PATZ1

Summary

PATZ1 (POZ/BTB and AT hook containing zinc finger 1, HGNC:13071) is a protein-coding gene on chromosome 22q12.2, encoding POZ-, AT hook-, and zinc finger-containing protein 1 (Q9HBE1). Transcriptional regulator that plays a role in many biological processes such as embryogenesis, senescence, T-cell development or neurogenesis.

The protein encoded by this gene contains an A-T hook DNA binding motif which usually binds to other DNA binding structures to play an important role in chromatin modeling and transcription regulation. Its Poz domain is thought to function as a site for protein-protein interaction and is required for transcriptional repression, and the zinc-fingers comprise the DNA binding domain. Since the encoded protein has typical features of a transcription factor, it is postulated to be a repressor of gene expression. In small round cell sarcoma, this gene is fused to EWS by a small inversion of 22q, then the hybrid is thought to be translocated (t(1;22)(p36.1;q12). The rearrangement of chromosome 22 involves intron 8 of EWS and exon 1 of this gene creating a chimeric sequence containing the transactivation domain of EWS fused to zinc finger domain of this protein. This is a distinct example of an intra-chromosomal rearrangement of chromosome 22. Four alternatively spliced transcript variants are described for this gene.

Source: NCBI Gene 23598 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 81 total
• Transcription factor: yes — 12 downstream targets (CollecTRI)
• MANE Select transcript: NM_014323

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13071
Approved symbol	PATZ1
Name	POZ/BTB and AT hook containing zinc finger 1
Location	22q12.2
Locus type	gene with protein product
Status	Approved
Aliases	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ
Ensembl gene	ENSG00000100105
Ensembl biotype	protein_coding
OMIM	605165
Entrez	23598

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 retained_intron

ENST00000215919, ENST00000266269, ENST00000351933, ENST00000405309, ENST00000465287, ENST00000494109, ENST00000930048, ENST00000930049, ENST00000930050, ENST00000941424

RefSeq mRNA: 4 — MANE Select: NM_014323 NM_014323, NM_032050, NM_032051, NM_032052

CCDS: CCDS13894, CCDS13895, CCDS13896, CCDS46691

Canonical transcript exons

ENST00000266269 — 5 exons

Exon	Start	End
ENSE00000653152	31335692	31335863
ENSE00000911167	31342897	31342960
ENSE00001361736	31328787	31328924
ENSE00001742345	31325804	31327309
ENSE00003846833	31344332	31346346

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 95.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.1531 / max 123.4444, expressed in 1766 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193706	13.6811	1763
193707	1.0763	362
193699	0.5759	224
193708	0.3260	197
193704	0.1174	66
193701	0.1133	57
193702	0.1072	61
193705	0.0938	47
193698	0.0367	18
193700	0.0253	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	95.23	gold quality
ganglionic eminence	UBERON:0004023	95.00	gold quality
embryo	UBERON:0000922	94.10	gold quality
endometrium epithelium	UBERON:0004811	92.60	gold quality
cortical plate	UBERON:0005343	92.57	gold quality
right lobe of thyroid gland	UBERON:0001119	92.37	gold quality
right uterine tube	UBERON:0001302	91.99	gold quality
left lobe of thyroid gland	UBERON:0001120	91.06	gold quality
thyroid gland	UBERON:0002046	90.77	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.43	gold quality
minor salivary gland	UBERON:0001830	89.12	gold quality
metanephros cortex	UBERON:0010533	88.89	gold quality
saliva-secreting gland	UBERON:0001044	88.35	gold quality
paraflocculus	UBERON:0005351	88.06	gold quality
mouth mucosa	UBERON:0003729	87.17	gold quality
ovary	UBERON:0000992	86.65	gold quality
body of pancreas	UBERON:0001150	86.51	gold quality
granulocyte	CL:0000094	86.35	gold quality
body of stomach	UBERON:0001161	86.29	gold quality
prostate gland	UBERON:0002367	86.16	gold quality
left ovary	UBERON:0002119	86.09	gold quality
body of uterus	UBERON:0009853	85.61	gold quality
right ovary	UBERON:0002118	85.53	gold quality
fundus of stomach	UBERON:0001160	85.35	gold quality
endocervix	UBERON:0000458	85.15	gold quality
stomach	UBERON:0000945	85.08	gold quality
pancreatic ductal cell	CL:0002079	85.04	silver quality
lymph node	UBERON:0000029	84.92	gold quality
left uterine tube	UBERON:0001303	84.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.77

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

12 targets.

Target	Regulation
BAX
BCL6	Repression
CD8A	Unknown
CDKN2A
FGF4	Activation
MYC	Activation
PRKAR1A
RNF4
STK36
TP53
TPSAB1	Activation
TPSB2

JASPAR motifs

Motif	Name	Family
MA1961.1	PATZ1	Factors with multiple dispersed zinc fingers
MA1961.2	PATZ1	Factors with multiple dispersed zinc fingers

JASPAR matrix evidence (PMIDs): PMID:24380431

miRNA regulators (miRDB)

192 targeting PATZ1, 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-3646	100.00	73.56	5283
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-652-5P	99.91	67.49	505
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-3663-3P	99.84	70.39	798

Literature-anchored findings (GeneRIF, showing 22)

• The short isoform of the Zinc finger Sarcoma Gene (ZSG) was isolated as a RNF4 interacting protein. (PMID:10949935)
• We report here the isolation and characterization of two novel nuclear BTB/POZ domain zinc finger isoformsthat are specifically expressed in early hippocampal neurons, cerebellar granule cells, and gliogenic progenitors as well as in differentiated glia (PMID:11744704)
• MAZR and MITF synergistically transactivated the mMCP-6 gene. MAZR appeared to play important roles in the normal phenotypic expression of mast cells in association with MITF (PMID:11751862)
• The results show that ZNF278 promotes cell growth, and its knockdown suppresses cell proliferation. ZNF278 could be a potential proto-oncogene in colorectal cancer. (PMID:18401526)
• these results showed a potentially novel mechanism of cAMP signaling mediated through the interaction of RIalpha with PATZ1. (PMID:20026299)
• PATZ1 may have an important role in the regulation of EC senescence through an ROS-mediated p53-dependent pathway and contribute to vascular diseases associated with aging. (PMID:22052190)
• The data support a PATZ1 tumour-suppressive function based on its ability to enhance p53-dependent transcription and apoptosis. (PMID:24336083)
• these results propose that Patz1 is important for ESC pluripotency. (PMID:24380431)
• Loss of PATZ1 expression is associated with thyroid cancer progression. (PMID:25595894)
• Results show that PATZ1 binds to p53 and inhibits p53-dependent transcription activation. (PMID:25755280)
• this study show that PATZ1 expression correlates positively with BAX and negatively with BCL6 and survival in human diffuse large B cell lymphomas (PMID:27494852)
• The derived allele of rs174557, which is the common variant in most populations, diminishes binding of PATZ1, a transcription factor conferring allele-specific downregulation of FADS1. (PMID:27932482)
• ZNF278 played a prominent role in the pathogenesis of colorectal cancer (CRC), and promoted CRC cell proliferation via the ERK/MAPK pathway, suggesting that it may act as a potential target in the diagnosis or treatment of CRC (PMID:29039562)
• The results of IHC and qPCR analyses showed that the expression of PATZ1 in cancerous tissue was significantly lower than that in non-cancerous tissues. Meanwhile, PATZ1 expression was significantly associated with tumor differentiation and LN metastasis. (PMID:29926841)
• EWSR1-PATZ1 fusion positive spindle and round cell sarcomas show abundant intratumoral fibrosis and polyphenotypic differentiation (PMID:30379650)
• It has been shown that PATZ1 is a novel regulator of HIV-1 infection. (PMID:31060775)
• The Transcription Factor MAZR/PATZ1 Regulates the Development of FOXP3(+) Regulatory T Cells. (PMID:31875552)
• EWSR1-PATZ1-rearranged sarcoma: a report of nine cases of spindle and round cell neoplasms with predilection for thoracoabdominal soft tissues and frequent expression of neural and skeletal muscle markers. (PMID:33012788)
• Expanding the spectrum of EWSR1-PATZ1 rearranged CNS tumors: An infantile case with leptomeningeal dissemination. (PMID:33378126)
• PATZ1 fusions define a novel molecularly distinct neuroepithelial tumor entity with a broad histological spectrum. (PMID:34417833)
• POZ/BTB and AT hook containing zinc finger 1 (PATZ1) suppresses differentiation and regulates metabolism in human embryonic stem cells. (PMID:38385086)
• Transcription factor PATZ1 promotes adipogenesis by controlling promoter regulatory loci of adipogenic factors. (PMID:39358382)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	patz1	ENSDARG00000076584
mus_musculus	Patz1	ENSMUSG00000020453
rattus_norvegicus	Patz1	ENSRNOG00000018709

Paralogs (36): ZBTB32 (ENSG00000011590), SNAI2 (ENSG00000019549), PRDM1 (ENSG00000057657), PRDM6 (ENSG00000061455), ZNF76 (ENSG00000065029), MAZ (ENSG00000103495), ZBTB16 (ENSG00000109906), ZNF451 (ENSG00000112200), ZBTB45 (ENSG00000119574), ZNF410 (ENSG00000119725), SNAI1 (ENSG00000124216), ZNF384 (ENSG00000126746), ZBTB1 (ENSG00000126804), VEZF1 (ENSG00000136451), PRDM14 (ENSG00000147596), ZNF276 (ENSG00000158805), ZNF362 (ENSG00000160094), ZNF653 (ENSG00000161914), ZNF281 (ENSG00000162702), ZNF148 (ENSG00000163848), ZNF143 (ENSG00000166478), HIC2 (ENSG00000169635), PRDM10 (ENSG00000170325), ZNF296 (ENSG00000170684), ZNF692 (ENSG00000171163), ZNF575 (ENSG00000176472), HIC1 (ENSG00000177374), ZBTB18 (ENSG00000179456), ZBTB42 (ENSG00000179627), ZBTB20 (ENSG00000181722), ZBTB7C (ENSG00000184828), SNAI3 (ENSG00000185669), ZFP91 (ENSG00000186660), MTF1 (ENSG00000188786), SCRT2 (ENSG00000215397), SCRT1 (ENSG00000261678)

Protein

Protein identifiers

POZ-, AT hook-, and zinc finger-containing protein 1 — Q9HBE1 (reviewed: Q9HBE1)

Alternative names: BTB/POZ domain zinc finger transcription factor, Protein kinase A RI subunit alpha-associated protein, Zinc finger and BTB domain-containing protein 19, Zinc finger protein 278, Zinc finger sarcoma gene protein

All UniProt accessions (1): Q9HBE1

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional regulator that plays a role in many biological processes such as embryogenesis, senescence, T-cell development or neurogenesis. Interacts with the TP53 protein to control genes that are important in proliferation and in the DNA-damage response. Mechanistically, the interaction inhibits the DNA binding and transcriptional activity of TP53/p53. Part of the transcriptional network modulating regulatory T-cell development and controls the generation of the regulatory T-cell pool under homeostatic conditions. (Microbial infection) Plays a positive role in viral cDNA synthesis.

Subunit / interactions. Homodimer. Interacts with RNF4. Interacts (via C-terminus) with TP53; this interaction inhibits TP53 ability to activate transcription.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous.

Disease relevance. A chromosomal aberration involving PATZ1 is associated with small round cell sarcoma. Translocation t(1;22)(p36.1;q12) with EWSR1.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9HBE1-1	1, C	yes
Q9HBE1-2	2, B
Q9HBE1-3	3, A
Q9HBE1-4	4, Short

RefSeq proteins (4): NP_055138, NP_114439, NP_114440, NP_114441 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000210	BTB/POZ_dom	Domain
IPR000637	HMGI/Y_DNA-bd_CS	Conserved_site
IPR011333	SKP1/BTB/POZ_sf	Homologous_superfamily
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF00651, PF13912, PF16637

UniProt features (42 total): strand 7, zinc finger region 7, helix 5, splice variant 4, turn 4, region of interest 3, sequence conflict 3, compositionally biased region 2, cross-link 2, chain 1, domain 1, modified residue 1, DNA-binding region 1, sequence variant 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
2EPP	SOLUTION NMR
2EPQ	SOLUTION NMR
2EPR	SOLUTION NMR
2EPS	SOLUTION NMR
2YT9	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HBE1-F1	60.98	0.02

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 (3): 282, 112, 272

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 277 (showing top): AGGAAGC_MIR5163P, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN, E2F_Q4_01, YANG_BREAST_CANCER_ESR1_LASER_UP, SP3_Q3, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GCM_ZNF198, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, AP2_Q3, GOBP_MALE_GAMETE_GENERATION, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22, AATGGAG_MIR136, YY1_Q6

GO Biological Process (11): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of cytokine production (GO:0001817), regulation of immune system process (GO:0002682), regulation of DNA-templated transcription (GO:0006355), spermatogenesis (GO:0007283), male gonad development (GO:0008584), negative regulation of endothelial cell migration (GO:0010596), T cell differentiation (GO:0030217), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), regulation of gene expression (GO:0010468)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), chromatin binding (GO:0003682), zinc ion binding (GO:0008270), ubiquitin protein ligase binding (GO:0031625), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): male germ cell nucleus (GO:0001673), nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	3
regulation of gene expression	2
regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
binding	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
cytokine production	1
regulation of multicellular organismal process	1
immune system process	1
regulation of biological process	1
regulation of RNA biosynthetic process	1
developmental process involved in reproduction	1
male gamete generation	1
gonad development	1
development of primary male sexual characteristics	1
regulation of endothelial cell migration	1
negative regulation of cell migration	1
endothelial cell migration	1
lymphocyte differentiation	1
T cell activation	1
negative regulation of RNA biosynthetic process	1
positive regulation of RNA biosynthetic process	1
gene expression	1
regulation of macromolecule biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
nucleic acid binding	1
transition metal ion binding	1
ubiquitin-like protein ligase binding	1
cation binding	1
germ cell nucleus	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1040 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PATZ1	EWSR1	Q01844	880
PATZ1	RNF4	P78317	832
PATZ1	E9PD41	E9PD41	814
PATZ1	NCOR1	O75376	698
PATZ1	ETV4	P43268	622
PATZ1	ETV1	P50549	622
PATZ1	FUS	P35637	611
PATZ1	CD99	P14209	611
PATZ1	SATB1	Q01826	575
PATZ1	NR4A3	Q92570	567
PATZ1	TAF15	Q92804	539
PATZ1	GATA3	P23771	510
PATZ1	CD8A	P01732	502
PATZ1	TP53	P04637	498
PATZ1	CD8B2	A6NJW9	494

IntAct

81 interactions, top by confidence:

A	B	Type	Score
FBXL17	BACH1	psi-mi:“MI:0914”(association)	0.730
SCRIB	NOS1AP	psi-mi:“MI:0914”(association)	0.690
P4HA3	FAM171A2	psi-mi:“MI:0914”(association)	0.640
CLEC11A	VWA8	psi-mi:“MI:0914”(association)	0.530
FGF3	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
MACROH2A2	PPM1G	psi-mi:“MI:0914”(association)	0.530
RPL18A	RRP8	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
RPL18	NAP1L1	psi-mi:“MI:0914”(association)	0.530
ZBTB24	CBX6	psi-mi:“MI:0914”(association)	0.530
LIN28B	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPL13A	NVL	psi-mi:“MI:0914”(association)	0.530
ZNF460	ZNF324	psi-mi:“MI:0914”(association)	0.530
CBX6	ZBTB24	psi-mi:“MI:0914”(association)	0.530
AIPL1	SUPT5H	psi-mi:“MI:0914”(association)	0.510
PATZ1	YWHAE	psi-mi:“MI:0915”(physical association)	0.400
SFN	PATZ1	psi-mi:“MI:0915”(physical association)	0.400
PATZ1	NDUFA3	psi-mi:“MI:0915”(physical association)	0.400
PATZ1	ACOT1	psi-mi:“MI:0915”(physical association)	0.400
FOXJ2	TCERG1	psi-mi:“MI:0914”(association)	0.350
RBPJ	SAMD1	psi-mi:“MI:0914”(association)	0.350
PB2	PIK3R2	psi-mi:“MI:0914”(association)	0.350
PB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
PB2	IPO5	psi-mi:“MI:0914”(association)	0.350
PB2	HAX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (200): PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Biochemical Activity), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-MS), PATZ1 (Affinity Capture-Western), TP53 (Affinity Capture-Western), PATZ1 (Affinity Capture-Western)

ESM2 similar proteins: A1L2U9, A2BID7, B1WAZ8, B4F6U4, E9Q8T2, F1QLG5, H2L008, O08785, O15164, P57071, P70121, Q05516, Q08BR4, Q0IH98, Q0P5J0, Q0VCJ6, Q2M1K9, Q2TAL8, Q3U288, Q3UA37, Q3UTQ7, Q53TQ3, Q56R14, Q5NBY9, Q5RAX9, Q5RGA4, Q5XJV7, Q64127, Q6E2N3, Q6INA9, Q6YND2, Q7Z3K3, Q8BZH4, Q8K0L9, Q8N1W2, Q8QGQ6, Q8R515, Q91YB0, Q91YB2, Q96BR9

Diamond homologs: A0JN76, A1L2U9, A1YEX3, A1YPR0, A2AAX3, B1WAZ8, B1WBS3, B1WBU4, B2RXF5, D3ZA50, E9Q4F2, O15062, O15156, O15209, O43167, O88282, O88939, O93567, O94889, O95365, P10074, P24278, P41182, P41183, P52739, P97302, Q0D2K2, Q0IH98, Q0IJ29, Q0P4X6, Q0VCJ6, Q13105, Q14526, Q1H9T6, Q1L8W0, Q3B725, Q3B7M1, Q3B7N9, Q3SWU4, Q53HC5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
PATZ1	down-regulates	RNF4	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 89 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Peptide chain elongation	10	20.1×	5e-09
Viral mRNA Translation	10	20.1×	5e-09
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	10	19.9×	5e-09
Selenocysteine synthesis	10	19.1×	5e-09
Eukaryotic Translation Termination	10	19.1×	5e-09
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	10	18.7×	5e-09
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	10	18.7×	5e-09
Formation of a pool of free 40S subunits	10	17.8×	7e-09

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	10	22.6×	1e-08
negative regulation of translation	5	11.9×	7e-03
translation	9	11.3×	3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

952 predictions. Top by Δscore:

Variant	Effect	Δscore
22:31327307:CTT:C	acceptor_gain	1.0000
22:31327310:C:CC	acceptor_gain	1.0000
22:31327310:C:CG	acceptor_loss	1.0000
22:31327313:C:CT	acceptor_gain	1.0000
22:31335686:GATTA:G	donor_loss	1.0000
22:31335687:ATTAC:A	donor_loss	1.0000
22:31335688:TTA:T	donor_loss	1.0000
22:31335689:TA:T	donor_loss	1.0000
22:31335690:A:AG	donor_loss	1.0000
22:31335859:CAGGT:C	acceptor_gain	1.0000
22:31335860:AGGT:A	acceptor_gain	1.0000
22:31335861:GGT:G	acceptor_gain	1.0000
22:31335862:GT:G	acceptor_gain	1.0000
22:31335862:GTCT:G	acceptor_loss	1.0000
22:31335863:TCTG:T	acceptor_loss	1.0000
22:31335864:C:CC	acceptor_gain	1.0000
22:31335871:C:CT	acceptor_gain	1.0000
22:31342956:CAGGC:C	acceptor_gain	1.0000
22:31342957:AGGCC:A	acceptor_loss	1.0000
22:31342958:GGC:G	acceptor_gain	1.0000
22:31342959:GC:G	acceptor_gain	1.0000
22:31342959:GCC:G	acceptor_loss	1.0000
22:31342960:CC:C	acceptor_gain	1.0000
22:31342961:C:CC	acceptor_gain	1.0000
22:31342961:C:CG	acceptor_loss	1.0000
22:31342962:T:A	acceptor_loss	1.0000
22:31344326:CCTCA:C	donor_loss	1.0000
22:31344327:CTCAC:C	donor_loss	1.0000
22:31344328:TCAC:T	donor_loss	1.0000
22:31344329:CACCT:C	donor_loss	1.0000

AlphaMissense

4509 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:31327136:A:G	C607R	1.000
22:31328920:G:C	F504L	1.000
22:31328920:G:T	F504L	1.000
22:31328921:A:G	F504S	1.000
22:31328922:A:G	F504L	1.000
22:31335701:A:G	C500R	1.000
22:31335708:G:C	C497W	1.000
22:31335710:A:G	C497R	1.000
22:31335744:G:C	H485Q	1.000
22:31335744:G:T	H485Q	1.000
22:31335746:G:C	H485D	1.000
22:31335781:C:G	C473S	1.000
22:31335781:C:T	C473Y	1.000
22:31335782:A:G	C473R	1.000
22:31335782:A:T	C473S	1.000
22:31335789:G:C	C470W	1.000
22:31335791:A:G	C470R	1.000
22:31335817:A:G	L461P	1.000
22:31335819:G:C	H460Q	1.000
22:31335819:G:T	H460Q	1.000
22:31335820:T:C	H460R	1.000
22:31335821:G:C	H460D	1.000
22:31335821:G:T	H460N	1.000
22:31335829:A:G	L457P	1.000
22:31335832:C:G	R456P	1.000
22:31335833:G:T	R456S	1.000
22:31335846:A:C	F451L	1.000
22:31335846:A:T	F451L	1.000
22:31335847:A:C	F451C	1.000
22:31335847:A:G	F451S	1.000

dbSNP variants (sampled 300 via entrez): RS1000102672 (22:31329286 G>A), RS1000364268 (22:31327868 C>T), RS1000470935 (22:31332674 G>A), RS1000502099 (22:31332944 T>C), RS1000584165 (22:31325381 C>G), RS1000586455 (22:31335521 G>A,C), RS1000677291 (22:31340166 G>T), RS1000769266 (22:31325710 G>C), RS1000807942 (22:31342329 G>A), RS1000846164 (22:31346888 C>A,T), RS1000847840 (22:31346762 G>A), RS1000883385 (22:31328221 G>T), RS1000958812 (22:31346902 G>A,C), RS1001092996 (22:31341948 T>C), RS1001110964 (22:31340529 G>A,T)

Disease associations

OMIM: gene MIM:605165 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): ependymoma (MONDO:0016698)

Orphanet (1): Ependymoma (Orphanet:251636)

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST004619_67	Reticulocyte fraction of red cells	6.000000e-10
GCST004622_96	Reticulocyte count	7.000000e-10
GCST006804_141	Red cell distribution width	9.000000e-10
GCST008839_268	Height	3.000000e-08
GCST010135_20	Oily fish consumption	3.000000e-10
GCST010135_5	Oily fish consumption	1.000000e-15
GCST010140_12	Pork consumption	3.000000e-10
GCST010140_49	Pork consumption	1.000000e-15
GCST010142_11	Fish- and plant-related diet	1.000000e-11
GCST010142_79	Fish- and plant-related diet	3.000000e-08
GCST90002382_503	Eosinophil percentage of white cells	5.000000e-37
GCST90002405_417	Reticulocyte count	4.000000e-15
GCST90002406_570	Reticulocyte fraction of red cells	3.000000e-14

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count
EFO:0009188	Red cell distribution width
EFO:0008111	diet measurement
EFO:0007991	eosinophil percentage of leukocytes

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D004806	Ependymoma	C04.557.465.625.600.380.290; C04.557.470.670.380.290; C04.557.580.625.600.380.290

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	8
trichostatin A	affects cotreatment, decreases expression	4
Tobacco Smoke Pollution	decreases expression, decreases methylation	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
bisphenol A	increases expression	1
methylselenic acid	decreases expression	1
quercitrin	decreases expression	1
arsenite	increases methylation	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
testosterone-3-carboxymethyloxime-bovine serum albumin conjugate	affects expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
entinostat	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
NSC 689534	affects binding, decreases expression	1
Bortezomib	decreases expression	1
Vorinostat	decreases expression	1
Asbestos	affects expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression	1
Caffeine	decreases phosphorylation	1
Copper	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Folic Acid	decreases expression	1
Methotrexate	decreases expression	1

Cellosaurus cell lines

7 cell lines: 3 embryonic stem cell, 3 spontaneously immortalized cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A5C6	SEES3-1V human PATZ1, clone1	Embryonic stem cell	Male
CVCL_A5C7	SEES3-1V human PATZ1, clone2	Embryonic stem cell	Male
CVCL_A5C8	SEES3-1V human PATZ1, clone3	Embryonic stem cell	Male
CVCL_E5UB	FRTL5-Ras-PATZ1 clone 22	Spontaneously immortalized cell line	Sex unspecified
CVCL_E5UC	FRTL5-Ras-PATZ1 clone 28	Spontaneously immortalized cell line	Sex unspecified
CVCL_E5UD	FRTL5-Ras-PATZ1 clone 33	Spontaneously immortalized cell line	Sex unspecified
CVCL_XV72	HEK293 eGFP-PATZ1	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00517959	PHASE3	UNKNOWN	SCRT Versus Conventional RT in Children and Young Adults With Low Grade and Benign Brain Tumors
NCT01096368	PHASE3	COMPLETED	Maintenance Chemotherapy or Observation Following Induction Chemotherapy and Radiation Therapy in Treating Patients With Newly Diagnosed Ependymoma
NCT00003479	PHASE2	TERMINATED	Antineoplaston Therapy in Treating Patients With Ependymoma
NCT00520936	PHASE2	COMPLETED	A Study of Pemetrexed in Children With Recurrent Cancer
NCT00840047	PHASE2	ACTIVE_NOT_RECRUITING	Methionine PET/CT Studies In Patients With Cancer
NCT01088035	PHASE2	TERMINATED	Carboplatin as a Radiosensitizer in Treating Childhood Ependymoma
NCT01247922	PHASE2	TERMINATED	Single-agent Erlotinib in Patients Previously Treated With Oral Etoposide in Protocol OSI-774-205
NCT01288235	PHASE2	COMPLETED	Proton Radiotherapy for Pediatric Brain Tumors Requiring Partial Brain Irradiation
NCT01295944	PHASE2	COMPLETED	Carboplatin and Bevacizumab for Recurrent Ependymoma
NCT01356290	PHASE2	RECRUITING	Antiangiogenic Therapy for Children With Recurrent Medulloblastoma, Ependymoma, ATRT and Rare CNS Tumors
NCT01836549	PHASE2	TERMINATED	Imetelstat Sodium in Treating Younger Patients With Recurrent or Refractory Brain Tumors
NCT02125786	PHASE2	ACTIVE_NOT_RECRUITING	A Trial of Surgery and Fractionated Re-Irradiation for Recurrent Ependymoma
NCT02689336	PHASE2	WITHDRAWN	Erlotinib in Combination With Temozolomide in Treating Relapsed/Recurrent/Refractory Pediatric Solid Tumors
NCT03095248	PHASE2	TERMINATED	Trial of Selumetinib in Patients With Neurofibromatosis Type II Related Tumors
NCT03155620	PHASE2	ACTIVE_NOT_RECRUITING	Targeted Therapy Directed by Genetic Testing in Treating Pediatric Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphomas, or Histiocytic Disorders (The Pediatric MATCH Screening Trial)
NCT03173950	PHASE2	COMPLETED	Immune Checkpoint Inhibitor Nivolumab in People With Recurrent Select Rare CNS Cancers
NCT03194906	PHASE2	COMPLETED	Memantine for Prevention of Cognitive Late Effects in Pediatric Patients Receiving Cranial Radiation Therapy for Localized Brain Tumors
NCT03210714	PHASE2	ACTIVE_NOT_RECRUITING	Erdafitinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With FGFR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213652	PHASE2	ACTIVE_NOT_RECRUITING	Ensartinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With ALK or ROS1 Genomic Alterations (A Pediatric MATCH Treatment Trial)
NCT03213665	PHASE2	COMPLETED	Tazemetostat in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With EZH2, SMARCB1, or SMARCA4 Gene Mutations (A Pediatric MATCH Treatment Trial)
NCT03213678	PHASE2	COMPLETED	Samotolisib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With TSC or PI3K/MTOR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213704	PHASE2	ACTIVE_NOT_RECRUITING	Larotrectinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With NTRK Fusions (A Pediatric MATCH Treatment Trial)
NCT03220035	PHASE2	COMPLETED	Vemurafenib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With BRAF V600 Mutations (A Pediatric MATCH Treatment Trial)
NCT03233204	PHASE2	COMPLETED	Olaparib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Defects in DNA Damage Repair Genes (A Pediatric MATCH Treatment Trial)
NCT03526250	PHASE2	COMPLETED	Palbociclib in Treating Patients With Relapsed or Refractory Rb Positive Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Activating Alterations in Cell Cycle Genes (A Pediatric MATCH Treatment Trial)
NCT03698994	PHASE2	ACTIVE_NOT_RECRUITING	Ulixertinib in Treating Patients With Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With MAPK Pathway Mutations (A Pediatric MATCH Treatment Trial)
NCT03727841	PHASE2	TERMINATED	Marizomib for Recurrent Low-Grade and Anaplastic Supratentorial, Infratentorial, and Spinal Cord Ependymoma
NCT04049669	PHASE2	ACTIVE_NOT_RECRUITING	Pediatric Trial of Indoximod With Chemotherapy and Radiation for Relapsed Brain Tumors or Newly Diagnosed DIPG
NCT04195555	PHASE2	ACTIVE_NOT_RECRUITING	Ivosidenib in Treating Patients With Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With IDH1 Mutations (A Pediatric MATCH Treatment Trial)
NCT04284774	PHASE2	ACTIVE_NOT_RECRUITING	Tipifarnib for the Treatment of Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With HRAS Gene Alterations, a Pediatric MATCH Treatment Trial
NCT04320888	PHASE2	ACTIVE_NOT_RECRUITING	Selpercatinib for the Treatment of Advanced Solid Tumors, Lymphomas, or Histiocytic Disorders With Activating RET Gene Alterations, a Pediatric MATCH Treatment Trial
NCT04374305	PHASE2	RECRUITING	Innovative Trial for Understanding the Impact of Targeted Therapies in NF2-Related Schwannomatosis (INTUITT-NF2)
NCT04743661	PHASE2	ACTIVE_NOT_RECRUITING	131I-Omburtamab, in Recurrent Medulloblastoma and Ependymoma
NCT06804655	PHASE2	NOT_YET_RECRUITING	Pharmacoscopy for Patients With Refractory Primary Brain Tumors
NCT07424092	PHASE2	RECRUITING	Intratumoral DNX-2401 for High Grade Pediatric Brain Tumors
NCT00634231	PHASE1	COMPLETED	A Phase I Study of AdV-tk + Prodrug Therapy in Combination With Radiation Therapy for Pediatric Brain Tumors
NCT00994071	PHASE1	COMPLETED	A Phase I Study of ABT-888, an Oral Inhibitor of Poly(ADP-ribose) Polymerase and Temozolomide in Children With Recurrent/Refractory CNS Tumors
NCT01171469	PHASE1	COMPLETED	Vaccination With Dendritic Cells Loaded With Brain Tumor Stem Cells for Progressive Malignant Brain Tumor
NCT01331135	PHASE1	COMPLETED	Aflac ST0901 CHOANOME - Sirolimus in Solid Tumors
NCT01498783	PHASE1	COMPLETED	Phase I Study of 5-Fluorouracil in Children and Young Adults With Recurrent Ependymoma