ZNF7

Summary

ZNF7 (zinc finger protein 7, HGNC:13139) is a protein-coding gene on chromosome 8q24.3, encoding Zinc finger protein 7 (P17097). 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 located in membrane. Predicted to be active in nucleus.

Source: NCBI Gene 7553 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_003416

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13139
Approved symbol	ZNF7
Name	zinc finger protein 7
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	KOX4, HF.16
Ensembl gene	ENSG00000147789
Ensembl biotype	protein_coding
OMIM	194531
Entrez	7553

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 24 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000325217, ENST00000446747, ENST00000525266, ENST00000527218, ENST00000528017, ENST00000528130, ENST00000528372, ENST00000529767, ENST00000529819, ENST00000530082, ENST00000530682, ENST00000530776, ENST00000532051, ENST00000532382, ENST00000532393, ENST00000532777, ENST00000533314, ENST00000544249, ENST00000908822, ENST00000908823, ENST00000908824, ENST00000908825, ENST00000908826, ENST00000908827, ENST00000908828, ENST00000933362, ENST00000933363, ENST00000933364, ENST00000933365, ENST00000955409, ENST00000955410, ENST00000955411

RefSeq mRNA: 10 — MANE Select: NM_003416 NM_001282795, NM_001282796, NM_001282797, NM_001330623, NM_001349805, NM_001349806, NM_001349807, NM_001349808, NM_001349809, NM_003416

CCDS: CCDS6435, CCDS64996, CCDS64998, CCDS64999, CCDS83336, CCDS94368

Canonical transcript exons

ENST00000532777 — 5 exons

Exon	Start	End
ENSE00001131910	144829478	144829604
ENSE00002187571	144841355	144843772
ENSE00002197456	144827560	144827609
ENSE00003489033	144837391	144837507
ENSE00003497741	144829043	144829090

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 90.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.4677 / max 89.2489, expressed in 1797 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91537	11.4478	1797
91538	0.0199	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	90.38	gold quality
cerebellar hemisphere	UBERON:0002245	90.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.34	gold quality
cerebellar cortex	UBERON:0002129	90.18	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.25	gold quality
gastrocnemius	UBERON:0001388	89.20	gold quality
granulocyte	CL:0000094	88.98	gold quality
apex of heart	UBERON:0002098	88.89	gold quality
muscle of leg	UBERON:0001383	88.86	gold quality
right lobe of thyroid gland	UBERON:0001119	88.00	gold quality
left uterine tube	UBERON:0001303	87.67	gold quality
cerebellum	UBERON:0002037	87.63	gold quality
skin of leg	UBERON:0001511	87.59	gold quality
tibial nerve	UBERON:0001323	87.50	gold quality
skin of abdomen	UBERON:0001416	87.44	gold quality
left lobe of thyroid gland	UBERON:0001120	87.34	gold quality
endocervix	UBERON:0000458	87.31	gold quality
muscle layer of sigmoid colon	UBERON:0035805	87.30	gold quality
body of uterus	UBERON:0009853	87.21	gold quality
left ovary	UBERON:0002119	87.17	gold quality
body of pancreas	UBERON:0001150	87.15	gold quality
ectocervix	UBERON:0012249	86.98	gold quality
mucosa of stomach	UBERON:0001199	86.95	gold quality
right ovary	UBERON:0002118	86.94	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.89	gold quality
lower esophagus	UBERON:0013473	86.88	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.87	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	86.82	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.61	gold quality
tibial artery	UBERON:0007610	86.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.45

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Single-cell imaging revealed that RIPK3-dependent death caused inflammasome-dependent IL-1beta release from lipopolysaccharide-stimulated A20-deficient macrophages. Importantly, mutation of the A20 ZnF7 ubiquitin binding domain caused arthritis in mice, arguing that ZnF7-dependent inhibition of necroptosis is critical for A20 anti-inflammatory function in vivo. (PMID:31086261)
• RNA sequencing and Immunohistochemistry Reveal ZFN7 as a Stronger Marker of Survival than Molecular Subtypes in G-CIMP-negative Glioblastoma. (PMID:33106291)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp7	ENSMUSG00000033669
rattus_norvegicus	Zfp7	ENSRNOG00000050695

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), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 7 — P17097 (reviewed: P17097)

Alternative names: Zinc finger protein HF.16, Zinc finger protein KOX4

All UniProt accessions (8): P17097, E9PIH3, E9PJX9, E9PJZ3, E9PM16, E9PPK0, E9PQI2, F5H290

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitously present in many human cell lines of different embryological derivation.

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

Isoforms (3)

UniProt ID	Names	Canonical?
P17097-1	1	yes
P17097-2	2
P17097-3	3

RefSeq proteins (10): NP_001269724, NP_001269725, NP_001269726, NP_001317552, NP_001336734, NP_001336735, NP_001336736, NP_001336737, NP_001336738, NP_003407* (*=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

Pfam: PF00096, PF01352

UniProt features (30 total): zinc finger region 15, cross-link 5, splice variant 3, sequence variant 3, modified residue 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17097-F1	68.17	0.14

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 (7): 126, 138, 81, 101, 279, 292, 393

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, ONKEN_UVEAL_MELANOMA_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, BROWNE_HCMV_INFECTION_14HR_DN, MARTIN_VIRAL_GPCR_SIGNALING_DN, ACEVEDO_LIVER_CANCER_UP, DANG_BOUND_BY_MYC, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN, KANNAN_TP53_TARGETS_UP, BENPORATH_MYC_MAX_TARGETS, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, STEIN_ESRRA_TARGETS_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, chr8q24

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

GO Molecular Function (5): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA binding (GO:0003677), zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), membrane (GO:0016020)

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
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

27 interactions, top by confidence:

A	B	Type	Score
MAPK6	HERC2	psi-mi:“MI:0914”(association)	0.840
ZNF71	NVL	psi-mi:“MI:0914”(association)	0.530
ZNF7	IPO8	psi-mi:“MI:0914”(association)	0.530
NIFK	RSL1D1	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF16	ZNF7	psi-mi:“MI:0915”(physical association)	0.370
IPO8	BIN1	psi-mi:“MI:0914”(association)	0.350
Kif19		psi-mi:“MI:0914”(association)	0.350
DGCR8	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
NIFK	RRP8	psi-mi:“MI:0914”(association)	0.350
ATG16L1		psi-mi:“MI:0914”(association)	0.350
SCRIB	C1orf226	psi-mi:“MI:0914”(association)	0.350
NOP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
CBX6	ZNF316	psi-mi:“MI:0914”(association)	0.350
RPS6	CCDC85C	psi-mi:“MI:0914”(association)	0.350
ANOS1	ZNF724	psi-mi:“MI:0914”(association)	0.350
REXO4	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
NEIL1	U2SURP	psi-mi:“MI:0914”(association)	0.350
ZNF7	SOX5	psi-mi:“MI:0914”(association)	0.350
RBM11	ZNF7	psi-mi:“MI:0915”(physical association)	0.000
ZNF7	TADA3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (31): ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), TADA3 (Two-hybrid), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), SOX13 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS), ZNF7 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

Diamond homologs: A1L1L7, A3KN32, A3KN36, A6NFI3, A6NM28, A6NN14, A6QLU5, A7MBI1, A8K8V0, A8MTY0, A8MWA4, B4DU55, C9JBD0, G3X9G7, O60765, O75290, O94892, O95780, P0C7X2, P10072, P15622, P16373, P16374, P17023, P17032, P17097, P17098, P21506, P52742, P59923, Q06730, Q08DG8, Q16587, Q29RZ4, Q2TL60, Q3V080, Q49AA0, Q4R6C2, Q4V8A8, Q5FWF6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 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.

GO biological processes:

GO term	Partners	Fold	FDR
rRNA processing	5	23.6×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1739 predictions. Top by Δscore:

Variant	Effect	Δscore
8:144827879:GGGCC:G	donor_gain	1.0000
8:144837383:A:AG	acceptor_gain	1.0000
8:144837384:C:G	acceptor_gain	1.0000
8:144827730:A:T	donor_gain	0.9900
8:144827880:GGCC:G	donor_gain	0.9900
8:144827881:GCC:G	donor_gain	0.9900
8:144827887:G:GG	donor_gain	0.9900
8:144827921:GCC:G	donor_gain	0.9900
8:144829565:G:T	donor_gain	0.9900
8:144837380:C:A	acceptor_gain	0.9900
8:144837385:A:AG	acceptor_gain	0.9900
8:144837386:C:G	acceptor_gain	0.9900
8:144837389:A:AG	acceptor_gain	0.9900
8:144837389:AGCAG:A	acceptor_gain	0.9900
8:144837390:G:GG	acceptor_gain	0.9900
8:144837390:GCA:G	acceptor_gain	0.9900
8:144837390:GCAGG:G	acceptor_gain	0.9900
8:144841349:TTTCA:T	acceptor_loss	0.9900
8:144841350:TTCAG:T	acceptor_loss	0.9900
8:144841352:CA:C	acceptor_loss	0.9900
8:144841353:A:AC	acceptor_loss	0.9900
8:144841353:A:AG	acceptor_gain	0.9900
8:144841354:G:GG	acceptor_gain	0.9900
8:144841354:G:GT	acceptor_loss	0.9900
8:144837387:A:AG	acceptor_gain	0.9800
8:144837387:ACAGC:A	acceptor_loss	0.9800
8:144837389:A:AC	acceptor_loss	0.9800
8:144837505:CAG:C	donor_loss	0.9800
8:144837507:GG:G	donor_loss	0.9800
8:144837508:G:GA	donor_loss	0.9800

AlphaMissense

1582 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:144829528:G:C	W18C	0.995
8:144829528:G:T	W18C	0.995
8:144829526:T:A	W18R	0.993
8:144829526:T:C	W18R	0.993
8:144829559:T:G	Y29D	0.990
8:144829512:T:C	F13S	0.986
8:144829490:T:C	F6L	0.985
8:144829492:T:A	F6L	0.985
8:144829492:T:G	F6L	0.985
8:144829536:T:C	L21P	0.985
8:144829527:G:C	W18S	0.980
8:144829559:T:A	Y29N	0.978
8:144829572:T:C	M33T	0.976
8:144829491:T:G	F6C	0.974
8:144829575:T:C	L34P	0.971
8:144829572:T:A	M33K	0.970
8:144829549:G:C	Q25H	0.969
8:144829549:G:T	Q25H	0.969
8:144829560:A:C	Y29S	0.969
8:144837430:T:C	L57P	0.969
8:144829552:G:C	R26S	0.967
8:144829552:G:T	R26S	0.967
8:144829572:T:G	M33R	0.966
8:144829511:T:C	F13L	0.964
8:144829513:C:A	F13L	0.964
8:144829513:C:G	F13L	0.964
8:144829557:T:C	L28P	0.961
8:144829559:T:C	Y29H	0.960
8:144829491:T:C	F6S	0.958
8:144829502:G:C	A10P	0.958

dbSNP variants (sampled 300 via entrez): RS1000025187 (8:144839454 G>A), RS1000078481 (8:144839663 G>A), RS1000119752 (8:144838619 G>C), RS1000231786 (8:144834837 T>C,G), RS1000338509 (8:144844275 C>A,T), RS1000357134 (8:144828759 C>T), RS1000367074 (8:144828545 A>G), RS1000527140 (8:144827426 T>C,G), RS1000601947 (8:144835043 A>C,G), RS1000767357 (8:144847567 T>C), RS1000784246 (8:144833780 TTTAA>T), RS1000798496 (8:144847244 T>C), RS1001010064 (8:144838464 C>G,T), RS1001017319 (8:144841909 C>T), RS1001338858 (8:144846692 GGGA>G)

Disease associations

OMIM: gene MIM:194531 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST007005_3	Logical memory (immediate recall) in normal cognition	5.000000e-07
GCST007005_4	Logical memory (immediate recall) in normal cognition	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	2
Formaldehyde	decreases expression, increases expression	2
Valproic Acid	affects expression, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
pirinixic acid	increases activity, affects binding, decreases expression	1
beta-lapachone	increases expression	1
cobaltous chloride	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
tebuconazole	decreases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Ethyl Methanesulfonate	increases expression	1
Hydrogen Peroxide	affects expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Potassium Chloride	decreases expression, decreases response to substance	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases response to substance, decreases expression	1
Thiram	decreases expression	1
Cyclosporine	increases expression	1
Magnetite Nanoparticles	increases expression	1

Clinical trials (associated diseases)

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