ZNF789

Summary

ZNF789 (zinc finger protein 789, HGNC:27801) is a protein-coding gene on chromosome 7q22.1, encoding Zinc finger protein 789 (Q5FWF6). 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. Located in nucleoplasm.

Source: NCBI Gene 285989 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 14 total
• MANE Select transcript: NM_213603

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27801
Approved symbol	ZNF789
Name	zinc finger protein 789
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000198556
Ensembl biotype	protein_coding
Entrez	285989

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 11 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000331410, ENST00000379724, ENST00000447047, ENST00000448667, ENST00000465438, ENST00000468705, ENST00000481108, ENST00000481472, ENST00000483089, ENST00000488485, ENST00000493485, ENST00000494186, ENST00000877987, ENST00000918757, ENST00000918758, ENST00000951819, ENST00000951820, ENST00000951821

RefSeq mRNA: 7 — MANE Select: NM_213603 NM_001013258, NM_001350999, NM_001351000, NM_001351001, NM_001351002, NM_001351004, NM_213603

CCDS: CCDS34693, CCDS34694

Canonical transcript exons

ENST00000331410 — 5 exons

Exon	Start	End
ENSE00001324331	99486476	99487605
ENSE00001595287	99472890	99473056
ENSE00003469445	99479661	99479787
ENSE00003533423	99484030	99484143
ENSE00003646167	99476403	99476480

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 89.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2563 / max 198.2184, expressed in 1731 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
79879	6.0056	1658
79880	2.0051	971
204539	0.2456	110

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	89.50	gold quality
right uterine tube	UBERON:0001302	89.39	gold quality
cerebellar cortex	UBERON:0002129	89.38	gold quality
adenohypophysis	UBERON:0002196	89.03	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.03	gold quality
cerebellum	UBERON:0002037	88.52	gold quality
pituitary gland	UBERON:0000007	87.96	gold quality
small intestine Peyer’s patch	UBERON:0003454	87.78	gold quality
sural nerve	UBERON:0015488	87.54	gold quality
mucosa of transverse colon	UBERON:0004991	87.33	gold quality
rectum	UBERON:0001052	87.32	gold quality
transverse colon	UBERON:0001157	87.09	gold quality
prostate gland	UBERON:0002367	86.87	gold quality
right testis	UBERON:0004534	86.83	gold quality
left testis	UBERON:0004533	86.76	gold quality
small intestine	UBERON:0002108	86.55	gold quality
metanephros cortex	UBERON:0010533	86.44	gold quality
left ovary	UBERON:0002119	86.19	gold quality
right ovary	UBERON:0002118	85.86	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.47	gold quality
spleen	UBERON:0002106	85.47	gold quality
body of uterus	UBERON:0009853	85.43	gold quality
right lobe of thyroid gland	UBERON:0001119	85.40	gold quality
left lobe of thyroid gland	UBERON:0001120	85.39	gold quality
thyroid gland	UBERON:0002046	85.17	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.90	gold quality
body of pancreas	UBERON:0001150	84.67	gold quality
testis	UBERON:0000473	84.62	gold quality
intestine	UBERON:0000160	84.17	gold quality
cortical plate	UBERON:0005343	84.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting ZNF789, 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-8485	100.00	77.57	4731
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-4635	98.74	67.63	1339
HSA-MIR-603	98.58	68.28	1603
HSA-MIR-216B-3P	98.55	67.19	1223
HSA-MIR-4275	97.96	68.42	1549
HSA-MIR-5585-5P	97.95	68.80	1024
HSA-MIR-12127	97.93	66.67	793

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), 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 789 — Q5FWF6 (reviewed: Q5FWF6)

All UniProt accessions (5): Q5FWF6, C9J3R7, C9J487, C9JUE3, F8WEN0

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?
Q5FWF6-1	1	yes
Q5FWF6-2	2
Q5FWF6-3	3

RefSeq proteins (7): NP_001013276, NP_001337928, NP_001337929, NP_001337930, NP_001337931, NP_001337933, NP_998768* (*=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
IPR050826	Krueppel_C2H2_ZnFinger	Family

Pfam: PF00096, PF01352

UniProt features (15 total): zinc finger region 8, splice variant 3, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5FWF6-F1	68.50	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 51 (showing top): LIAO_METASTASIS, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MYC_UP.V1_DN, SRC_UP.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GLI3_TARGET_GENES, SNIP1_TARGET_GENES, ZNF407_TARGET_GENES, ZNF528_TARGET_GENES, MIR4261, MIR147B_5P, MIR548AV_5P_MIR548K, MIR8054, MIR603

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

674 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF789	ACOT6	Q3I5F7	524
ZNF789	FAM222B	Q8WU58	453
ZNF789	ZBED8L	Q8TCP9	446
ZNF789	POU1F1	P28069	418
ZNF789	SSC4D	Q8WTU2	416
ZNF789	AGO3	Q9H9G7	410
ZNF789	SREBF2	Q12772	406
ZNF789	CHD8	Q9HCK8	400
ZNF789	TOP2B	Q02880	398
ZNF789	MAP2K7	O14733	396
ZNF789	KMT5A	Q9NQR1	396
ZNF789	MGLL	Q99685	389
ZNF789	CAPN1	P07384	388
ZNF789	COL2A1	P02458	373
ZNF789	PTK2B	Q14289	371
ZNF789	TET1	Q8NFU7	371

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ZNF789	HEXIM2	psi-mi:“MI:0915”(physical association)	0.560
HEXIM2	ZNF789	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): ZNF789 (Two-hybrid), ZNF789 (Affinity Capture-RNA), ZNF789 (Cross-Linking-MS (XL-MS)), ZNF789 (Affinity Capture-MS), ZNF789 (Affinity Capture-RNA)

ESM2 similar proteins: A0JPL0, A3KN36, A7MBI1, A8MT65, B2RXC5, D3ZVT0, P08042, P21506, P51508, P52738, Q02525, Q06730, Q12901, Q2KI58, Q2M218, Q2M3W8, Q2M3X9, Q2VY69, Q49AA0, Q4R6J4, Q4V8A8, Q5FWF6, Q5HY98, Q5RB33, Q5RC79, Q5REF1, Q5T5D7, Q5VIY5, Q61967, Q6P2D0, Q6ZN11, Q86XU0, Q86Y25, Q8N782, Q8N859, Q8NB42, Q8TF39, Q8TF47, Q8WXB4, Q95K49

Diamond homologs: A0JPL0, A2A761, A3KN32, A3KN36, A6NFI3, A6NM28, A6QLU5, A6QPT6, A7MBI1, A8MTY0, B2RXC5, B4DU55, E9PYI1, O14978, O60765, O75467, O75820, O95780, P0C7X2, P0DKX0, P0DPD5, P10072, P15622, P16374, P17014, P17023, P17032, P17098, P51523, P51786, P52738, P52742, Q02975, Q06732, Q08DG8, Q08ER8, Q0VCB0, Q14590, Q14929, Q29RZ4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1257 predictions. Top by Δscore:

Variant	Effect	Δscore
7:99473607:GGAAA:G	donor_gain	1.0000
7:99476401:A:AG	acceptor_gain	1.0000
7:99476402:G:GG	acceptor_gain	1.0000
7:99479771:G:GT	donor_gain	1.0000
7:99479772:A:T	donor_gain	1.0000
7:99494629:AACC:A	acceptor_loss	1.0000
7:99494630:ACCT:A	acceptor_loss	1.0000
7:99494632:C:A	acceptor_loss	1.0000
7:99494633:T:G	acceptor_loss	1.0000
7:99498714:A:AC	donor_gain	1.0000
7:99498715:C:CC	donor_gain	1.0000
7:99498715:CT:C	donor_gain	1.0000
7:99498715:CTCGG:C	donor_gain	1.0000
7:99498838:ATCCC:A	acceptor_gain	1.0000
7:99498839:TCCC:T	acceptor_gain	1.0000
7:99498840:CCC:C	acceptor_gain	1.0000
7:99498840:CCCC:C	acceptor_gain	1.0000
7:99498841:CC:C	acceptor_gain	1.0000
7:99498841:CCC:C	acceptor_gain	1.0000
7:99498841:CCCT:C	acceptor_loss	1.0000
7:99498842:CC:C	acceptor_gain	1.0000
7:99498842:CCTGG:C	acceptor_loss	1.0000
7:99498843:C:CC	acceptor_gain	1.0000
7:99498843:CTGGA:C	acceptor_loss	1.0000
7:99498844:T:C	acceptor_loss	1.0000
7:99499634:TCAC:T	donor_loss	1.0000
7:99499636:A:AC	donor_gain	1.0000
7:99499637:C:CC	donor_gain	1.0000
7:99499637:C:CG	donor_loss	1.0000
7:99473063:G:GT	donor_gain	0.9900

AlphaMissense

2860 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:99487090:T:C	F294L	0.997
7:99487092:T:A	F294L	0.997
7:99487092:T:G	F294L	0.997
7:99487174:T:C	F322L	0.997
7:99487176:T:A	F322L	0.997
7:99487176:T:G	F322L	0.997
7:99487342:T:C	F378L	0.996
7:99487344:T:A	F378L	0.996
7:99487344:T:G	F378L	0.996
7:99487115:G:C	R302P	0.995
7:99487258:T:C	F350L	0.994
7:99487260:T:A	F350L	0.994
7:99487260:T:G	F350L	0.994
7:99479746:G:C	R37P	0.993
7:99486922:T:C	F238L	0.993
7:99486924:C:A	F238L	0.993
7:99486924:C:G	F238L	0.993
7:99487006:T:C	F266L	0.993
7:99487008:T:A	F266L	0.993
7:99487008:T:G	F266L	0.993
7:99487119:T:A	H303Q	0.993
7:99487119:T:G	H303Q	0.993
7:99487109:T:C	L300P	0.992
7:99487426:T:C	F406L	0.992
7:99487428:C:A	F406L	0.992
7:99487428:C:G	F406L	0.992
7:99487277:T:C	L356P	0.991
7:99487367:G:C	R386P	0.991
7:99487371:T:A	H387Q	0.991
7:99487371:T:G	H387Q	0.991

dbSNP variants (sampled 300 via entrez): RS1000117569 (7:99474332 C>A,G,T), RS1000352984 (7:99483456 C>T), RS1000357490 (7:99484904 G>A), RS1000466105 (7:99477713 AG>A,AGG), RS1000541800 (7:99472230 T>A,G), RS1000711935 (7:99478322 G>A), RS1000764112 (7:99478561 C>T), RS1000995788 (7:99472464 G>A), RS1001067464 (7:99485052 A>G), RS1001618019 (7:99471728 T>C), RS1001670500 (7:99471963 CTTTT>C,CT,CTT,CTTT,CTTTTT,CTTTTTT), RS1001771130 (7:99479953 C>A,T), RS1002354713 (7:99486254 G>A,C), RS1002406002 (7:99482581 T>C), RS1002513013 (7:99474693 T>A)

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

6 associations (top):

Study	Trait	p-value
GCST002925_1	Sex hormone levels	2.000000e-14
GCST002925_10	Sex hormone levels	5.000000e-07
GCST002925_9	Sex hormone levels	3.000000e-13
GCST004730_2	Facial emotion recognition (sad faces)	3.000000e-06
GCST005144_1	Tacrolimus trough concentration in kidney transplant patients	2.000000e-17
GCST006249_21	Serum metabolite levels	4.000000e-11

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004730	hormone measurement
EFO:0007001	dehydroepiandrosterone sulphate measurement
EFO:0004908	testosterone measurement
EFO:0008329	facial emotion recognition measurement
EFO:0008458	tacrolimus measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects cotreatment, decreases expression	4
Cyclosporine	decreases expression	3
bisphenol A	decreases expression	2
trichostatin A	decreases expression, increases expression	1
beta-lapachone	decreases expression	1
manganese chloride	increases abundance, increases expression	1
beta-methylcholine	affects 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	decreases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Atrazine	decreases expression	1
Folic Acid	decreases expression	1
Manganese	increases abundance, increases expression	1
Niclosamide	decreases expression	1
Quercetin	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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