ZNF280A

Summary

ZNF280A (zinc finger protein 280A, HGNC:18597) is a protein-coding gene on chromosome 22q11.22, encoding Zinc finger protein 280A (P59817). May function as a transcription factor.

This gene encodes a zinc finger protein. The encoded protein contains 4 C2H2-type zinc fingers, which are commonly found in transcription factors. A variety of functions may be performed by this type of zinc finger protein, including the binding of DNA or RNA.

Source: NCBI Gene 129025 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_080740

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18597
Approved symbol	ZNF280A
Name	zinc finger protein 280A
Location	22q11.22
Locus type	gene with protein product
Status	Approved
Aliases	3’OY11.1, ZNF636
Ensembl gene	ENSG00000169548
Ensembl biotype	protein_coding
Entrez	129025

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000302097

RefSeq mRNA: 1 — MANE Select: NM_080740 NM_080740

CCDS: CCDS13800

Canonical transcript exons

ENST00000302097 — 2 exons

Exon	Start	End
ENSE00001135391	22513736	22515701
ENSE00001256153	22520089	22520270

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 88.42.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4499 / max 68.3181, expressed in 155 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193277	0.4499	155

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.42	gold quality
right adrenal gland cortex	UBERON:0035827	64.64	gold quality
left adrenal gland	UBERON:0001234	63.98	gold quality
right adrenal gland	UBERON:0001233	62.83	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	62.14	gold quality
left adrenal gland cortex	UBERON:0035825	62.06	gold quality
adrenal gland	UBERON:0002369	59.05	gold quality
stromal cell of endometrium	CL:0002255	41.19	silver quality
placenta	UBERON:0001987	37.90	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
endometrium	UBERON:0001295	36.90	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
apex of heart	UBERON:0002098	35.38	gold quality
sural nerve	UBERON:0015488	35.27	gold quality
granulocyte	CL:0000094	34.92	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
vermiform appendix	UBERON:0001154	32.18	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
urinary bladder	UBERON:0001255	31.70	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
leukocyte	CL:0000738	30.25	gold quality
prefrontal cortex	UBERON:0000451	30.16	gold quality
monocyte	CL:0000576	29.96	gold quality
islet of Langerhans	UBERON:0000006	29.70	gold quality
liver	UBERON:0002107	29.28	gold quality
tonsil	UBERON:0002372	28.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting ZNF280A, 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-8075	99.97	67.20	962
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-5088-5P	97.97	64.28	487
HSA-MIR-6818-5P	97.50	67.10	1167
HSA-MIR-6726-5P	95.97	63.72	841
HSA-MIR-920	95.97	63.95	811
HSA-MIR-4300	95.85	64.56	1003
HSA-MIR-5591-5P	95.85	64.76	1002
HSA-MIR-6874-5P	95.73	64.94	545

Literature-anchored findings (GeneRIF, showing 2)

• ZNF280A promotes lung adenocarcinoma development by regulating the expression of EIF3C. (PMID:33414445)
• Knockdown of ZNF280A inhibits cell proliferation and promotes cell apoptosis of bladder cancer. (PMID:37345848)

Cross-species orthologs

0 orthologs

Paralogs (28): ZNF280C (ENSG00000056277), ZBTB25 (ENSG00000089775), PRDM13 (ENSG00000112238), BCL6 (ENSG00000113916), FEZF1 (ENSG00000128610), ZBTB46 (ENSG00000130584), PRDM12 (ENSG00000130711), ZNF280D (ENSG00000137871), NACC2 (ENSG00000148411), FEZF2 (ENSG00000153266), ZBTB7B (ENSG00000160685), NACC1 (ENSG00000160877), BCL6B (ENSG00000161940), GFI1 (ENSG00000162676), GFI1B (ENSG00000165702), ZBTB49 (ENSG00000168826), ZNF581 (ENSG00000171425), ZNF524 (ENSG00000171443), ZBTB26 (ENSG00000171448), ZBTB21 (ENSG00000173276), ZNF683 (ENSG00000176083), ZBTB33 (ENSG00000177485), ZBTB3 (ENSG00000185670), ZBTB6 (ENSG00000186130), ZBTB14 (ENSG00000198081), ZBTB12 (ENSG00000204366), ZNF580 (ENSG00000213015), ZNF280B (ENSG00000275004)

Protein

Protein identifiers

Zinc finger protein 280A — P59817 (reviewed: P59817)

Alternative names: 3’OY11.1, Suppressor of hairy wing homolog 1, Zinc finger protein 636

All UniProt accessions (1): P59817

UniProt curated annotations — full annotation on UniProt →

Function. May function as a transcription factor.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_542778* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR025243	DUF4195	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050527

Pfam: PF13836

UniProt features (20 total): sequence variant 9, zinc finger region 4, compositionally biased region 4, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P59817-F1	60.84	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP, YAGI_AML_WITH_11Q23_REARRANGED, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, HES2_TARGET_GENES, LCORL_TARGET_GENES, SNRNP70_TARGET_GENES, MIR6801_5P, MIR10393_3P, GSE13411_NAIVE_VS_IGM_MEMORY_BCELL_UP, GSE22886_NAIVE_VS_IGG_IGA_MEMORY_BCELL_UP, CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_UP, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING

GO Biological Process (2): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

378 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF280A	POM121L1P	Q3SYA9	624
ZNF280A	GGTLC2	Q14390	621
ZNF280A	ZNF200	P98182	595
ZNF280A	PRAME	P78395	582
ZNF280A	IQANK1	A8MXQ7	580
ZNF280A	ZNF668	Q96K58	565
ZNF280A	ZNF382	Q96SR6	511
ZNF280A	OR1L3	Q8NH93	506
ZNF280A	ZNF84	P51523	504
ZNF280A	OR1L1	Q8NH94	496
ZNF280A	RIMBP3B	A6NNM3	446
ZNF280A	CCDC71L	Q8N9Z2	446
ZNF280A	ZNF285	Q96NJ3	417
ZNF280A	ZNF276	Q8N554	407
ZNF280A	HSFY1	Q96LI6	402

IntAct

22 interactions, top by confidence:

A	B	Type	Score
PDE4C	ZNF280A	psi-mi:“MI:0915”(physical association)	0.560
ZNF280A	ENOPH1	psi-mi:“MI:0915”(physical association)	0.560
	ZNF280A	psi-mi:“MI:0915”(physical association)	0.560
ZNF280A	CABP5	psi-mi:“MI:0915”(physical association)	0.560
ZNF280A	EIF1AD	psi-mi:“MI:0915”(physical association)	0.560
ZNF280A	PDE4C	psi-mi:“MI:0915”(physical association)	0.560
ZNF280A	H2BC20P	psi-mi:“MI:0915”(physical association)	0.400
ZNF280A	NUCB2	psi-mi:“MI:0915”(physical association)	0.400
ZNF280A	KDM1A	psi-mi:“MI:0915”(physical association)	0.370
ZNF280A	NUCB2	psi-mi:“MI:0914”(association)	0.350
	ZNF280A	psi-mi:“MI:0915”(physical association)	0.000
ENOPH1	ZNF280A	psi-mi:“MI:0915”(physical association)	0.000
CABP5	ZNF280A	psi-mi:“MI:0915”(physical association)	0.000
EIF1AD	ZNF280A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (31): ZNF280B (Affinity Capture-MS), NUCB2 (Affinity Capture-MS), HDGFRP3 (Affinity Capture-MS), RBM42 (Affinity Capture-MS), UPF3B (Affinity Capture-MS), ZNF280A (Two-hybrid), ZNF280A (Two-hybrid), ZNF280A (Two-hybrid), ZNF280A (Two-hybrid), ZNF280A (Two-hybrid), EIF1AD (Two-hybrid), CALM1 (Two-hybrid), ZNF280A (Proximity Label-MS), NUCB2 (Affinity Capture-MS), ZNF280A (Proximity Label-MS)

ESM2 similar proteins: A0A0R4IYX6, A0A1D5NVS8, A0AVK6, A4QP16, A5GFT6, A7XYJ6, B8A5Y1, D4A666, E1B7L7, E1BKK0, F1LMN3, F1QLG5, F1QZ88, F6NSX9, F7EA39, O73590, P12757, P59817, Q0VEE6, Q2IBF7, Q2TB10, Q53TQ3, Q566I1, Q58FA4, Q5R431, Q5ZIX8, Q60665, Q63679, Q68FE9, Q69ZF8, Q6IQ32, Q6P2L6, Q6PCM1, Q6ZSZ6, Q6ZU65, Q7Z3K3, Q80WC1, Q86UP3, Q8BHZ4, Q8BZH4

Diamond homologs: P59817, Q5PPG4, Q68FE8, Q6N043, Q6P3Y5, Q7Z3K3, Q86YH2, Q8BZH4, Q8ND82, Q99KZ6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

313 predictions. Top by Δscore:

Variant	Effect	Δscore
22:22520083:G:C	donor_gain	1.0000
22:22520178:T:TA	donor_gain	1.0000
22:22517774:T:C	donor_gain	0.9900
22:22517778:AGAT:A	donor_gain	0.9900
22:22520083:GCTCA:G	donor_loss	0.9900
22:22520084:CTCAC:C	donor_loss	0.9900
22:22520085:TCACC:T	donor_loss	0.9900
22:22520086:CA:C	donor_loss	0.9900
22:22520087:A:AC	donor_gain	0.9900
22:22520087:A:AT	donor_loss	0.9900
22:22520088:C:CC	donor_gain	0.9900
22:22520088:C:T	donor_loss	0.9900
22:22520093:T:TA	donor_gain	0.9800
22:22520088:CCAG:C	donor_gain	0.9600
22:22520087:AC:A	donor_gain	0.9400
22:22520088:CC:C	donor_gain	0.9400
22:22515702:C:A	acceptor_loss	0.9100
22:22515703:T:G	acceptor_loss	0.9100
22:22516501:C:A	donor_gain	0.9000
22:22515704:A:C	acceptor_loss	0.8800
22:22515710:A:T	acceptor_loss	0.8800
22:22516493:TGC:T	donor_gain	0.8800
22:22520082:AGCT:A	donor_gain	0.8800
22:22520088:CCA:C	donor_gain	0.8800
22:22520088:CCAGT:C	donor_gain	0.8600
22:22515713:C:CT	acceptor_loss	0.8500
22:22516527:C:CA	donor_gain	0.8400
22:22515712:CCA:C	acceptor_loss	0.7700
22:22515716:G:C	acceptor_loss	0.7000
22:22520090:AGTT:A	donor_gain	0.6900

AlphaMissense

3605 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000277935 (22:22519104 A>G), RS1000873439 (22:22517155 C>T), RS1001326753 (22:22517356 G>A), RS1001955195 (22:22515312 C>G), RS1002004419 (22:22521520 T>C), RS1002058209 (22:22521805 G>A), RS1002183698 (22:22520482 C>T), RS1002286186 (22:22515847 A>G), RS1003518844 (22:22520657 G>A,T), RS1004112042 (22:22516288 C>T), RS1004846375 (22:22513599 C>T), RS1005116407 (22:22514828 T>C,G), RS1005578997 (22:22513488 C>CG), RS1005786395 (22:22521456 C>T), RS1006076608 (22:22520451 T>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009391_1468	Metabolite levels	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010406	triacylglycerol 48:3 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, decreases methylation, increases expression	8
Benzo(a)pyrene	increases methylation, affects methylation, increases expression	3
entinostat	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
methylmercuric chloride	increases expression	1
trichostatin A	decreases expression, increases expression	1
butyraldehyde	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	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
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Leflunomide	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Quercetin	increases expression	1
Urethane	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	affects expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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