ZNF17

Summary

ZNF17 (zinc finger protein 17, HGNC:12958) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 17 (P17021). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-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 7565 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 96 total
• MANE Select transcript: NM_001330617

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12958
Approved symbol	ZNF17
Name	zinc finger protein 17
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615
Ensembl gene	ENSG00000186272
Ensembl biotype	protein_coding
OMIM	619254
Entrez	7565

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000307658, ENST00000595162, ENST00000595206, ENST00000597350, ENST00000599867, ENST00000601808, ENST00000602050, ENST00000878542, ENST00000964805, ENST00000964806

RefSeq mRNA: 2 — MANE Select: NM_001330617 NM_001330617, NM_006959

CCDS: CCDS42636, CCDS82405

Canonical transcript exons

ENST00000307658 — 4 exons

Exon	Start	End
ENSE00001170822	57419635	57421934
ENSE00003160959	57411161	57411406
ENSE00003686570	57413596	57413636
ENSE00003784919	57417912	57418038

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 85.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9803 / max 50.1750, expressed in 1507 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177772	3.9803	1507

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.64	gold quality
corpus callosum	UBERON:0002336	80.34	gold quality
ventricular zone	UBERON:0003053	79.26	gold quality
cortical plate	UBERON:0005343	79.26	gold quality
calcaneal tendon	UBERON:0003701	77.98	gold quality
embryo	UBERON:0000922	77.73	gold quality
ganglionic eminence	UBERON:0004023	77.73	gold quality
skeletal muscle tissue	UBERON:0001134	77.12	gold quality
tonsil	UBERON:0002372	76.84	gold quality
endometrium	UBERON:0001295	76.00	gold quality
muscle tissue	UBERON:0002385	75.86	gold quality
smooth muscle tissue	UBERON:0001135	75.75	gold quality
skeletal muscle organ	UBERON:0014892	75.48	gold quality
muscle of leg	UBERON:0001383	75.42	gold quality
gastrocnemius	UBERON:0001388	75.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	75.18	gold quality
apex of heart	UBERON:0002098	75.12	gold quality
islet of Langerhans	UBERON:0000006	74.89	gold quality
stromal cell of endometrium	CL:0002255	74.67	gold quality
urinary bladder	UBERON:0001255	74.66	gold quality
granulocyte	CL:0000094	74.65	gold quality
adrenal tissue	UBERON:0018303	74.17	gold quality
ovary	UBERON:0000992	74.09	gold quality
lymph node	UBERON:0000029	73.98	gold quality
heart left ventricle	UBERON:0002084	73.98	gold quality
heart	UBERON:0000948	73.91	gold quality
superior frontal gyrus	UBERON:0002661	73.83	gold quality
descending thoracic aorta	UBERON:0002345	73.81	gold quality
left ovary	UBERON:0002119	73.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting ZNF17, 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-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-302B-5P	99.50	69.49	1857
HSA-MIR-302D-5P	99.50	69.34	1863
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-4777-5P	99.33	67.53	1148
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-449B-3P	99.20	67.24	1047
HSA-MIR-1257	98.97	68.02	1133
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-4317	98.49	67.09	987
HSA-MIR-1912-5P	97.94	67.98	832
HSA-MIR-630	97.50	66.38	921
HSA-MIR-6831-3P	97.49	69.29	505

Cross-species orthologs

0 orthologs

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), ZNF319 (ENSG00000166188), 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), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein 17 — P17021 (reviewed: P17021)

Alternative names: Zinc finger protein HPF3, Zinc finger protein KOX10

All UniProt accessions (3): P17021, M0QZR3, M0R2T2

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 (3)

UniProt ID	Names	Canonical?
P17021-1	1	yes
P17021-2	2
P17021-3	3

RefSeq proteins (2): NP_001317546, NP_008890 (=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

Pfam: PF00096, PF01352

UniProt features (24 total): zinc finger region 16, sequence conflict 3, splice variant 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17021-F1	73.17	0.16

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 37 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ACACTGG_MIR199A_MIR199B, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, DLX4_TARGET_GENES, MIR10527_5P, MIR497_3P, MIR302B_5P, MIR302D_5P, MIR329_5P, MIR1257, MIR449B_3P, MIR630, MIR6831_3P, SMN1_SMN2_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, 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)

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
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

580 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF17	OR10G2	Q8NGC3	447
ZNF17	EFCAB8	A8MWE9	396
ZNF17	C5orf15	Q8NC54	395
ZNF17	ABHD1	Q96SE0	311
ZNF17	MAMDC4	Q6UXC1	306
ZNF17	SPAG17	Q6Q759	291
ZNF17	CEP20	Q96NB1	290
ZNF17	TMCC1	O94876	276
ZNF17	SVIL	O95425	272
ZNF17	HOGA1	Q86XE5	261
ZNF17	CORO2B	Q9UQ03	256
ZNF17	UNC79	Q9P2D8	254
ZNF17	GPR107	Q5VW38	252
ZNF17	FAM111B	Q6SJ93	248
ZNF17	SLC26A11	Q86WA9	247

IntAct

41 interactions, top by confidence:

A	B	Type	Score
ZNF17	ZNF837	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF17	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	PICK1	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	CEP70	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	OPTN	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	ZRANB1	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	KRT40	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	SET	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF17	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	AIRIM	psi-mi:“MI:0915”(physical association)	0.560
ZNF17	ZNF438	psi-mi:“MI:0915”(physical association)	0.560
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF17	TRIM24	psi-mi:“MI:0914”(association)	0.350
ZNF17	NDEL1	psi-mi:“MI:0915”(physical association)	0.000
NDEL1	ZNF17	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	ZNF837	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	MTUS2	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	PICK1	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	CEP70	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	OPTN	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	ZRANB1	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	KRT40	psi-mi:“MI:0915”(physical association)	0.000
AIRIM	ZNF17	psi-mi:“MI:0915”(physical association)	0.000
SET	ZNF17	psi-mi:“MI:0915”(physical association)	0.000
ZNF17	YJU2B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (38): ZNF17 (Synthetic Growth Defect), ZNF17 (Affinity Capture-RNA), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), ZNF17 (Two-hybrid), GOLGA6L9 (Two-hybrid), KRT40 (Two-hybrid), DAP3 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, B2RUI1, O43296, O75123, P10072, P17020, P17021, P17097, P51814, P52740, P52741, Q07230, Q08ER8, Q13398, Q14590, Q32KN0, Q3KQV3, Q3MIS6, Q4V8A8, Q5CZA5, Q5RBQ3, Q5RBX0, Q5RCD9, Q5RCX4, Q6GQR8, Q6NX45, Q6P9A3, Q6PK81, Q7TSH9, Q7TSI0, Q7Z7L9, Q86UD4, Q8BFS8, Q8BLB0, Q8IVP9, Q8IZ26, Q8TAU3

Diamond homologs: A2RRD8, A6NFI3, A6NM28, A8MUZ8, A8MWA4, B2RUI1, B4DU55, E9Q8G5, O43296, O43361, O75467, O75820, P0CH99, P0CI00, P10078, P16373, P16374, P17021, P17023, P17032, P17097, P17098, P21506, P51786, P52740, Q06732, Q08ER8, Q13106, Q13360, Q13398, Q14592, Q147U1, Q32M78, Q3KQV3, Q3MIS6, Q3SY52, Q571J5, Q5CZA5, Q5HY98, Q5R7I8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

866 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57418035:GTAG:G	donor_gain	1.0000
19:57411402:CTGAG:C	donor_loss	0.9900
19:57411403:TGAG:T	donor_loss	0.9900
19:57411405:AGGTG:A	donor_loss	0.9900
19:57411407:G:GA	donor_loss	0.9900
19:57411408:T:G	donor_loss	0.9900
19:57411006:C:T	donor_gain	0.9800
19:57411015:T:G	donor_gain	0.9800
19:57411015:T:TG	donor_gain	0.9800
19:57411010:T:G	donor_gain	0.9700
19:57417911:GGATT:G	acceptor_gain	0.9700
19:57418034:AGTAG:A	donor_loss	0.9700
19:57418037:AG:A	donor_loss	0.9700
19:57418038:GGTAA:G	donor_loss	0.9700
19:57418039:GTAA:G	donor_loss	0.9700
19:57418040:T:G	donor_loss	0.9700
19:57419634:GGTT:G	acceptor_gain	0.9700
19:57411409:GGGT:G	donor_loss	0.9600
19:57411410:GGTG:G	donor_loss	0.9600
19:57417910:A:AG	acceptor_gain	0.9600
19:57417910:AG:A	acceptor_gain	0.9600
19:57417911:G:GG	acceptor_gain	0.9600
19:57417911:GG:G	acceptor_gain	0.9600
19:57419628:GTTTT:G	acceptor_loss	0.9600
19:57419629:TTTTA:T	acceptor_loss	0.9600
19:57419630:TTTA:T	acceptor_loss	0.9600
19:57419631:TTA:T	acceptor_loss	0.9600
19:57419631:TTAG:T	acceptor_loss	0.9600
19:57419632:TA:T	acceptor_loss	0.9600
19:57419633:A:AC	acceptor_loss	0.9600

AlphaMissense

4492 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57421011:T:C	F507L	0.994
19:57421013:T:A	F507L	0.994
19:57421013:T:G	F507L	0.994
19:57421431:T:C	F647L	0.994
19:57421433:T:A	F647L	0.994
19:57421433:T:G	F647L	0.994
19:57420423:T:C	F311L	0.993
19:57420425:C:A	F311L	0.993
19:57420425:C:G	F311L	0.993
19:57420790:A:C	Q433P	0.991
19:57421347:T:C	F619L	0.991
19:57421349:T:A	F619L	0.991
19:57421349:T:G	F619L	0.991
19:57420255:T:C	F255L	0.990
19:57420257:C:A	F255L	0.990
19:57420257:C:G	F255L	0.990
19:57420786:C:G	H432D	0.990
19:57420956:T:A	H488Q	0.990
19:57420956:T:G	H488Q	0.990
19:57420958:A:C	Q489P	0.990
19:57420339:T:C	F283L	0.989
19:57420341:T:A	F283L	0.989
19:57420341:T:G	F283L	0.989
19:57420538:A:C	Q349P	0.989
19:57420954:C:G	H488D	0.989
19:57420507:T:C	F339L	0.988
19:57420509:T:A	F339L	0.988
19:57420509:T:G	F339L	0.988
19:57420704:T:A	H404Q	0.988
19:57420704:T:G	H404Q	0.988

dbSNP variants (sampled 300 via entrez): RS1000400318 (19:57414190 T>C), RS1000755043 (19:57412442 TAA>T), RS1000774038 (19:57419703 G>A), RS1001003663 (19:57413918 A>T), RS1001170822 (19:57417279 G>A,C), RS1001280690 (19:57411241 C>A,T), RS1001363243 (19:57418445 T>A), RS1001449104 (19:57416920 G>A), RS1002187054 (19:57417796 G>A,C), RS1002275343 (19:57412414 C>G,T), RS1002480799 (19:57412660 G>A), RS1002645763 (19:57417449 A>G), RS1002732895 (19:57410178 A>G), RS1002966800 (19:57421634 C>A,T), RS1003123889 (19:57415517 G>A)

Disease associations

OMIM: gene MIM:619254 | 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

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects cotreatment	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
manganese chloride	increases abundance, increases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression	1
Ozone	affects expression, increases abundance	1
Urethane	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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