ZNF19

Summary

ZNF19 (zinc finger protein 19, HGNC:12981) is a protein-coding gene on chromosome 16q22.2, encoding Zinc finger protein 19 (P17023). May be involved in transcriptional regulation.

The protein encoded by this gene contains a zinc finger, a nucleic acid-binding domain present in many transcription factors. This gene is located in a region next to ZNF23, a gene also encoding a zinc finger protein, on chromosome 16.

Source: NCBI Gene 7567 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_006961

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12981
Approved symbol	ZNF19
Name	zinc finger protein 19
Location	16q22.2
Locus type	gene with protein product
Status	Approved
Aliases	KOX12, MGC51021
Ensembl gene	ENSG00000157429
Ensembl biotype	protein_coding
OMIM	194525
Entrez	7567

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 14 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000288177, ENST00000561469, ENST00000562210, ENST00000564225, ENST00000564230, ENST00000565100, ENST00000565541, ENST00000565637, ENST00000566202, ENST00000567225, ENST00000568446, ENST00000568815, ENST00000569072, ENST00000569717, ENST00000617615, ENST00000866316, ENST00000866317, ENST00000866318, ENST00000948558

RefSeq mRNA: 1 — MANE Select: NM_006961 NM_006961

CCDS: CCDS10901

Canonical transcript exons

ENST00000288177 — 6 exons

Exon	Start	End
ENSE00001106008	71473583	71476272
ENSE00001351646	71489272	71489324
ENSE00003459065	71478228	71478341
ENSE00003489794	71478879	71479005
ENSE00003569092	71484589	71484748
ENSE00003670752	71482082	71482143

Expression profiles

Bgee: expression breadth ubiquitous, 189 present calls, max score 91.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.6087 / max 75.5710, expressed in 1279 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
158007	2.0280	1115
158010	1.0097	398
158006	0.5490	81
158008	0.0146	3
158009	0.0074	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	91.07	gold quality
ileal mucosa	UBERON:0000331	82.78	silver quality
pancreatic ductal cell	CL:0002079	82.69	silver quality
tibialis anterior	UBERON:0001385	82.65	silver quality
right testis	UBERON:0004534	81.75	gold quality
left testis	UBERON:0004533	81.51	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.50	gold quality
adenohypophysis	UBERON:0002196	80.96	gold quality
testis	UBERON:0000473	80.40	gold quality
pituitary gland	UBERON:0000007	80.24	gold quality
right lobe of thyroid gland	UBERON:0001119	80.22	gold quality
left lobe of thyroid gland	UBERON:0001120	80.09	gold quality
thyroid gland	UBERON:0002046	79.62	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.87	gold quality
bronchial epithelial cell	CL:0002328	78.72	gold quality
mucosa of paranasal sinus	UBERON:0005030	78.10	silver quality
sural nerve	UBERON:0015488	77.91	gold quality
bronchus	UBERON:0002185	77.71	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	76.93	gold quality
islet of Langerhans	UBERON:0000006	76.56	gold quality
metanephros	UBERON:0000081	76.34	gold quality
ventricular zone	UBERON:0003053	76.34	gold quality
fallopian tube	UBERON:0003889	76.24	gold quality
colonic epithelium	UBERON:0000397	75.86	gold quality
right lung	UBERON:0002167	75.58	gold quality
metanephros cortex	UBERON:0010533	75.54	gold quality
body of pancreas	UBERON:0001150	75.32	gold quality
cortical plate	UBERON:0005343	74.99	gold quality
pancreas	UBERON:0001264	74.94	gold quality
oviduct epithelium	UBERON:0004804	74.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

48 targeting ZNF19, 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-499A-5P	99.98	70.79	1323
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-1273H-3P	99.29	67.55	980
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-4711-3P	98.97	66.87	1020

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 19 — P17023 (reviewed: P17023)

Alternative names: Zinc finger protein KOX12

All UniProt accessions (10): P17023, H3BMU5, H3BNH9, H3BNI0, H3BQ26, H3BQI6, H3BR98, J3KRI7, J3KSN3, J3KT56

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?
P17023-1	1	yes
P17023-2	2

RefSeq proteins (1): NP_008892* (*=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
IPR050589	Ikaros_C2H2-ZF	Family

Pfam: PF00096, PF01352

UniProt features (17 total): zinc finger region 10, sequence variant 2, sequence conflict 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17023-F1	71.76	0.13

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 33 (showing top): chr16q22, XU_GH1_EXOGENOUS_TARGETS_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, BCL6B_TARGET_GENES, CENPT_TARGET_GENES, CSHL1_TARGET_GENES, DLX4_TARGET_GENES, FOXN3_TARGET_GENES, SNIP1_TARGET_GENES, TERF1_TARGET_GENES, ZIM3_TARGET_GENES, ZNF410_TARGET_GENES, MIR4310

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

Protein interactions and networks

STRING

518 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF19	NOX4	Q9NPH5	772
ZNF19	TTC39A	Q5SRH9	543
ZNF19	CCDC71	Q8IV32	490
ZNF19	CREB5	Q02930	464
ZNF19	NIPAL2	Q9H841	450
ZNF19	LEMD3	Q9Y2U8	443
ZNF19	TMBIM4	Q9HC24	442
ZNF19	SPDYE6	P0CI01	434
ZNF19	ZNF292	O60281	422
ZNF19	KLF11	O14901	411
ZNF19	FRA10AC1	Q70Z53	399
ZNF19	MEPE	Q9NQ76	391
ZNF19	SNAI2	O43623	379
ZNF19	C1orf21	Q9H246	377
ZNF19	NBPF20	P0DPF2	373

IntAct

88 interactions, top by confidence:

A	B	Type	Score
CTNNA3	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
CSNK2B	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
FAM72D	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
LMO2	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
SCNM1	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
MAGOHB	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
LMO1	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
NUDT22	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
CINP	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
ZNF417	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
BCCIP	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
BEX2	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
CARD9	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
NDUFAB1	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
ZNF19	RFC5	psi-mi:“MI:0915”(physical association)	0.560
ZNF19	SPANXN2	psi-mi:“MI:0915”(physical association)	0.560
ZNF19	ZNF417	psi-mi:“MI:0915”(physical association)	0.560
ZNF19	AP1M1	psi-mi:“MI:0915”(physical association)	0.560
ZNF19	ATPAF2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (30): TRIM28 (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), TRIM28 (Affinity Capture-MS), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid), ZNF19 (Two-hybrid)

ESM2 similar proteins: A1L1L7, A3KN36, D3ZVT0, O43296, P08042, P13682, P16373, P17023, P17097, P52738, P85977, Q02975, Q12901, Q14590, Q14592, Q2M3W8, Q2VY69, Q4V8A8, Q571J5, Q5CZA5, Q5R7I8, Q5RB33, Q5RBX0, Q61751, Q61967, Q6GQR8, Q6PF04, Q6ZNG0, Q6ZS27, Q86Y25, Q8BFS8, Q8BQC8, Q8IZ26, Q8N782, Q8N9Z0, Q8R1D1, Q8TF47, Q8WTR7, Q96LW1, Q9BS31

Diamond homologs: A0JPL0, A1L1L7, A2A761, A2VDP4, A3KN36, A6QLU5, A6QPT6, A7MBI1, A8MT65, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, O95780, P10076, P17014, P17023, P17025, P17030, P17032, P17098, P51523, P51814, P52736, P52742, P58317, Q02975, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14584, Q14587, Q14590, Q147U1, Q16587, Q29RZ4, Q2M218

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	57
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1675 predictions. Top by Δscore:

Variant	Effect	Δscore
16:71478224:CTA:C	donor_loss	1.0000
16:71478225:TA:T	donor_loss	1.0000
16:71478226:A:AT	donor_loss	1.0000
16:71478227:C:CT	donor_loss	1.0000
16:71478340:CC:C	acceptor_gain	1.0000
16:71478341:CC:C	acceptor_gain	1.0000
16:71478342:C:CC	acceptor_gain	1.0000
16:71525376:G:GT	donor_gain	1.0000
16:71476091:TGGA:T	donor_gain	0.9900
16:71476100:T:A	donor_gain	0.9900
16:71476270:CAT:C	acceptor_gain	0.9900
16:71476271:ATCTG:A	acceptor_loss	0.9900
16:71476273:C:A	acceptor_loss	0.9900
16:71476277:C:CT	acceptor_gain	0.9900
16:71476278:A:C	acceptor_gain	0.9900
16:71478338:TACC:T	acceptor_gain	0.9900
16:71478340:CCCT:C	acceptor_loss	0.9900
16:71478342:C:CA	acceptor_loss	0.9900
16:71478343:T:A	acceptor_loss	0.9900
16:71478872:GCCTT:G	donor_loss	0.9900
16:71478873:CCTTA:C	donor_loss	0.9900
16:71478874:CTT:C	donor_loss	0.9900
16:71478875:TTA:T	donor_loss	0.9900
16:71478875:TTAC:T	donor_loss	0.9900
16:71478876:TA:T	donor_loss	0.9900
16:71478877:AC:A	donor_gain	0.9900
16:71478877:ACCC:A	donor_loss	0.9900
16:71478878:CC:C	donor_gain	0.9900
16:71484750:T:C	acceptor_gain	0.9900
16:71488965:C:A	donor_gain	0.9900

AlphaMissense

3062 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:71475701:A:C	F282L	0.998
16:71475701:A:T	F282L	0.998
16:71475703:A:G	F282L	0.998
16:71475869:A:C	F226L	0.998
16:71475869:A:T	F226L	0.998
16:71475871:A:G	F226L	0.998
16:71475953:A:C	F198L	0.998
16:71475953:A:T	F198L	0.998
16:71475955:A:G	F198L	0.998
16:71475533:G:C	F338L	0.997
16:71475533:G:T	F338L	0.997
16:71475535:A:G	F338L	0.997
16:71475617:A:C	F310L	0.997
16:71475617:A:T	F310L	0.997
16:71475619:A:G	F310L	0.997
16:71475785:G:C	F254L	0.997
16:71475785:G:T	F254L	0.997
16:71475787:A:G	F254L	0.997
16:71475585:C:G	R321P	0.996
16:71475756:T:G	Q264P	0.996
16:71475842:A:C	H235Q	0.996
16:71475842:A:T	H235Q	0.996
16:71475844:G:C	H235D	0.996
16:71475852:A:G	L232P	0.996
16:71475449:G:C	F366L	0.995
16:71475449:G:T	F366L	0.995
16:71475451:A:G	F366L	0.995
16:71475600:A:G	L316P	0.995
16:71475674:A:C	H291Q	0.995
16:71475674:A:T	H291Q	0.995

dbSNP variants (sampled 300 via entrez): RS1000058973 (16:71488985 C>G,T), RS1000300451 (16:71488579 G>A,C), RS1000317683 (16:71488343 G>A,T), RS1000328498 (16:71488681 C>T), RS1000532036 (16:71477145 G>T), RS1000928887 (16:71490070 A>C,T), RS1001022300 (16:71490335 T>C), RS1001052893 (16:71477446 T>C), RS1001118780 (16:71484034 C>A,T), RS1001231214 (16:71489331 C>A,G), RS1001464933 (16:71490512 T>C), RS1001599068 (16:71489602 G>A), RS1001607316 (16:71474251 C>T), RS1001639544 (16:71487292 G>A), RS1001693596 (16:71487575 A>G)

Disease associations

OMIM: gene MIM:194525 | 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
GCST005316_209	Intelligence (MTAG)	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence

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, increases methylation	2
Esketamine	decreases expression	1
methylmercuric chloride	decreases expression	1
terbufos	decreases methylation	1
trichostatin A	decreases expression	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	increases reaction, affects binding	1
abrine	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Leflunomide	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Fonofos	decreases methylation	1
Parathion	decreases methylation	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	decreases 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_XW14	HEK293 eGFP-ZNF19	Transformed cell line	Female

Clinical trials (associated diseases)

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