clinical data on the patient's phenotype specificity for EZHIP-related disease are available for assessment.
PP5 This variant is absent from ClinVar; no expert panel or reputable source has classified it as pathogenic.
Benign
BA1 The variant's maximum population frequency (gnomAD v4.1 South Asian AF = 4.70×10⁻⁵, 0.0047%) is far below the BA1 threshold of >1%.
BS1 The variant's maximum population frequency (gnomAD v4.1 South Asian AF = 4.70×10⁻⁵, 0.0047%) is far below the BS1 threshold of >0.3%.
BS2 No systematic observation of this variant in healthy homozygous or hemizygous adult individuals has been documented.
BS3 The only functional study available (PMID 29909548) demonstrates that p.Tyr184Cys retains EZHIP-mediated PRC2 inhibitory function, reducing H3K27me3 levels in cellular assays.
BS4 No segregation data demonstrating lack of co-segregation with disease are available for this variant.
BP1 There is no evidence that EZHIP-related disease is caused exclusively by truncating variants.
BP2 No observation of this variant in trans with a known pathogenic EZHIP variant has been reported.
BP5 No observation of this variant in a case with an alternate molecular basis for disease has been reported.
BP6 This variant is absent from ClinVar; no expert panel or reputable source has classified it as benign.
N/A · 4 PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 5.40362e-06; MAF= 0.00054%, 3/555183 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 4.69616e-05; MAF= 0.00470%, 2/42588 alleles, homozygotes = 0); grpmax FAF= 7.78e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 6.59652e-06; MAF= 0.00066%, 1/151595 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 6.39509e-05; MAF= 0.00640%, 1/15637 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00054% · 3 / 555,183
0 hom · FAF 0.00078%
South Asian
2 / 42,588
0.0047%
European (non-Finnish)
1 / 300,845
0.00033%
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.00066% · 1 / 151,595
0 hom
South Asian
1 / 15,637
0.0064%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). BayesDel score = -0.923011.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas.
Searched
c.551A>Gp.Tyr184CysY184CTyr184551A
Found
The p.Tyr184Cys (Y184C) variant in EZHIP/CXorf67 was identified among 22 somatic SNVs in a cohort of 675 PFA ependymomas. Lentiviral expression of Y184C in NSCs and HEK293 cells produced reduction in H3K27me3 levels comparable to wildtype CXorf67 and hotspot mutants T73S and I88F, demonstrating retained PRC2 inhibitory function. Y184C lies outside the main hotspot region (codons 71–122).
Variant
✓ Names this variant — characterised directly
Applied to
PS3 supports · met
Why
Variant-specific functional data confirmed in somatic cancer context (PFA ependymoma); applied as PS3_Supporting with acknowledgement of uncertain germline disease relevance.
Lentiviral infection with constructs containing three mutant variants of CXorf67 produced the same effect on H3 K27-me3. The three mutant variants were SNVs found in our series of PFA ependymomas; two within and one outside the hotspot region (T73S, I88F, Y184C).
Location Results; Figure 7  ·  Context Lentiviral expression in neural stem cells (NSCs) and HEK293 cells; H3K27me3 measurement by immunofluorescence and immunoblotting  ·  full text
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots