ZNF383

Summary

ZNF383 (zinc finger protein 383, HGNC:18609) is a protein-coding gene on chromosome 19q13.13, encoding Zinc finger protein 383 (Q8NA42). May function as a transcriptional repressor, suppressing transcriptional activities mediated by MAPK signaling pathways.

The protein encoded by this gene is a KRAB-related zinc finger protein that inhibits the transcription of some MAPK signaling pathway genes. The repressor activity resides in the KRAB domain of the encoded protein.

Source: NCBI Gene 163087 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_001387601

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18609
Approved symbol	ZNF383
Name	zinc finger protein 383
Location	19q13.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35863, Zfp383
Ensembl gene	ENSG00000188283
Ensembl biotype	protein_coding
OMIM	619499
Entrez	163087

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 16 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000352998, ENST00000585441, ENST00000586068, ENST00000586658, ENST00000588250, ENST00000588371, ENST00000589413, ENST00000590503, ENST00000684119, ENST00000882182, ENST00000882183, ENST00000938216, ENST00000938217, ENST00000938218, ENST00000938219, ENST00000938220, ENST00000938221, ENST00000952120, ENST00000952121, ENST00000952122

RefSeq mRNA: 14 — MANE Select: NM_001387601 NM_001345947, NM_001345948, NM_001345949, NM_001387593, NM_001387594, NM_001387595, NM_001387596, NM_001387597, NM_001387598, NM_001387599, NM_001387600, NM_001387601, NM_001387602, NM_152604

CCDS: CCDS12501

Canonical transcript exons

ENST00000684119 — 6 exons

Exon	Start	End
ENSE00002435646	37235549	37235675
ENSE00002820334	37224818	37224939
ENSE00003500339	37230409	37230462
ENSE00003690165	37235979	37236074
ENSE00003917444	37218214	37218274
ENSE00003917887	37242469	37248740

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 82.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.7395 / max 71.7681, expressed in 1453 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175542	3.1858	1335
175541	0.5536	320

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	82.05	gold quality
calcaneal tendon	UBERON:0003701	81.76	gold quality
colonic epithelium	UBERON:0000397	81.74	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.08	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.00	gold quality
bone marrow cell	CL:0002092	79.29	gold quality
muscle of leg	UBERON:0001383	78.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.63	gold quality
gastrocnemius	UBERON:0001388	78.49	gold quality
smooth muscle tissue	UBERON:0001135	77.38	gold quality
cortical plate	UBERON:0005343	77.19	gold quality
ganglionic eminence	UBERON:0004023	76.84	gold quality
leukocyte	CL:0000738	76.56	gold quality
stromal cell of endometrium	CL:0002255	76.26	gold quality
ventricular zone	UBERON:0003053	76.15	gold quality
monocyte	CL:0000576	76.03	gold quality
mucosa of stomach	UBERON:0001199	75.94	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.69	gold quality
islet of Langerhans	UBERON:0000006	75.63	gold quality
rectum	UBERON:0001052	75.33	gold quality
popliteal artery	UBERON:0002250	75.03	gold quality
tibial artery	UBERON:0007610	75.03	gold quality
skin of leg	UBERON:0001511	74.69	gold quality
adrenal tissue	UBERON:0018303	74.69	gold quality
left ovary	UBERON:0002119	74.61	gold quality
skin of abdomen	UBERON:0001416	74.41	gold quality
muscle layer of sigmoid colon	UBERON:0035805	74.30	gold quality
descending thoracic aorta	UBERON:0002345	74.11	gold quality
aorta	UBERON:0000947	74.08	gold quality
endocervix	UBERON:0000458	74.00	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-7303	no	23.15
E-ANND-3	no	5.92

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
JUN	Repression

JASPAR motifs

Motif	Name	Family
MA1979.1	ZNF416	More than 3 adjacent zinc fingers
MA1979.2	ZNF416	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:25690854

Literature-anchored findings (GeneRIF, showing 2)

• Overexpression of ZNF383 in cells inhibits the transcriptional activities of AP-1 and SRE, suggesting that ZNF383 may act as a negative regulator in MAPK-mediated signaling pathways. (PMID:15964543)
• 19q13.12 KRAB zinc-finger protein ZNF383 represses p53 signaling pathway by interacting with p53. (PMID:35835334)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp383	ENSMUSG00000099689
rattus_norvegicus	Zfp420	ENSRNOG00000020774

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 383 — Q8NA42 (reviewed: Q8NA42)

All UniProt accessions (3): Q8NA42, K7EJN0, K7ELW4

UniProt curated annotations — full annotation on UniProt →

Function. May function as a transcriptional repressor, suppressing transcriptional activities mediated by MAPK signaling pathways.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Expressed in heart, placenta, liver, pancreas and with a higher level in skeletal muscle.

Domain organisation. The KRAB domain is responsible for the transcriptional repressor activity.

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

RefSeq proteins (14): NP_001332876, NP_001332877, NP_001332878, NP_001374522, NP_001374523, NP_001374524, NP_001374525, NP_001374526, NP_001374527, NP_001374528, NP_001374529, NP_001374530, NP_001374531, NP_689817 (=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, PF13465

UniProt features (16 total): zinc finger region 11, sequence conflict 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NA42-F1	73.36	0.30

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 62 (showing top): IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_MEMBRANE, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOCC_ORGANELLE_ENVELOPE, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, IRF5_TARGET_GENES, NCOA2_TARGET_GENES, NFE2L1_TARGET_GENES, RYBP_TARGET_GENES, ZBTB12_TARGET_GENES, ZBTB18_TARGET_GENES, ZNF33A_TARGET_GENES, ZNF391_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 cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear membrane (GO:0031965), 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
regulation of DNA-templated transcription	2
cellular anatomical structure	2
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
nuclear lumen	1
intracellular anatomical structure	1
nucleus	1
nuclear envelope	1
organelle membrane	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

882 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF383	CEP170	Q5SW79	446
ZNF383	USP6	P35125	418
ZNF383	TMBIM6	P55061	391
ZNF383	YPEL3	P61236	387
ZNF383	ACOT13	Q9NPJ3	383
ZNF383	PCMT1	P22061	379
ZNF383	UGGT2	Q9NYU1	377
ZNF383	PARS2	Q7L3T8	371
ZNF383	EMG1	Q92979	371
ZNF383	TDP2	O95551	366
ZNF383	BAG4	O95429	364
ZNF383	RPL6	Q02878	363
ZNF383	ZNF326	Q5BKZ1	362
ZNF383	HSPA8	P11142	354
ZNF383	NEK7	Q8TDX7	353
ZNF383	PHB2	Q99623	353

IntAct

21 interactions, top by confidence:

A	B	Type	Score
ZNF572	ZNF383	psi-mi:“MI:0915”(physical association)	0.560
TLE5	ZNF383	psi-mi:“MI:0915”(physical association)	0.560
ZNF383	ZIM2	psi-mi:“MI:0915”(physical association)	0.560
ZNF383	RCOR3	psi-mi:“MI:0915”(physical association)	0.560
NOL4	ZNF383	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
EWSR1	ZNF383	psi-mi:“MI:0915”(physical association)	0.370
ZNF383	ZNF195	psi-mi:“MI:0914”(association)	0.350
SLC7A9	CDC7	psi-mi:“MI:0914”(association)	0.350
NRAS	IGKV2D-24	psi-mi:“MI:0914”(association)	0.350
ZNF572	ZNF383	psi-mi:“MI:0915”(physical association)	0.000
TLE5	ZNF383	psi-mi:“MI:0915”(physical association)	0.000
ZIM2	ZNF383	psi-mi:“MI:0915”(physical association)	0.000
RCOR3	ZNF383	psi-mi:“MI:0915”(physical association)	0.000
NOL4	ZNF383	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (21): ZNF383 (Affinity Capture-RNA), ZNF383 (Two-hybrid), ZNF383 (Two-hybrid), ZNF383 (Two-hybrid), ZNF383 (Two-hybrid), ZIM2 (Two-hybrid), LRP4 (Affinity Capture-MS), ZNF195 (Affinity Capture-MS), ZNF644 (Affinity Capture-MS), LRP5 (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), IKBIP (Affinity Capture-MS), LRP6 (Affinity Capture-MS), TRIM24 (Affinity Capture-MS), UBR1 (Affinity Capture-MS)

ESM2 similar proteins: A2RRD8, A6NHJ4, B4DX44, O75346, P10077, P10755, P15621, P16372, P16373, P51786, P52737, P85977, Q0VGE8, Q14588, Q147U1, Q15928, Q15973, Q2M3X9, Q3KNS6, Q3MIS6, Q494X3, Q5HY98, Q5RBQ3, Q5REK1, Q5VIY5, Q60585, Q61751, Q6GQR8, Q7L2R6, Q7TSH9, Q8IYX0, Q8N782, Q8N823, Q8N988, Q8N9F8, Q8NA42, Q8NCK3, Q8NDP4, Q8NEP9, Q8TC21

Diamond homologs: A0JPL0, A2VDP4, A6QLU5, A6QPT6, A8MQ14, A8MUZ8, A8MWA4, B1APH4, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, P08042, P0CH99, P0CI00, P17014, P17025, P17030, P17031, P17032, P17098, P21506, P51508, P51523, P51786, P51814, P52736, P52738, Q02525, Q03923, Q03936, Q06730, Q06732, Q0VCB0, Q13401, Q14587, Q16587, Q2M218, Q2M3X9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1046 predictions. Top by Δscore:

Variant	Effect	Δscore
19:37227991:G:GT	donor_gain	1.0000
19:37230461:AGG:A	donor_loss	1.0000
19:37230463:G:GC	donor_loss	1.0000
19:37230464:T:A	donor_loss	1.0000
19:37232725:A:T	donor_gain	1.0000
19:37235545:TCA:T	acceptor_loss	1.0000
19:37235546:CAG:C	acceptor_loss	1.0000
19:37235547:A:AG	acceptor_gain	1.0000
19:37235547:A:G	acceptor_loss	1.0000
19:37235547:AG:A	acceptor_gain	1.0000
19:37235547:AGG:A	acceptor_gain	1.0000
19:37235548:G:GC	acceptor_gain	1.0000
19:37235548:GG:G	acceptor_gain	1.0000
19:37235548:GGG:G	acceptor_gain	1.0000
19:37235672:ATGGG:A	donor_loss	1.0000
19:37235673:TGGGT:T	donor_loss	1.0000
19:37235674:GG:G	donor_gain	1.0000
19:37235675:GG:G	donor_gain	1.0000
19:37235675:GGTAA:G	donor_loss	1.0000
19:37235676:G:GG	donor_gain	1.0000
19:37235676:G:GT	donor_loss	1.0000
19:37235677:TAAG:T	donor_loss	1.0000
19:37218272:CAGG:C	donor_loss	0.9900
19:37218275:G:C	donor_loss	0.9900
19:37218276:T:A	donor_loss	0.9900
19:37235541:T:TA	acceptor_gain	0.9900
19:37235548:GGGAT:G	acceptor_gain	0.9900
19:37242467:A:AG	acceptor_gain	0.9900
19:37242468:G:GG	acceptor_gain	0.9900
19:37230460:GAG:G	donor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000051839 (19:37220425 T>C,G), RS1000083133 (19:37244820 T>C), RS1000159617 (19:37220967 A>G), RS1000324243 (19:37233215 C>G,T), RS1000351940 (19:37227345 C>T), RS1000423178 (19:37233782 T>C), RS1000511620 (19:37221206 A>G), RS1000578243 (19:37239346 A>G), RS1000640417 (19:37237375 GA>G,GAA), RS1001090729 (19:37244888 TTTCATG>T), RS1001121747 (19:37222588 G>A), RS1001225507 (19:37245578 G>A,T), RS1001468987 (19:37235091 G>A), RS1001530673 (19:37241278 C>T), RS1001544908 (19:37244637 C>T)

Disease associations

OMIM: gene MIM:619499 | 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
GCST002097_45	Coronary artery calcification	7.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004723	coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	increases expression, increases methylation	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
trichostatin A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
jinfukang	decreases expression	1
MT19c compound	increases expression	1
Temozolomide	increases expression	1
Arsenic Trioxide	affects cotreatment, decreases expression	1
Antimycin A	increases expression	1
Benzo(a)pyrene	increases expression	1
Camptothecin	increases expression	1
Cytarabine	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Tretinoin	affects cotreatment, decreases expression	1
Valproic Acid	decreases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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