ZNF394

Summary

ZNF394 (zinc finger protein 394, HGNC:18832) is a protein-coding gene on chromosome 7q22.1, encoding Zinc finger protein 394 (Q53GI3). May be involved in transcriptional regulation.

The protein encoded by this gene is a zinc finger protein that inhibits the transcription of mitogen-activated protein kinase signaling pathways. The encoded protein may be involved in cardiac function.

Source: NCBI Gene 84124 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 116 total
• MANE Select transcript: NM_032164

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18832
Approved symbol	ZNF394
Name	zinc finger protein 394
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Aliases	ZKSCAN14, FLJ12298, ZSCAN46
Ensembl gene	ENSG00000160908
Ensembl biotype	protein_coding
OMIM	619300
Entrez	84124

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 7 protein_coding, 3 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000337673, ENST00000394177, ENST00000426306, ENST00000462024, ENST00000464401, ENST00000481881, ENST00000485576, ENST00000651061, ENST00000651364, ENST00000926066, ENST00000970609, ENST00000970610, ENST00000970611

RefSeq mRNA: 2 — MANE Select: NM_032164 NM_001345967, NM_032164

CCDS: CCDS5666, CCDS87524

Canonical transcript exons

ENST00000337673 — 3 exons

Exon	Start	End
ENSE00001797465	99493240	99494631
ENSE00003569812	99498716	99498842
ENSE00003660774	99499638	99500281

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 92.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.9570 / max 193.0262, expressed in 1775 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85108	11.9570	1775

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mononuclear cell	CL:0000842	92.44	gold quality
monocyte	CL:0000576	92.42	gold quality
blood	UBERON:0000178	92.36	gold quality
leukocyte	CL:0000738	92.22	gold quality
bone marrow	UBERON:0002371	91.93	gold quality
granulocyte	CL:0000094	91.57	gold quality
bone marrow cell	CL:0002092	91.51	gold quality
calcaneal tendon	UBERON:0003701	90.94	gold quality
diaphragm	UBERON:0001103	89.58	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.25	gold quality
sural nerve	UBERON:0015488	87.92	gold quality
tendon	UBERON:0000043	87.58	gold quality
mucosa of urinary bladder	UBERON:0001259	87.58	gold quality
palpebral conjunctiva	UBERON:0001812	86.93	gold quality
spleen	UBERON:0002106	86.31	gold quality
parotid gland	UBERON:0001831	85.84	gold quality
blood vessel layer	UBERON:0004797	85.13	gold quality
lower esophagus mucosa	UBERON:0035834	85.11	gold quality
skin of abdomen	UBERON:0001416	84.98	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.85	gold quality
left uterine tube	UBERON:0001303	84.76	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.74	gold quality
lymph node	UBERON:0000029	84.73	gold quality
tonsil	UBERON:0002372	84.71	gold quality
mucosa of stomach	UBERON:0001199	84.65	gold quality
left ovary	UBERON:0002119	84.41	gold quality
amniotic fluid	UBERON:0000173	84.40	gold quality
small intestine	UBERON:0002108	84.37	gold quality
popliteal artery	UBERON:0002250	84.24	gold quality
tibial artery	UBERON:0007610	84.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting ZNF394, 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-6778-3P	99.96	67.29	2693
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-27A-5P	97.01	65.63	528
HSA-MIR-4695-3P	96.71	67.21	836

Literature-anchored findings (GeneRIF, showing 1)

• Overexpression of ZNF394 in the cell inhibits the transcriptional activities of c-Jun and AP-1 reporters. (PMID:15249231)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zkscan14	ENSMUSG00000029627
rattus_norvegicus	Atp5mf	ENSRNOG00000027049

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZKSCAN3 (ENSG00000189298), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger protein 394 — Q53GI3 (reviewed: Q53GI3)

Alternative names: Zinc finger protein with KRAB and SCAN domains 14

All UniProt accessions (1): Q53GI3

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 (2)

UniProt ID	Names	Canonical?
Q53GI3-1	1	yes
Q53GI3-3	2

RefSeq proteins (2): NP_001332896, NP_115540* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily

Pfam: PF00096, PF01352, PF02023

UniProt features (28 total): zinc finger region 7, cross-link 6, region of interest 3, sequence conflict 3, domain 2, compositionally biased region 2, splice variant 2, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q53GI3-F1	62.01	0.06

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): 12, 40, 203, 228, 254, 282, 443

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 149 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, TSENG_IRS1_TARGETS_DN, GNF2_DDX5, GNF2_PTPRC, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, SCGGAAGY_ELK1_02, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MTOR_UP.N4.V1_DN, PDGF_UP.V1_UP, HOXA9_DN.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

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

GO Molecular Function (7): 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), sequence-specific double-stranded DNA binding (GO:1990837)

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

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

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
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

600 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF394	ARHGAP11B	Q3KRB8	461
ZNF394	CMC2	Q9NRP2	452
ZNF394	A0A087WTG0	A0A087WTG0	447
ZNF394	NBPF26	B4DH59	447
ZNF394	ARHGAP11A	Q6P4F7	445
ZNF394	DUSP22	Q9NRW4	437
ZNF394	USP19	O94966	418
ZNF394	TCAF1	Q9Y4C2	407
ZNF394	PTPN20	Q4JDL3	404
ZNF394	JHY	Q6NUN7	403
ZNF394	SCML1	Q9UN30	402
ZNF394	GABPA	Q06546	398
ZNF394	BEND2	Q8NDZ0	398
ZNF394	ANKRD65	E5RJM6	397
ZNF394	NEK4	P51957	371
ZNF394	C1orf53	Q5VUE5	371

IntAct

35 interactions, top by confidence:

A	B	Type	Score
ZNF394	SCAND1	psi-mi:“MI:0914”(association)	0.740
SCAND1	ZNF394	psi-mi:“MI:0915”(physical association)	0.740
ZNF394	CLK2	psi-mi:“MI:0915”(physical association)	0.560
CCNDBP1	ZNF394	psi-mi:“MI:0915”(physical association)	0.560
CLK2	ZNF394	psi-mi:“MI:0915”(physical association)	0.560
ZNF394	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.560
ZNF394	ZBTB47	psi-mi:“MI:0915”(physical association)	0.560
RNPS1	ZNF394	psi-mi:“MI:0915”(physical association)	0.560
	ZNF394	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN32	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZNF397	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZSCAN20	ZNF197	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
ZBTB47	ZNF394	psi-mi:“MI:0915”(physical association)	0.000
SCAND1	ZNF394	psi-mi:“MI:0915”(physical association)	0.000
ZNF394	SCAND1	psi-mi:“MI:0915”(physical association)	0.000
RNPS1	ZNF394	psi-mi:“MI:0915”(physical association)	0.000
	ZNF394	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (21): ZNF394 (Two-hybrid), ZNF394 (Two-hybrid), ZNF394 (Affinity Capture-MS), ZNF394 (Affinity Capture-MS), ZNF394 (Affinity Capture-MS), ZNF394 (Affinity Capture-MS), ZNF394 (Affinity Capture-MS), CTNNBL1 (Affinity Capture-MS), ZNF394 (Affinity Capture-MS), ZNF394 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), ZNF394 (Affinity Capture-MS), ZNF394 (Two-hybrid), ZNF394 (Two-hybrid), SCAND1 (Two-hybrid)

ESM2 similar proteins: A1YEP8, A1YEV9, A1YFW2, A1YG26, A1YG48, A1YG60, A2T6E3, A2T6V8, A2T712, A2T736, A2T7D2, A2T7F4, A2T7L7, A2T812, A6QNZ0, O14709, O15535, O43296, O43309, P10073, P17023, P17097, P49910, Q07231, Q12901, Q15776, Q16670, Q1LZ87, Q3MJ62, Q53GI3, Q571J5, Q5JNZ3, Q5RAE6, Q5RBX0, Q5RCD9, Q5RJ54, Q7Z7L9, Q86W11, Q8IZ26, Q8NF99

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	111
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1089 predictions. Top by Δscore:

Variant	Effect	Δscore
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
7:99504731:GAG:G	donor_gain	1.0000
7:99476398:TCCA:T	acceptor_loss	0.9900

AlphaMissense

3724 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:99493613:A:C	F534L	0.998
7:99493613:A:T	F534L	0.998
7:99493615:A:G	F534L	0.998
7:99493697:G:C	F506L	0.998
7:99493697:G:T	F506L	0.998
7:99493699:A:G	F506L	0.998
7:99493946:G:C	F423L	0.998
7:99493946:G:T	F423L	0.998
7:99493948:A:G	F423L	0.998
7:99494030:G:C	F395L	0.998
7:99494030:G:T	F395L	0.998
7:99494032:A:G	F395L	0.998
7:99493781:G:C	F478L	0.997
7:99493781:G:T	F478L	0.997
7:99493783:A:G	F478L	0.997
7:99493670:G:C	H515Q	0.996
7:99493670:G:T	H515Q	0.996
7:99493764:A:G	L484P	0.996
7:99493929:A:G	L429P	0.996
7:99494114:G:C	F367L	0.996
7:99494114:G:T	F367L	0.996
7:99494116:A:G	F367L	0.996
7:99493658:G:C	H519Q	0.995
7:99493658:G:T	H519Q	0.995
7:99493668:T:G	Q516P	0.995
7:99493672:G:C	H515D	0.995
7:99493680:A:G	L512P	0.995
7:99493698:A:G	F506S	0.995
7:99494003:G:C	H404Q	0.995
7:99494003:G:T	H404Q	0.995

dbSNP variants (sampled 300 via entrez): RS1000067207 (7:99496379 C>T), RS1000078532 (7:99489575 T>C), RS1000243877 (7:99502019 T>C,G), RS1000298523 (7:99495733 G>A), RS1000415466 (7:99496072 T>C), RS1000799410 (7:99491247 A>G), RS1000911617 (7:99489931 G>T), RS1001030208 (7:99497684 T>C), RS1001083502 (7:99490994 T>C), RS1001376030 (7:99494606 T>A,C), RS1001428344 (7:99494785 A>G), RS1001497581 (7:99495887 G>T), RS1001801298 (7:99492922 C>T), RS1001990582 (7:99499316 C>T), RS1002057189 (7:99500314 G>A,C)

Disease associations

OMIM: gene MIM:619300 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004730_2	Facial emotion recognition (sad faces)	3.000000e-06
GCST008667_7	Smoking status (heavy vs never)	8.000000e-08
GCST90000047_140	Age at first sexual intercourse	2.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008329	facial emotion recognition measurement
EFO:0006527	smoking status measurement
EFO:0009749	age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Doxorubicin	decreases expression, decreases response to substance	2
Tobacco Smoke Pollution	increases expression	2
Cadmium Chloride	increases expression	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
geraniol	increases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	increases expression	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
abrine	increases expression	1
elesclomol	increases expression, decreases reaction	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1
PCI 5002	affects cotreatment, 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
Temozolomide	decreases expression	1
Acetylcysteine	decreases reaction, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XW40	HEK293 eGFP-ZNF394	Transformed cell line	Female

Clinical trials (associated diseases)

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