ZNF780B

Summary

ZNF780B (zinc finger protein 780B, HGNC:33109) is a protein-coding gene on chromosome 19q13.2, encoding Zinc finger protein 780B (Q9Y6R6). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription activator 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 163131 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 80 total
• MANE Select transcript: NM_001005851

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33109
Approved symbol	ZNF780B
Name	zinc finger protein 780B
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000128000
Ensembl biotype	protein_coding
Entrez	163131

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 retained_intron

ENST00000221355, ENST00000434248, ENST00000593605, ENST00000594811, ENST00000598845, ENST00000884302, ENST00000884303, ENST00000884304, ENST00000884305, ENST00000933461, ENST00000956875, ENST00000956876

RefSeq mRNA: 1 — MANE Select: NM_001005851 NM_001005851

CCDS: CCDS46077

Canonical transcript exons

ENST00000434248 — 5 exons

Exon	Start	End
ENSE00001604984	40028260	40036626
ENSE00001796978	40056189	40056231
ENSE00002479328	40047375	40047470
ENSE00003529005	40050324	40050377
ENSE00003534055	40048670	40048796

Expression profiles

Bgee: expression breadth ubiquitous, 139 present calls, max score 93.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.7532 / max 172.2434, expressed in 1685 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180938	9.7532	1685

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	93.88	gold quality
adrenal tissue	UBERON:0018303	86.80	gold quality
calcaneal tendon	UBERON:0003701	85.40	gold quality
endometrium	UBERON:0001295	82.76	gold quality
tonsil	UBERON:0002372	82.59	gold quality
apex of heart	UBERON:0002098	82.13	gold quality
cortical plate	UBERON:0005343	82.00	gold quality
pituitary gland	UBERON:0000007	81.86	gold quality
bone marrow cell	CL:0002092	81.39	gold quality
sural nerve	UBERON:0015488	81.39	gold quality
ovary	UBERON:0000992	81.08	gold quality
left ovary	UBERON:0002119	81.03	gold quality
adenohypophysis	UBERON:0002196	80.93	gold quality
right uterine tube	UBERON:0001302	80.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.54	gold quality
cerebellar cortex	UBERON:0002129	80.49	gold quality
cerebellum	UBERON:0002037	80.47	gold quality
right atrium auricular region	UBERON:0006631	80.44	gold quality
cerebellar hemisphere	UBERON:0002245	80.41	gold quality
monocyte	CL:0000576	80.34	gold quality
thyroid gland	UBERON:0002046	80.21	gold quality
leukocyte	CL:0000738	80.11	gold quality
right lobe of thyroid gland	UBERON:0001119	80.07	gold quality
heart	UBERON:0000948	79.96	gold quality
heart left ventricle	UBERON:0002084	79.87	gold quality
lymph node	UBERON:0000029	79.83	gold quality
right ovary	UBERON:0002118	79.80	gold quality
left lobe of thyroid gland	UBERON:0001120	79.68	gold quality
ganglionic eminence	UBERON:0004023	79.57	gold quality
smooth muscle tissue	UBERON:0001135	79.46	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.80

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2532.1	ZNF780B	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

miRNA regulators (miRDB)

224 targeting ZNF780B, 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-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
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-3646	100.00	73.56	5283
HSA-MIR-4776-3P	100.00	68.73	1340
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-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
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-5696	99.98	72.36	4487
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4803	99.98	71.99	3117

Cross-species orthologs

0 orthologs

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), 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), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 780B — Q9Y6R6 (reviewed: Q9Y6R6)

Alternative names: Zinc finger protein 779

All UniProt accessions (4): Q9Y6R6, C9JTJ1, M0R0W9, M0R168

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.

RefSeq proteins (1): NP_001005851* (*=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352, PF13912

UniProt features (25 total): zinc finger region 23, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6R6-F1	73.23	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 97 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MULLIGHAN_NPM1_SIGNATURE_3_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION, BASAKI_YBX1_TARGETS_DN, OSMAN_BLADDER_CANCER_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP, KARLSSON_TGFB1_TARGETS_DN, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY, ZWANG_DOWN_BY_2ND_EGF_PULSE, BRCA1_DN.V1_UP

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), zinc ion binding (GO:0008270), DNA binding (GO:0003677), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

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

GO top-level categories

Rollup of top GO terms by namespace:

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

Protein interactions and networks

STRING

374 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF780B	TMEM235	A6NFC5	537
ZNF780B	ZNF438	Q7Z4V0	535
ZNF780B	CIMIP2B	A8MTA8	511
ZNF780B	TACC2	O95359	461
ZNF780B	TRIOBP	Q9H2D6	458
ZNF780B	C19orf47	Q8N9M1	417
ZNF780B	ACTMAP	Q5BKX5	398
ZNF780B	CCDC74B	Q96LY2	397
ZNF780B	ZNF511	Q8NB15	390
ZNF780B	TMCO1	Q9UM00	379
ZNF780B	CCDC169	A6NNP5	373
ZNF780B	CCDC190	Q86UF4	368
ZNF780B	UBTF	P17480	353
ZNF780B	UBTFL1	P0CB47	353
ZNF780B	PC	P11498	353

IntAct

1 interactions, top by confidence:

A	B	Type	Score
STING1	ZSWIM8	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): ZNF780B (Affinity Capture-MS), ZNF780B (Affinity Capture-RNA)

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

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1106 predictions. Top by Δscore:

Variant	Effect	Δscore
19:40048664:CCTTA:C	donor_loss	1.0000
19:40048665:CTTA:C	donor_loss	1.0000
19:40048666:TTA:T	donor_loss	1.0000
19:40048667:TACCC:T	donor_loss	1.0000
19:40048668:A:AC	donor_gain	1.0000
19:40048668:AC:A	donor_gain	1.0000
19:40048669:C:CC	donor_gain	1.0000
19:40048669:C:CT	donor_loss	1.0000
19:40048669:CC:C	donor_gain	1.0000
19:40048669:CCCA:C	donor_gain	1.0000
19:40048794:TCC:T	acceptor_gain	1.0000
19:40048795:CC:C	acceptor_gain	1.0000
19:40048795:CCC:C	acceptor_gain	1.0000
19:40048795:CCCT:C	acceptor_loss	1.0000
19:40048796:CC:C	acceptor_gain	1.0000
19:40048797:C:CC	acceptor_gain	1.0000
19:40048797:C:CG	acceptor_loss	1.0000
19:40048798:T:C	acceptor_loss	1.0000
19:40048804:C:CT	acceptor_gain	1.0000
19:40048804:C:T	acceptor_gain	1.0000
19:40050322:A:AC	donor_gain	1.0000
19:40050323:C:CC	donor_gain	1.0000
19:40048709:C:A	donor_gain	0.9900
19:40048792:GATCC:G	acceptor_gain	0.9900
19:40048793:ATCC:A	acceptor_gain	0.9900
19:40055414:AC:A	donor_gain	0.9900
19:40055415:CC:C	donor_gain	0.9900
19:40056074:T:TA	donor_gain	0.9900
19:40036623:AAATC:A	acceptor_loss	0.9800
19:40036625:ATCT:A	acceptor_loss	0.9800

AlphaMissense

5628 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:40035581:A:C	F426L	0.995
19:40035581:A:T	F426L	0.995
19:40035583:A:G	F426L	0.995
19:40035413:A:C	F482L	0.994
19:40035413:A:T	F482L	0.994
19:40035415:A:G	F482L	0.994
19:40035665:A:C	F398L	0.993
19:40035665:A:T	F398L	0.993
19:40035667:A:G	F398L	0.993
19:40035749:A:C	F370L	0.993
19:40035749:A:T	F370L	0.993
19:40035751:A:G	F370L	0.993
19:40035329:G:C	F510L	0.992
19:40035329:G:T	F510L	0.992
19:40035331:A:G	F510L	0.992
19:40035660:C:G	R400P	0.992
19:40036001:A:C	F286L	0.992
19:40036001:A:T	F286L	0.992
19:40036003:A:G	F286L	0.992
19:40035324:C:G	R512P	0.990
19:40035833:A:C	F342L	0.990
19:40035833:A:T	F342L	0.990
19:40035835:A:G	F342L	0.990
19:40034993:G:C	F622L	0.989
19:40034993:G:T	F622L	0.989
19:40034995:A:G	F622L	0.989
19:40035497:A:C	F454L	0.989
19:40035497:A:T	F454L	0.989
19:40035499:A:G	F454L	0.989
19:40035077:A:C	F594L	0.987

dbSNP variants (sampled 300 via entrez): RS1000120460 (19:40050964 C>T), RS1000187760 (19:40049651 T>C), RS1000456325 (19:40042676 T>G), RS1000488720 (19:40042475 T>C,G), RS1000862566 (19:40055573 C>T), RS1000867734 (19:40029331 A>G), RS1001179564 (19:40035865 G>C,T), RS1001181022 (19:40047754 C>A,T), RS1001197326 (19:40030731 C>A,T), RS1001199896 (19:40054663 C>T), RS1001359171 (19:40041823 T>C), RS1001786746 (19:40036792 T>C), RS1001795198 (19:40041576 G>C), RS1001837400 (19:40036405 AAG>A), RS1002101126 (19:40054402 C>A,T)

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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
sodium arsenite	decreases expression	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
pentabromodiphenyl ether	decreases expression	1
ICG 001	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Vorinostat	decreases expression	1
Air Pollutants, Occupational	decreases expression	1
Cadmium	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

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