ZNF780A

Summary

ZNF780A (zinc finger protein 780A, HGNC:27603) is a protein-coding gene on chromosome 19q13.2, encoding Zinc finger protein 780A (O75290). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 284323 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 112 total
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• MANE Select transcript: NM_001142578

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27603
Approved symbol	ZNF780A
Name	zinc finger protein 780A
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	ZNF780
Ensembl gene	ENSG00000197782
Ensembl biotype	protein_coding
Entrez	284323

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 22 protein_coding, 3 non_stop_decay

ENST00000340963, ENST00000414720, ENST00000450241, ENST00000455521, ENST00000594395, ENST00000595687, ENST00000595773, ENST00000599368, ENST00000599972, ENST00000601688, ENST00000601715, ENST00000683561, ENST00000907463, ENST00000907464, ENST00000907465, ENST00000907466, ENST00000907467, ENST00000937711, ENST00000937712, ENST00000937713, ENST00000937714, ENST00000937715, ENST00000970365, ENST00000970366, ENST00000970367

RefSeq mRNA: 4 — MANE Select: NM_001142578 NM_001010880, NM_001142577, NM_001142578, NM_001142579

CCDS: CCDS33026, CCDS46078, CCDS46079

Canonical transcript exons

ENST00000628273 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 90.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.5956 / max 58.5584, expressed in 1672 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180941	3.1222	1448
180940	2.4233	1251
180939	0.0502	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	90.45	gold quality
leukocyte	CL:0000738	90.20	gold quality
calcaneal tendon	UBERON:0003701	89.98	gold quality
body of pancreas	UBERON:0001150	86.21	gold quality
tonsil	UBERON:0002372	86.14	gold quality
corpus callosum	UBERON:0002336	86.01	gold quality
right lobe of liver	UBERON:0001114	85.87	gold quality
granulocyte	CL:0000094	85.32	gold quality
pancreas	UBERON:0001264	85.20	gold quality
lower esophagus mucosa	UBERON:0035834	84.68	gold quality
blood	UBERON:0000178	84.52	gold quality
liver	UBERON:0002107	84.23	gold quality
islet of Langerhans	UBERON:0000006	84.13	gold quality
lymph node	UBERON:0000029	83.31	gold quality
mucosa of stomach	UBERON:0001199	83.15	gold quality
esophagus mucosa	UBERON:0002469	82.86	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.74	gold quality
adrenal tissue	UBERON:0018303	82.49	gold quality
vermiform appendix	UBERON:0001154	82.47	gold quality
spleen	UBERON:0002106	82.34	gold quality
endometrium	UBERON:0001295	82.30	gold quality
left adrenal gland cortex	UBERON:0035825	82.07	gold quality
body of stomach	UBERON:0001161	81.85	gold quality
cortical plate	UBERON:0005343	81.78	gold quality
saliva-secreting gland	UBERON:0001044	81.71	gold quality
stomach	UBERON:0000945	81.66	gold quality
adrenal gland	UBERON:0002369	81.62	gold quality
bone marrow cell	CL:0002092	81.51	gold quality
minor salivary gland	UBERON:0001830	81.47	gold quality
left adrenal gland	UBERON:0001234	81.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting ZNF780A, 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-4262	100.00	73.26	3931
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp607a	ENSMUSG00000020420
mus_musculus	Zfp626	ENSMUSG00000030604
mus_musculus	Zfp60	ENSMUSG00000037640
mus_musculus	Zfp607b	ENSMUSG00000057093
mus_musculus	Zfp59	ENSMUSG00000078779
mus_musculus	Zfp850	ENSMUSG00000096916
rattus_norvegicus	Zfp780b	ENSRNOG00000018885
rattus_norvegicus	LOC102553760	ENSRNOG00000018928
rattus_norvegicus	Zfp780b	ENSRNOG00000050995
rattus_norvegicus	Zfp59	ENSRNOG00000053366
rattus_norvegicus		ENSRNOG00000079029

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 780A — O75290 (reviewed: O75290)

All UniProt accessions (7): A0A075B791, A0A075B796, A0A075B7B0, A0A0C4DG08, O75290, M0QXV4, M0QYL2

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

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

Isoforms (3)

UniProt ID	Names	Canonical?
O75290-1	1	yes
O75290-2	2
O75290-3	3

RefSeq proteins (4): NP_001010880, NP_001136049, NP_001136050, NP_001136051 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352

UniProt features (24 total): zinc finger region 17, splice variant 4, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75290-F1	74.67	0.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION, ZAMORA_NOS2_TARGETS_UP, RODRIGUES_DCC_TARGETS_DN, LEIN_ASTROCYTE_MARKERS, SANSOM_APC_TARGETS, GEORGES_TARGETS_OF_MIR192_AND_MIR215, WANG_TUMOR_INVASIVENESS_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, BAKKER_FOXO3_TARGETS_UP, RAO_BOUND_BY_SALL4_ISOFORM_A, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, H1_6_TARGET_GENES

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

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 (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	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
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF780A	ZNF438	Q7Z4V0	567
ZNF780A	GRTP1	Q5TC63	537
ZNF780A	MYOZ3	Q8TDC0	519
ZNF780A	MICOS10	Q5TGZ0	513
ZNF780A	TRIM68	Q6AZZ1	511
ZNF780A	UTP20	O75691	508
ZNF780A	TIMM21	Q9BVV7	491
ZNF780A	DHRS4	Q9BTZ2	482
ZNF780A	KRTAP10-7	P60409	471
ZNF780A	FBXO15	Q8NCQ5	458
ZNF780A	ITGA11	Q9UKX5	445
ZNF780A	C19orf47	Q8N9M1	445
ZNF780A	ACTMAP	Q5BKX5	431
ZNF780A	GSTO1	P78417	425
ZNF780A	OR11A1	Q9GZK7	418
ZNF780A	A0A0U1RQV1	A0A0U1RQV1	418

IntAct

13 interactions, top by confidence:

A	B	Type	Score
ZNF780A	TRIM41	psi-mi:“MI:0915”(physical association)	0.560
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
ZNF780A	HSP90B1	psi-mi:“MI:0915”(physical association)	0.400
ZNF780A	TXNDC5	psi-mi:“MI:0915”(physical association)	0.400
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF346	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
ZNF780A	GAPDHS	psi-mi:“MI:0914”(association)	0.350
TRIM41	ZNF780A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (26): ZNF780A (Affinity Capture-RNA), ZNF780A (Affinity Capture-RNA), ZNF780A (Affinity Capture-MS), ZNF780A (Proximity Label-MS), ZNF780A (Proximity Label-MS), ZNF780A (Two-hybrid), HSP90B1 (Proximity Label-MS), TXNDC5 (Proximity Label-MS), ZNF780A (Proximity Label-MS), ZNF780A (Proximity Label-MS), ZNF780A (Proximity Label-MS), ZNF780A (Proximity Label-MS), ZNF780A (Affinity Capture-MS), RPS27A (Affinity Capture-MS), GAPDHS (Affinity Capture-MS)

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — NPC.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	102
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

874 predictions. Top by Δscore:

Variant	Effect	Δscore
19:40076208:ATC:A	acceptor_loss	1.0000
19:40076209:TCT:T	acceptor_loss	1.0000
19:40076210:C:CA	acceptor_loss	1.0000
19:40076210:C:CC	acceptor_gain	1.0000
19:40081919:T:C	acceptor_gain	1.0000
19:40083105:CCTTA:C	donor_loss	1.0000
19:40083106:CTTA:C	donor_loss	1.0000
19:40083107:TTACC:T	donor_loss	1.0000
19:40083108:TA:T	donor_loss	1.0000
19:40083109:A:AC	donor_gain	1.0000
19:40083109:A:AG	donor_loss	1.0000
19:40083109:AC:A	donor_gain	1.0000
19:40083110:C:CC	donor_gain	1.0000
19:40083110:CC:C	donor_gain	1.0000
19:40083245:C:T	acceptor_gain	1.0000
19:40084741:TTA:T	donor_loss	1.0000
19:40084743:A:AC	donor_gain	1.0000
19:40084743:AC:A	donor_loss	1.0000
19:40084744:C:CC	donor_gain	1.0000
19:40084746:TGG:T	donor_gain	1.0000
19:40084794:CTCCC:C	acceptor_gain	1.0000
19:40084796:CCC:C	acceptor_gain	1.0000
19:40084797:CC:C	acceptor_gain	1.0000
19:40084797:CCC:C	acceptor_gain	1.0000
19:40084798:CC:C	acceptor_gain	1.0000
19:40084798:CCTG:C	acceptor_loss	1.0000
19:40084799:C:CA	acceptor_loss	1.0000
19:40084799:C:CC	acceptor_gain	1.0000
19:40084800:T:A	acceptor_loss	1.0000
19:40084808:A:T	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000292012 (19:40091716 A>G), RS1000360503 (19:40085610 G>A), RS1000384518 (19:40069700 G>A), RS1000549972 (19:40088752 G>A), RS1000664052 (19:40091964 A>G), RS1000677794 (19:40083440 G>T), RS1000788853 (19:40086814 T>C), RS1000869986 (19:40080449 C>A,T), RS1000973881 (19:40074072 G>A,T), RS1001300865 (19:40080049 A>T), RS1001507117 (19:40081528 A>C), RS1001571550 (19:40070789 T>C), RS1001599066 (19:40082135 T>C), RS1001640566 (19:40069844 T>C), RS1002008031 (19:40070268 G>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	2
Acrolein	affects cotreatment, increases oxidation, increases abundance	2
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
Ozone	affects cotreatment, increases oxidation, increases abundance	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
propionaldehyde	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
pentabromodiphenyl ether	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Resveratrol	increases expression, affects cotreatment	1
Sunitinib	increases expression	1
Arsenic	increases abundance, increases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Coal	decreases expression, increases abundance	1
Manganese	increases abundance, increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A8K6	SEES3-1V human ZNF780A, clone1	Embryonic stem cell	Male
CVCL_A8K7	SEES3-1V human ZNF780A, clone2	Embryonic stem cell	Male
CVCL_A8K8	SEES3-1V human ZNF780A, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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