EZHIP

Summary

EZHIP (EZH inhibitory protein, HGNC:33738) is a protein-coding gene on chromosome Xp11.22, encoding EZH inhibitory protein (Q86X51). Inhibits PRC2/EED-EZH1 and PRC2/EED-EZH2 complex function by inhibiting EZH1/EZH2 methyltransferase activity, thereby causing down-regulation of histone H3 trimethylation on ‘Lys-27’ (H3K27me3).

Enables histone methyltransferase inhibitor activity. Involved in epigenetic regulation of gene expression. Located in cytosol and nucleoplasm.

Source: NCBI Gene 340602 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_203407

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33738
Approved symbol	EZHIP
Name	EZH inhibitory protein
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	CATACOMB
Ensembl gene	ENSG00000187690
Ensembl biotype	protein_coding
OMIM	301036
Entrez	340602

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000342995

RefSeq mRNA: 1 — MANE Select: NM_203407 NM_203407

CCDS: CCDS78485

Canonical transcript exons

ENST00000342995 — 1 exons

Exon	Start	End
ENSE00001365036	51406948	51408843

Expression profiles

Bgee: expression breadth broad, 85 present calls, max score 99.68.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0745 / max 34.1866, expressed in 19 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196363	0.0710	17
196364	0.0034	2

Top tissues by expression

209 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.68	gold quality
oocyte	CL:0000023	99.60	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.60	gold quality
right testis	UBERON:0004534	68.66	gold quality
left testis	UBERON:0004533	67.16	gold quality
testis	UBERON:0000473	66.56	gold quality
placenta	UBERON:0001987	58.69	gold quality
cerebellar hemisphere	UBERON:0002245	58.15	gold quality
cerebellar cortex	UBERON:0002129	57.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	57.48	gold quality
cerebellum	UBERON:0002037	56.76	gold quality
granulocyte	CL:0000094	53.12	gold quality
pituitary gland	UBERON:0000007	52.45	gold quality
adenohypophysis	UBERON:0002196	52.02	gold quality
spleen	UBERON:0002106	48.05	gold quality
ovary	UBERON:0000992	47.79	gold quality
adult organism	UBERON:0007023	46.88	gold quality
nucleus accumbens	UBERON:0001882	46.71	gold quality
left ovary	UBERON:0002119	46.31	gold quality
anterior cingulate cortex	UBERON:0009835	45.80	gold quality
lower esophagus mucosa	UBERON:0035834	45.60	silver quality
right ovary	UBERON:0002118	45.34	gold quality
hypothalamus	UBERON:0001898	45.14	gold quality
amniotic fluid	UBERON:0000173	45.01	gold quality
ascending aorta	UBERON:0001496	44.91	gold quality
brain	UBERON:0000955	44.89	gold quality
thoracic aorta	UBERON:0001515	44.72	gold quality
ventricular zone	UBERON:0003053	44.08	silver quality
caudate nucleus	UBERON:0001873	44.07	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting EZHIP, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-520D-3P	99.83	70.78	1676
HSA-MIR-657	99.48	66.02	848
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-606	98.72	67.34	960
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-1237-3P	98.55	67.65	1423
HSA-MIR-6880-5P	98.08	65.59	1282
HSA-MIR-3198	97.84	65.64	579
HSA-MIR-4309	97.84	65.45	588
HSA-MIR-6787-3P	97.75	66.17	1233
HSA-MIR-510-5P	97.66	65.82	916
HSA-MIR-890	97.47	68.67	982

Literature-anchored findings (GeneRIF, showing 11)

• The chimeric MBTD1-CXorf67 fusion identifies yet another cytogenetically distinct subgroup of low-grade Endometrial stromal sarcomas and offers the opportunity to shed light on the functions of two poorly characterized genes. (PMID:23959973)
• The data of this study suggested that heterogeneity among PFA ependymomas could have clinicopathologic utility and that CXorf67 may have a functional role in these tumors. (PMID:29909548)
• High EZHIP expression is associated with posterior fossa ependymoma. (PMID:30923826)
• Study revealed that CXORF67 contains a highly conserved “K27M-like” sequence that is necessary and sufficient to inhibit PRC2 activity and reduce cellular H3K27me3 levels. Biochemical and cell-based studies demonstrate that CXORF67 functions as a K27M-like peptidyl inhibitor of PRC2. Therefore, study propose the name EZHIP (Enhancer of Zeste Homologs Inhibitory Protein) as a more descriptive for the function of CXORF67. (PMID:31086175)
• CATACOMB as the potential interlocutor between DNA methylation and PRC2 activity. (PMID:31281901)
• Study reports the identification of a cofactor of PRC2, EZHIP (EZH1/2 Inhibitory Protein), expressed predominantly in the gonads. EZHIP limits the enzymatic activity of PRC2 and lessens the interaction between the core complex and its accessory subunits but does not interfere with PRC2 recruitment to chromatin. Study uncovers EZHIP as a regulator of chromatin landscape in gametes. (PMID:31451685)
• Histone H3 wild-type DIPG/DMG overexpressing EZHIP extend the spectrum diffuse midline gliomas with PRC2 inhibition beyond H3-K27M mutation. (PMID:32193787)
• EZH2 inhibitory protein (EZHIP/Cxorf67) expression correlates strongly with H3K27me3 loss in posterior fossa ependymomas and is mutually exclusive with H3K27M mutations. (PMID:33130928)
• EZHIP is a specific diagnostic biomarker for posterior fossa ependymomas, group PFA and diffuse midline gliomas H3-WT with EZHIP overexpression. (PMID:33153494)
• Elevated CXorf67 Expression in PFA Ependymomas Suppresses DNA Repair and Sensitizes to PARP Inhibitors. (PMID:33186520)
• [The value of CXorf67 and H3K27me3 for diagnosing germ cell tumors in central nervous system]. (PMID:35511635)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-14a11.2	ENSDARG00000093457
danio_rerio	si:ch211-14a11.1	ENSDARG00000095420
danio_rerio	si:ch211-221n20.2	ENSDARG00000095671
danio_rerio	si:ch211-221n20.1	ENSDARG00000110807
danio_rerio	si:ch211-221n20.4	ENSDARG00000111367
danio_rerio	si:dkey-235d18.7	ENSDARG00000113562
danio_rerio	si:ch211-221n20.7	ENSDARG00000114229
danio_rerio	si:dkey-235d18.6	ENSDARG00000115571

Protein

Protein identifiers

EZH inhibitory protein — Q86X51 (reviewed: Q86X51)

All UniProt accessions (2): A0A515VFR0, Q86X51

UniProt curated annotations — full annotation on UniProt →

Function. Inhibits PRC2/EED-EZH1 and PRC2/EED-EZH2 complex function by inhibiting EZH1/EZH2 methyltransferase activity, thereby causing down-regulation of histone H3 trimethylation on ‘Lys-27’ (H3K27me3). Probably inhibits methyltransferase activity by limiting the stimulatory effect of cofactors such as AEBP2 and JARID2. Inhibits H3K27me3 deposition during spermatogenesis and oogenesis.

Subunit / interactions. Interacts with PRC2/EED-EZH1 complex member EZH1 and with PRC2/EED-EZH2 complex member EZH2; the interaction blocks EZH1/EZH2 methyltransferase activity. Interacts (via C-terminus) with SUZ12 which is a member of the PRC2/EED-EZH1 and PRC2/EED-EZH2 complexes.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. In testis, detected in male germ cells inside the seminiferous tubules, especially in spermatogonia and round spermatids (at protein level). In the ovary, expressed in primordial follicles and oocytes but not the external follicle cells (at protein level).

RefSeq proteins (1): NP_981952* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR052882	EZH_Inhibitor	Family

UniProt features (25 total): mutagenesis site 11, compositionally biased region 6, region of interest 5, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86X51-F1	49.28	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 259

Mutagenesis-validated functional residues (11):

Position	Phenotype
73	decreases inhibition of h3k27me3.
81	no effect on h3k27me3 levels.
88	slightly decreases inhibition of h3k27me3.
184	decreases inhibition of h3k27me3.
394–417	abolishes interaction with the prc2 complex and causes increased h3k27me3 levels.
405	does not inhibit prc2/eed-ezh2 complex activity and abolishes ability to decrease h3k27me3 levels.
406	does not act as a substrate of the prc2/eed-ezh2 complex.
406	does not reduce h3k27me3 levels.
406	does not affect inhibition of h3k27me3 levels.
406	acts as a substrate of the prc2/eed-ezh2 complex and does not reduce h3k27me3 levels.
407	no effect on h3k27me3 levels.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212300	PRC2 methylates histones and DNA

MSigDB gene sets: 22 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOBP_CHROMATIN_REMODELING, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_ENZYME_INHIBITOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, chrXp11, FOSTER_KDM1A_TARGETS_UP, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, REACTOME_PRC2_METHYLATES_HISTONES_AND_DNA, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_UP, MIR302E, MIR193A_5P

GO Biological Process (2): chromatin organization (GO:0006325), epigenetic regulation of gene expression (GO:0040029)

GO Molecular Function (2): histone methyltransferase inhibitor activity (GO:0180000), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Epigenetic regulation of gene expression	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cellular component organization	1
chromatin remodeling	1
regulation of gene expression	1
enzyme inhibitor activity	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1170 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EZHIP	MBTD1	Q05BQ5	772
EZHIP	EZH2	Q15910	732
EZHIP	MEAF6	Q9HAF1	691
EZHIP	SUZ12	Q15022	658
EZHIP	PHF1	O43189	642
EZHIP	ZC3H7B	Q9UGR2	611
EZHIP	JAZF1	Q86VZ6	610
EZHIP	EPOP	A6NHQ4	583
EZHIP	NUTM2A	Q8IVF1	549
EZHIP	AEBP2	Q6ZN18	508
EZHIP	ZFTA	C9JLR9	486
EZHIP	ZC3H7A	Q8IWR0	482
EZHIP	BRD8	Q9H0E9	442
EZHIP	MTF2	Q9Y483	434
EZHIP	YWHAE	P29360	403
EZHIP	JARID2	Q92833	403

IntAct

18 interactions, top by confidence:

A	B	Type	Score
EZHIP	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
EZHIP	ENKD1	psi-mi:“MI:0915”(physical association)	0.560
EZHIP	ZNF417	psi-mi:“MI:0915”(physical association)	0.560
EZHIP	TRIM41	psi-mi:“MI:0915”(physical association)	0.560
EZHIP	TRAF4	psi-mi:“MI:0915”(physical association)	0.560
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
TP53BP1	PSMD14	psi-mi:“MI:2364”(proximity)	0.270
SCNM1	EZHIP	psi-mi:“MI:0915”(physical association)	0.000
ENKD1	EZHIP	psi-mi:“MI:0915”(physical association)	0.000
ZNF417	EZHIP	psi-mi:“MI:0915”(physical association)	0.000
TRIM41	EZHIP	psi-mi:“MI:0915”(physical association)	0.000
TRAF4	EZHIP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): CXorf67 (Proximity Label-MS), CXorf67 (Proximity Label-MS), CXorf67 (Affinity Capture-MS), CXorf67 (Two-hybrid), CXorf67 (Two-hybrid), CXorf67 (Two-hybrid), CXorf67 (Two-hybrid), CXorf67 (Two-hybrid), CXorf67 (Affinity Capture-MS), EZH2 (Affinity Capture-Western), SUZ12 (Affinity Capture-Western), CXorf67 (Affinity Capture-Western), CXorf67 (Affinity Capture-MS), CXorf67 (Affinity Capture-MS), CXorf67 (Proximity Label-MS)

ESM2 similar proteins: A0A172M4N0, A1YFC1, A1YGK6, A2T7F2, A5A6K1, A6NHN6, A8MU93, F5HAE6, O70561, P0DI83, P16531, P26377, P38469, P56958, P59797, P62521, P84996, Q02234, Q3URU2, Q5JRC9, Q5R7U0, Q5RKG3, Q5SF94, Q5SF96, Q6GZN9, Q6H236, Q6R0H6, Q6ZVQ6, Q7T2B3, Q80Y39, Q810T2, Q86X51, Q8BGJ3, Q8CH20, Q8CJI4, Q8N2A0, Q8N3K9, Q8N976, Q8NC38, Q8NHX4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

7 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

55 predictions. Top by Δscore:

Variant	Effect	Δscore
X:51407460:G:GT	donor_gain	0.8200
X:51407338:G:GT	donor_gain	0.4800
X:51407642:C:T	donor_gain	0.4500
X:51407675:T:TA	donor_gain	0.3900
X:51407676:A:AA	donor_gain	0.3900
X:51407999:CAAG:C	donor_loss	0.3700
X:51408000:AAG:A	donor_loss	0.3700
X:51408001:AGGTC:A	donor_loss	0.3700
X:51408002:GG:G	donor_loss	0.3700
X:51408003:GTCAG:G	donor_loss	0.3700
X:51408004:T:A	donor_loss	0.3700
X:51407600:C:T	donor_gain	0.3500
X:51407062:G:GT	donor_gain	0.3400
X:51408005:CAGAC:C	donor_loss	0.3400
X:51408042:C:T	donor_loss	0.3200
X:51408006:AGA:A	donor_loss	0.3100
X:51407320:G:GT	donor_gain	0.3000
X:51407074:G:GT	donor_gain	0.2900
X:51407352:T:A	donor_gain	0.2900
X:51407675:TAGC:T	acceptor_gain	0.2900
X:51408168:A:G	donor_gain	0.2800
X:51408230:G:GG	donor_gain	0.2800
X:51407677:G:T	acceptor_gain	0.2700
X:51407693:GAC:G	acceptor_gain	0.2700
X:51408197:GCC:G	donor_gain	0.2700
X:51408261:G:T	donor_gain	0.2600
X:51407075:G:T	donor_gain	0.2500
X:51407673:G:GA	acceptor_gain	0.2500
X:51407902:G:GA	acceptor_gain	0.2500
X:51408007:G:C	donor_loss	0.2500

AlphaMissense

3192 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:51408234:G:A	M406I	0.989
X:51408234:G:C	M406I	0.989
X:51408234:G:T	M406I	0.989
X:51408233:T:C	M406T	0.983
X:51408379:T:C	F455L	0.964
X:51408381:T:A	F455L	0.964
X:51408381:T:G	F455L	0.964
X:51408235:C:A	R407S	0.951
X:51408268:T:C	F418L	0.939
X:51408270:C:A	F418L	0.939
X:51408270:C:G	F418L	0.939
X:51408239:C:A	A408D	0.938
X:51408229:C:A	R405S	0.931
X:51408227:T:A	V404D	0.926
X:51408398:T:C	I461T	0.924
X:51408409:A:C	S465R	0.922
X:51408411:C:A	S465R	0.922
X:51408411:C:G	S465R	0.922
X:51408248:C:A	P411H	0.921
X:51408265:T:C	F417L	0.921
X:51408267:C:A	F417L	0.921
X:51408267:C:G	F417L	0.921
X:51408239:C:T	A408V	0.919
X:51408242:C:A	S409Y	0.918
X:51408263:G:T	R416M	0.916
X:51408242:C:T	S409F	0.914
X:51408224:C:A	A403E	0.908
X:51408259:G:T	G415W	0.904
X:51408398:T:A	I461N	0.897
X:51408247:C:T	P411S	0.892

dbSNP variants (sampled 300 via entrez): RS1002342784 (X:51406932 C>T), RS1002745842 (X:51406680 T>C), RS1005187482 (X:51405932 T>C), RS1005239939 (X:51406560 C>G,T), RS1006910285 (X:51407903 C>G,T), RS1009323230 (X:51405234 C>T), RS1014002870 (X:51406611 C>A), RS1015353955 (X:51405959 A>T), RS1016475292 (X:51405366 G>A), RS1016997314 (X:51407373 C>T), RS1017049702 (X:51407538 A>G), RS1025598410 (X:51406642 C>T), RS1028445139 (X:51405842 A>G), RS1033798883 (X:51406949 C>G,T), RS1033913433 (X:51406682 T>C)

Disease associations

OMIM: gene MIM:301036 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
TAK-243	increases sumoylation	1
arsenite	decreases methylation	1
benzo(e)pyrene	decreases methylation	1
ferrous chloride	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Benzo(a)pyrene	affects methylation	1
Methapyrilene	decreases methylation	1
Valproic Acid	increases methylation	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_C0BP	Abcam U2OS EZHIP KO	Cancer cell line	Female
CVCL_C8V5	Daoy EZHIP KO	Cancer cell line	Male
CVCL_C8V6	U2OS EZHIP KO	Cancer cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.