ZNF57

Summary

ZNF57 (zinc finger protein 57, HGNC:13125) is a protein-coding gene on chromosome 19p13.3, encoding Zinc finger protein 57 (Q68EA5). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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 126295 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 106 total
• MANE Select transcript: NM_173480

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13125
Approved symbol	ZNF57
Name	zinc finger protein 57
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000171970
Ensembl biotype	protein_coding
Entrez	126295

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000306908, ENST00000522294, ENST00000523428, ENST00000590305, ENST00000881773, ENST00000881774, ENST00000939111

RefSeq mRNA: 2 — MANE Select: NM_173480 NM_001319083, NM_173480

CCDS: CCDS12098, CCDS82274

Canonical transcript exons

ENST00000306908 — 4 exons

Exon	Start	End
ENSE00001148948	2916078	2916249
ENSE00002132197	2916924	2918473
ENSE00003513010	2915522	2915648
ENSE00003843091	2900928	2901048

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 90.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9154 / max 75.2110, expressed in 1454 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173132	3.9154	1454

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	90.51	gold quality
upper leg skin	UBERON:0004262	87.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.00	gold quality
amniotic fluid	UBERON:0000173	86.92	gold quality
endothelial cell	CL:0000115	85.62	gold quality
colonic mucosa	UBERON:0000317	84.21	gold quality
mucosa of sigmoid colon	UBERON:0004993	83.58	gold quality
skin of abdomen	UBERON:0001416	83.02	gold quality
gingival epithelium	UBERON:0001949	82.95	gold quality
skin of leg	UBERON:0001511	82.92	gold quality
gingiva	UBERON:0001828	82.82	gold quality
zone of skin	UBERON:0000014	82.41	gold quality
mucosa of transverse colon	UBERON:0004991	81.71	gold quality
oral cavity	UBERON:0000167	80.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.23	gold quality
jejunal mucosa	UBERON:0000399	80.11	gold quality
oocyte	CL:0000023	80.02	gold quality
rectum	UBERON:0001052	79.39	gold quality
secondary oocyte	CL:0000655	78.98	gold quality
body of stomach	UBERON:0001161	78.88	gold quality
esophagus squamous epithelium	UBERON:0006920	78.32	gold quality
mammalian vulva	UBERON:0000997	78.26	gold quality
esophagus mucosa	UBERON:0002469	78.08	gold quality
duodenum	UBERON:0002114	77.19	gold quality
testis	UBERON:0000473	77.18	gold quality
left testis	UBERON:0004533	77.09	gold quality
penis	UBERON:0000989	77.03	gold quality
skin of hip	UBERON:0001554	76.72	gold quality
stomach	UBERON:0000945	76.64	gold quality
right testis	UBERON:0004534	76.64	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-CURD-7	no	418.25
E-ENAD-21	no	352.23
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2545.1	ZNF57	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605530

miRNA regulators (miRDB)

13 targeting ZNF57, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-4506	99.34	67.47	526
HSA-MIR-655-5P	98.74	65.93	888
HSA-MIR-1-5P	98.70	68.66	1017

Literature-anchored findings (GeneRIF, showing 3)

• ZNF424 protein may act as a transcriptional repressor that suppresses NFAT and p21 pathway to mediate cellular functions. (PMID:20356463)
• These are the first data to associate ZNF424 with tumorigenesis and demonstrate an inhibitory role in lung cancer, indicating the potential of ZNF424 expression as a diagnostic marker of lung tumorigenesis. (PMID:29974829)
• TMIGD2 is an orchestrator and therapeutic target on human acute myeloid leukemia stem cells. (PMID:38167704)

Cross-species orthologs

0 orthologs

Paralogs (15): ZNF14 (ENSG00000105708), ZNF791 (ENSG00000173875), ZNF443 (ENSG00000180855), ZNF101 (ENSG00000181896), ZNF563 (ENSG00000188868), ZNF799 (ENSG00000196466), ZNF700 (ENSG00000196757), ZNF441 (ENSG00000197044), ZNF433 (ENSG00000197647), ZNF44 (ENSG00000197857), ZNF823 (ENSG00000197933), ZNF442 (ENSG00000198342), ZNF844 (ENSG00000223547), ZNF709 (ENSG00000242852), ZNF878 (ENSG00000257446)

Protein

Protein identifiers

Zinc finger protein 57 — Q68EA5 (reviewed: Q68EA5)

Alternative names: Zinc finger protein 424

All UniProt accessions (5): Q68EA5, A5HJR3, E5RHE3, G3V131, K7ERB8

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 (2): NP_001306012, NP_775751* (*=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

UniProt features (19 total): zinc finger region 13, sequence variant 3, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q68EA5-F1	69.46	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 38 (showing top): GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, BARX1_TARGET_GENES, CEBPZ_TARGET_GENES, F10_TARGET_GENES, SOX3_TARGET_GENES, ZNF22_TARGET_GENES, ZNF528_TARGET_GENES, ZNF585B_TARGET_GENES, ZNF618_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 transcription regulatory region sequence-specific DNA binding (GO:0000977), 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
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
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	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

446 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF57	TRIM28	Q13263	791
ZNF57	DNMT1	P26358	517
ZNF57	TCF19	Q9Y242	453
ZNF57	SNRPN	P14648	437
ZNF57	CCHCR1	Q8TD31	437
ZNF57	RNF39	Q9H2S5	428
ZNF57	CDSN	Q15517	408
ZNF57	OR5D14	Q8NGL3	396
ZNF57	KLF17	Q5JT82	375
ZNF57	ZFP57	Q9NU63	365
ZNF57	MOG	Q16653	364
ZNF57	ID1	P41134	345
ZNF57	POU5F1	P31359	311
ZNF57	GIPC3	Q8TF64	310
ZNF57	CBX5	P45973	306

IntAct

88 interactions, top by confidence:

A	B	Type	Score
NDEL1	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	NDEL1	psi-mi:“MI:0915”(physical association)	0.560
EFEMP2	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	ZNF572	psi-mi:“MI:0915”(physical association)	0.560
ZNF250	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	CABP2	psi-mi:“MI:0915”(physical association)	0.560
U2AF2	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	MAGOHB	psi-mi:“MI:0915”(physical association)	0.560
DMWD	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
ZNF57		psi-mi:“MI:0915”(physical association)	0.560
ZNF57	GLE1	psi-mi:“MI:0915”(physical association)	0.560
GRN	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	NEFL	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	PMP22	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	PRPS1	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	WFS1	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	KIF1B	psi-mi:“MI:0915”(physical association)	0.560
RNF11	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
ZNF57	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
SNCA	ZNF57	psi-mi:“MI:0915”(physical association)	0.560
HTT	ZNF57	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (18): ZNF57 (Affinity Capture-RNA), ZNF57 (Two-hybrid), ZNF57 (Two-hybrid), ZNF57 (Two-hybrid), ZNF57 (Two-hybrid), EFEMP2 (Two-hybrid), ZNF572 (Two-hybrid), ZNF250 (Two-hybrid), ZNF57 (Proximity Label-MS), ZNF57 (Two-hybrid), ZNF57 (Two-hybrid), ZNF57 (Affinity Capture-MS), ZNF57 (Affinity Capture-MS), ZNF57 (Affinity Capture-MS), ZNF57 (Affinity Capture-MS)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 30 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
methylation	5	29.4×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	94
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

513 predictions. Top by Δscore:

Variant	Effect	Δscore
19:2901045:CATGG:C	donor_loss	1.0000
19:2901049:GTGA:G	donor_loss	1.0000
19:2915644:AGTAG:A	donor_loss	1.0000
19:2915645:GTAG:G	donor_gain	1.0000
19:2915649:G:GG	donor_gain	1.0000
19:2915654:G:GT	donor_gain	1.0000
19:2916076:A:AG	acceptor_gain	1.0000
19:2916076:A:G	acceptor_loss	1.0000
19:2916076:AGAT:A	acceptor_gain	1.0000
19:2916077:G:GT	acceptor_gain	1.0000
19:2916077:GA:G	acceptor_gain	1.0000
19:2916077:GAT:G	acceptor_gain	1.0000
19:2916077:GATG:G	acceptor_gain	1.0000
19:2916077:GATGA:G	acceptor_gain	1.0000
19:2916246:TGAG:T	donor_gain	1.0000
19:2916247:GAG:G	donor_gain	1.0000
19:2916247:GAGG:G	donor_gain	1.0000
19:2916248:AG:A	donor_gain	1.0000
19:2916248:AGG:A	donor_loss	1.0000
19:2916249:GG:G	donor_gain	1.0000
19:2916250:G:C	donor_loss	1.0000
19:2916250:G:GG	donor_gain	1.0000
19:2901049:G:GG	donor_gain	0.9900
19:2901050:T:A	donor_loss	0.9900
19:2901051:GAGT:G	donor_loss	0.9900
19:2901147:G:T	donor_gain	0.9900
19:2914702:G:GG	donor_gain	0.9900
19:2914808:G:GG	donor_gain	0.9900
19:2915519:TAG:T	acceptor_loss	0.9900
19:2915520:A:AG	acceptor_gain	0.9900

AlphaMissense

3704 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:2917738:T:C	F373L	0.997
19:2917740:C:A	F373L	0.997
19:2917740:C:G	F373L	0.997
19:2917906:T:C	F429L	0.996
19:2917908:C:A	F429L	0.996
19:2917908:C:G	F429L	0.996
19:2917486:T:C	F289L	0.995
19:2917488:C:A	F289L	0.995
19:2917488:C:G	F289L	0.995
19:2918074:T:C	F485L	0.995
19:2918076:C:A	F485L	0.995
19:2918076:C:G	F485L	0.995
19:2917402:T:C	F261L	0.994
19:2917404:C:A	F261L	0.994
19:2917404:C:G	F261L	0.994
19:2917654:T:C	F345L	0.994
19:2917656:T:A	F345L	0.994
19:2917656:T:G	F345L	0.994
19:2917935:T:A	H438Q	0.994
19:2917935:T:G	H438Q	0.994
19:2917570:T:C	F317L	0.993
19:2917572:C:A	F317L	0.993
19:2917572:C:G	F317L	0.993
19:2917683:T:A	H354Q	0.992
19:2917683:T:G	H354Q	0.992
19:2917822:T:C	F401L	0.992
19:2917824:T:A	F401L	0.992
19:2917824:T:G	F401L	0.992
19:2917990:T:C	F457L	0.992
19:2917992:T:A	F457L	0.992

dbSNP variants (sampled 300 via entrez): RS1000045535 (19:2901389 G>A,C), RS1000073561 (19:2913829 C>T), RS1000423627 (19:2914074 A>C), RS1000482647 (19:2912401 G>A,C), RS1000495396 (19:2908695 G>A,T), RS1000679513 (19:2899067 G>T), RS1000839091 (19:2903015 G>A), RS1000970805 (19:2907454 T>C,G), RS1001070042 (19:2904373 G>A,T), RS1001086658 (19:2907235 G>T), RS1001145864 (19:2906635 G>A), RS1001166816 (19:2906536 C>A), RS1001370810 (19:2918615 ATT>A,AT,ATTT,ATTTT), RS1001388136 (19:2901770 G>A), RS1001482670 (19:2915181 A>C,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
GCST003518_101	Daytime sleep phenotypes	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007828	daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
Tobacco Smoke Pollution	increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
butyraldehyde	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
epigallocatechin gallate	affects cotreatment, increases expression	1
microcystin RR	increases expression	1
di-n-butylphosphoric acid	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
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
licochalcone B	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Arsenic	increases expression, affects cotreatment, increases abundance	1
Dexamethasone	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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