ZNF319

Summary

ZNF319 (zinc finger protein 319, HGNC:13644) is a protein-coding gene on chromosome 16q21, encoding Zinc finger protein 319 (Q9P2F9). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 57567 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 73 total
• MANE Select transcript: NM_020807

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13644
Approved symbol	ZNF319
Name	zinc finger protein 319
Location	16q21
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1388, Zfp319
Ensembl gene	ENSG00000166188
Ensembl biotype	protein_coding
Entrez	57567

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000299237, ENST00000562909, ENST00000858170

RefSeq mRNA: 4 — MANE Select: NM_020807 NM_001384365, NM_001384366, NM_001384367, NM_020807

CCDS: CCDS32462

Canonical transcript exons

ENST00000299237 — 2 exons

Exon	Start	End
ENSE00001100746	57999493	58000672
ENSE00001100750	57994676	57998522

Expression profiles

Bgee: expression breadth ubiquitous, 189 present calls, max score 86.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.2528 / max 81.2420, expressed in 1755 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157592	6.2528	1755

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	86.71	gold quality
granulocyte	CL:0000094	85.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.63	gold quality
leukocyte	CL:0000738	82.56	gold quality
monocyte	CL:0000576	82.34	gold quality
blood	UBERON:0000178	81.38	gold quality
apex of heart	UBERON:0002098	80.27	gold quality
cortical plate	UBERON:0005343	79.22	gold quality
ganglionic eminence	UBERON:0004023	78.13	gold quality
embryo	UBERON:0000922	78.12	gold quality
ventricular zone	UBERON:0003053	78.12	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.97	gold quality
tibialis anterior	UBERON:0001385	77.96	silver quality
stromal cell of endometrium	CL:0002255	76.43	gold quality
lower esophagus muscularis layer	UBERON:0035833	76.20	gold quality
lower esophagus	UBERON:0013473	76.15	gold quality
gastrocnemius	UBERON:0001388	76.12	gold quality
muscle of leg	UBERON:0001383	75.84	gold quality
right lobe of thyroid gland	UBERON:0001119	75.68	gold quality
germinal epithelium of ovary	UBERON:0001304	75.62	silver quality
left lobe of thyroid gland	UBERON:0001120	75.29	gold quality
right coronary artery	UBERON:0001625	75.21	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	75.03	gold quality
right adrenal gland	UBERON:0001233	74.84	gold quality
bone marrow cell	CL:0002092	74.83	gold quality
heart left ventricle	UBERON:0002084	74.69	gold quality
right adrenal gland cortex	UBERON:0035827	74.68	gold quality
popliteal artery	UBERON:0002250	74.55	gold quality
smooth muscle tissue	UBERON:0001135	74.54	gold quality
tibial artery	UBERON:0007610	74.53	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.22

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Genome-wide CRISPR/Cas9 knockout screening uncovers ZNF319 as a novel tumor suppressor critical for breast cancer metastasis. (PMID:34902746)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf319b	ENSDARG00000062401
mus_musculus	Zfp319	ENSMUSG00000046556
rattus_norvegicus	Zfp319	ENSRNOG00000079756

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein 319 — Q9P2F9 (reviewed: Q9P2F9)

All UniProt accessions (2): Q9P2F9, H3BT69

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 (4): NP_001371294, NP_001371295, NP_001371296, NP_065858* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF13465

UniProt features (23 total): zinc finger region 16, region of interest 2, compositionally biased region 2, chain 1, modified residue 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2F9-F1	65.06	0.01

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 (2): 281, 130

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): ATGTTAA_MIR302C, AAAGACA_MIR511, chr16q21, CUI_TCF21_TARGETS_2_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DELACROIX_RARG_BOUND_MEF, PKCA_DN.V1_DN, ZNF711_TARGET_GENES, MIR153_5P, MIR4698, MIR10527_5P, MIR3143, MIR5196_5P, MIR4747_5P

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF319	RNF149	Q8NC42	517
ZNF319	UBN1	Q9NPG3	507
ZNF319	TMPPE	Q6ZT21	474
ZNF319	KIAA0040	Q15053	439
ZNF319	RNF25	Q96BH1	417
ZNF319	ZNF207	O43670	416
ZNF319	SPNS3	Q6ZMD2	414
ZNF319	C6orf136	Q5SQH8	397
ZNF319	TMEM273	Q5T292	396
ZNF319	UBE2Z	Q9H832	396
ZNF319	CCDC38	Q502W7	372
ZNF319	JOSD1	Q15040	369
ZNF319	UBA2	Q9UBT2	358
ZNF319	GSG1L	Q6UXU4	350
ZNF319	UBE2O	Q9C0C9	350

IntAct

64 interactions, top by confidence:

A	B	Type	Score
ZNF319	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-6	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
PLEKHG4	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
BEGAIN	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
DVL3	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
POU6F2	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
KRT40	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
KRT34	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLC	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
GRAP2	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
VWC2	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
RNF4	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
PIAS2	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
KRTAP13-3	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	ZNF319	psi-mi:“MI:0915”(physical association)	0.560
M		psi-mi:“MI:0914”(association)	0.350
KLF15		psi-mi:“MI:0914”(association)	0.350
ZNF319	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000
ZNF319	PLEKHG4	psi-mi:“MI:0915”(physical association)	0.000
ZNF319	BEGAIN	psi-mi:“MI:0915”(physical association)	0.000
ZNF319	DVL3	psi-mi:“MI:0915”(physical association)	0.000
ZNF319	TRIM41	psi-mi:“MI:0915”(physical association)	0.000
ZNF319	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.000
ZNF319	POU6F2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (28): ZNF319 (Affinity Capture-MS), ZNF319 (Affinity Capture-RNA), ZNF319 (Affinity Capture-MS), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), ZNF319 (Two-hybrid), BEGAIN (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-6 (Two-hybrid)

ESM2 similar proteins: A2CE44, A6NEF3, A6NEM1, A6NFI3, A6NI86, A6QR00, E9PXT9, G3V893, H0YKK7, O73823, O95201, P02861, P0CG23, P10075, P14590, P15714, P18174, P24710, P28698, P48998, Q07243, Q17RH7, Q28181, Q29RK0, Q3UH66, Q5EBL2, Q5TEC3, Q66K89, Q6PGE4, Q6ZN55, Q8BI66, Q8BY46, Q8CHD8, Q8CJ78, Q8IV76, Q8N693, Q8R0T2, Q8TF50, Q8TF68, Q95337

Diamond homologs: P21506, P30373, Q15697, Q5U4E2, Q8BGV5, Q8BZ34, Q96H86, Q96N20, Q96N77, Q9NWS9, Q9P2F9, Q9ERR8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 20 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	6	20.9×	1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

186 predictions. Top by Δscore:

Variant	Effect	Δscore
16:57999492:CCA:C	donor_gain	0.9900
16:57998523:C:CC	acceptor_gain	0.9800
16:57999487:ACTC:A	donor_loss	0.9700
16:57999488:CTCA:C	donor_loss	0.9700
16:57999489:TCA:T	donor_loss	0.9700
16:57999490:CAC:C	donor_loss	0.9700
16:57999491:ACCAC:A	donor_loss	0.9700
16:57999492:C:T	donor_loss	0.9700
16:57999709:T:TA	donor_gain	0.9700
16:57999486:AACT:A	donor_loss	0.9600
16:57999491:A:AC	donor_gain	0.9500
16:57999492:C:CC	donor_gain	0.9500
16:57999721:T:TA	donor_gain	0.9500
16:57998520:GTTCT:G	acceptor_loss	0.9400
16:57998521:TTCT:T	acceptor_loss	0.9400
16:57998522:TCTG:T	acceptor_loss	0.9400
16:57998523:C:T	acceptor_loss	0.9400
16:57998524:T:G	acceptor_loss	0.9400
16:57998519:CGTT:C	acceptor_gain	0.9200
16:57998518:CCGTT:C	acceptor_gain	0.9000
16:57998519:CGTTC:C	acceptor_gain	0.9000
16:57999492:CCACT:C	donor_gain	0.9000
16:57998521:TT:T	acceptor_gain	0.8900
16:57998373:T:TG	acceptor_gain	0.8800
16:57999589:A:C	donor_gain	0.8700
16:57999489:TCAC:T	donor_gain	0.8600
16:57999490:CACC:C	donor_gain	0.8600
16:57999491:AC:A	donor_gain	0.8600
16:57999491:ACCA:A	donor_gain	0.8600
16:57999492:CC:C	donor_gain	0.8600

AlphaMissense

3818 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:57996697:G:C	F523L	1.000
16:57996697:G:T	F523L	1.000
16:57996699:A:G	F523L	1.000
16:57997438:G:C	H276Q	1.000
16:57997438:G:T	H276Q	1.000
16:57997448:A:G	L273P	1.000
16:57997465:G:C	F267L	1.000
16:57997465:G:T	F267L	1.000
16:57997467:A:G	F267L	1.000
16:57997479:A:G	C263R	1.000
16:57997488:A:G	C260R	1.000
16:57997524:G:C	H248D	1.000
16:57997524:G:T	H248N	1.000
16:57997549:G:C	F239L	1.000
16:57997549:G:T	F239L	1.000
16:57997551:A:G	F239L	1.000
16:57996670:G:C	H532Q	0.999
16:57996670:G:T	H532Q	0.999
16:57996672:G:C	H532D	0.999
16:57996672:G:T	H532N	0.999
16:57996680:A:G	L529P	0.999
16:57996698:A:G	F523S	0.999
16:57996699:A:T	F523I	0.999
16:57996720:A:G	C516R	0.999
16:57996754:G:C	H504Q	0.999
16:57996754:G:T	H504Q	0.999
16:57996756:G:C	H504D	0.999
16:57996756:G:T	H504N	0.999
16:57996781:G:C	F495L	0.999
16:57996781:G:T	F495L	0.999

dbSNP variants (sampled 300 via entrez): RS1000234762 (16:57999466 C>T), RS1000461198 (16:58001461 C>A,G,T), RS1000465671 (16:57995359 T>C), RS1000795739 (16:57995066 C>T), RS1001072937 (16:57994847 T>C), RS1001102058 (16:58000736 C>T), RS1001638130 (16:58000546 C>G), RS1001777616 (16:57994368 A>G), RS1002077027 (16:57996249 GA>G), RS1002080046 (16:58001223 G>T), RS1003078490 (16:57997704 C>T), RS1003356242 (16:57999153 A>G), RS1003871990 (16:57999601 G>A,C,T), RS1004085517 (16:57998969 G>A,C), RS1004527649 (16:57998743 C>G,T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	3
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
TAK-243	decreases sumoylation	1
ferrous chloride	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Atrazine	decreases expression	1
Cisplatin	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Sodium Selenite	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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