ZNF20

Summary

ZNF20 (zinc finger protein 20, HGNC:12992) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 20 (P17024). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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 7568 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 55 total
• MANE Select transcript: NM_021143

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12992
Approved symbol	ZNF20
Name	zinc finger protein 20
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	KOX13
Ensembl gene	ENSG00000132010
Ensembl biotype	protein_coding
OMIM	194557
Entrez	7568

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000334213, ENST00000418866, ENST00000454949, ENST00000478942, ENST00000480477, ENST00000480770, ENST00000485451, ENST00000600335

RefSeq mRNA: 2 — MANE Select: NM_021143 NM_001203250, NM_021143

CCDS: CCDS45986

Canonical transcript exons

ENST00000334213 — 4 exons

Exon	Start	End
ENSE00001529999	12131350	12133985
ENSE00001844353	12140180	12140350
ENSE00003652812	12135500	12135560
ENSE00003666589	12135769	12135904

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 85.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.3161 / max 113.8635, expressed in 1511 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179286	4.2162	1499
179287	0.0999	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	85.33	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.43	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.58	gold quality
right testis	UBERON:0004534	81.50	gold quality
left testis	UBERON:0004533	80.79	gold quality
testis	UBERON:0000473	80.65	gold quality
right uterine tube	UBERON:0001302	80.61	gold quality
ganglionic eminence	UBERON:0004023	77.82	gold quality
endometrium	UBERON:0001295	75.26	gold quality
fallopian tube	UBERON:0003889	75.16	gold quality
rectum	UBERON:0001052	74.88	gold quality
islet of Langerhans	UBERON:0000006	74.77	gold quality
ventricular zone	UBERON:0003053	74.56	gold quality
adrenal tissue	UBERON:0018303	74.40	gold quality
leukocyte	CL:0000738	73.72	gold quality
lower esophagus mucosa	UBERON:0035834	73.63	gold quality
monocyte	CL:0000576	73.57	gold quality
blood	UBERON:0000178	73.27	gold quality
pancreas	UBERON:0001264	73.05	gold quality
urinary bladder	UBERON:0001255	72.86	gold quality
colonic epithelium	UBERON:0000397	72.54	gold quality
right adrenal gland cortex	UBERON:0035827	72.52	gold quality
body of pancreas	UBERON:0001150	72.46	gold quality
kidney	UBERON:0002113	72.37	gold quality
metanephros cortex	UBERON:0010533	72.17	gold quality
right adrenal gland	UBERON:0001233	72.01	gold quality
adult mammalian kidney	UBERON:0000082	71.99	gold quality
cortex of kidney	UBERON:0001225	71.81	gold quality
calcaneal tendon	UBERON:0003701	71.78	gold quality
mucosa of transverse colon	UBERON:0004991	71.38	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.28

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

Target	Regulation
ABCC3
MMP23B
SLC39A10
SLU7

JASPAR motifs

Motif	Name	Family
MA2580.1	ZNF20	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605530

Upstream regulators (CollecTRI, top): CTCF

miRNA regulators (miRDB)

75 targeting ZNF20, 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-4262	100.00	73.26	3931
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-6512-3P	99.65	66.07	1468

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp78	ENSMUSG00000055150
rattus_norvegicus		ENSRNOG00000083797
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), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), 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 20 — P17024 (reviewed: P17024)

Alternative names: Zinc finger protein KOX13

All UniProt accessions (4): C9JIP4, P17024, F8WDZ5, M0QYR3

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 (2): NP_001190179, NP_066966* (*=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
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352, PF13894, PF13912

UniProt features (17 total): zinc finger region 15, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17024-F1	72.48	0.35

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 47 (showing top): BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, ATTCTTT_MIR186, BROWNE_HCMV_INFECTION_14HR_UP, CHEN_HOXA5_TARGETS_9HR_UP, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, BROWNE_HCMV_INFECTION_48HR_UP, VERHAAK_GLIOBLASTOMA_CLASSICAL, CTIP_DN.V1_UP, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CIITA_TARGET_GENES, HMG20B_TARGET_GENES, MIR548AJ_3P_MIR548X_3P

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

264 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF20	ZNF518A	Q6AHZ1	371
ZNF20	COMMD5	Q9GZQ3	363
ZNF20	TNRC18	O15417	354
ZNF20	KIAA1549L	Q6ZVL6	349
ZNF20	RPS7	P23821	346
ZNF20	SLC66A1	Q6ZP29	321
ZNF20	JAZF1	Q86VZ6	313
ZNF20	NFXL1	Q6ZNB6	298
ZNF20	TSNARE1	Q96NA8	270
ZNF20	GNL3L	Q9NVN8	269
ZNF20	MFAP1	P55081	268
ZNF20	BFAR	Q9NZS9	252
ZNF20	TUBGCP4	Q9UGJ1	247
ZNF20	PELO	Q9BRX2	246
ZNF20	RNF34	Q969K3	246

IntAct

175 interactions, top by confidence:

A	B	Type	Score
CCDC102B	ZNF20	psi-mi:“MI:0915”(physical association)	0.720
CCNDBP1	ZNF20	psi-mi:“MI:0915”(physical association)	0.720
ZNF20	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.720
ZNF20	TRAF1	psi-mi:“MI:0915”(physical association)	0.720
ZNF20	CCDC102B	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-8	ZNF20	psi-mi:“MI:0915”(physical association)	0.720
TRAF1	ZNF20	psi-mi:“MI:0915”(physical association)	0.720
HEMGN	NPM1	psi-mi:“MI:0914”(association)	0.600
ZNF20	FSD2	psi-mi:“MI:0915”(physical association)	0.560
KRT38	ZNF20	psi-mi:“MI:0915”(physical association)	0.560
ZNF20	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.560
ZNF20	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	ZNF20	psi-mi:“MI:0915”(physical association)	0.560
KRT31	ZNF20	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	ZNF20	psi-mi:“MI:0915”(physical association)	0.560
ZNF20	KRT40	psi-mi:“MI:0915”(physical association)	0.560
ZNF20	CCDC136	psi-mi:“MI:0915”(physical association)	0.560
KRTAP4-12	ZNF20	psi-mi:“MI:0915”(physical association)	0.560
LZTS2	ZNF20	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (49): ZNF20 (Two-hybrid), ZNF20 (Two-hybrid), ZNF20 (Two-hybrid), KRT38 (Two-hybrid), MTUS2 (Two-hybrid), CCNDBP1 (Two-hybrid), CCDC136 (Two-hybrid), CCDC102B (Two-hybrid), KRTAP4-12 (Two-hybrid), LZTS2 (Two-hybrid), KRTAP4-2 (Two-hybrid), FSD2 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-9 (Two-hybrid)

ESM2 similar proteins: A6NK75, A6NNF4, A6NP11, A8MTY0, A8MUV8, B4DX44, B4DXR9, O43361, O75346, O75373, O75437, O95780, P0DKX0, P0DPD5, P17019, P17024, Q02386, Q03923, Q03924, Q03936, Q03938, Q14593, Q15928, Q3SXZ3, Q68DY1, Q6JLC9, Q6ZMV8, Q6ZN08, Q7L945, Q86T29, Q86V71, Q8BZW4, Q8IW36, Q8IYN0, Q8N8Z8, Q8NEM1, Q8TB69, Q8TC21, Q8TD23, Q8TF32

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 54 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	10	17.4×	2e-08

GO biological processes:

GO term	Partners	Fold	FDR
intermediate filament organization	5	28.7×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

3571 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12132890:G:C	F432L	0.994
19:12132890:G:T	F432L	0.994
19:12132892:A:G	F432L	0.994
19:12133142:G:C	F348L	0.993
19:12133142:G:T	F348L	0.993
19:12133144:A:G	F348L	0.993
19:12132722:A:C	F488L	0.991
19:12132722:A:T	F488L	0.991
19:12132724:A:G	F488L	0.991
19:12132806:G:C	F460L	0.991
19:12132806:G:T	F460L	0.991
19:12132808:A:G	F460L	0.991
19:12133226:A:C	F320L	0.991
19:12133226:A:T	F320L	0.991
19:12133228:A:G	F320L	0.991
19:12132641:A:C	F515L	0.990
19:12132641:A:T	F515L	0.990
19:12132643:A:G	F515L	0.990
19:12133058:A:C	F376L	0.990
19:12133058:A:T	F376L	0.990
19:12133060:A:G	F376L	0.990
19:12133478:A:C	F236L	0.988
19:12133478:A:T	F236L	0.988
19:12133480:A:G	F236L	0.988
19:12132767:G:C	H473Q	0.986
19:12132767:G:T	H473Q	0.986
19:12132851:G:C	H445Q	0.984
19:12132851:G:T	H445Q	0.984
19:12135860:G:C	F16L	0.984
19:12135860:G:T	F16L	0.984

dbSNP variants (sampled 300 via entrez): RS1000003116 (19:12131343 C>A), RS1000557516 (19:12142062 C>T), RS1000749406 (19:12136439 T>G), RS1000951901 (19:12134614 G>A,T), RS1001159276 (19:12140640 T>G), RS1001663241 (19:12137173 G>A), RS1001841059 (19:12131152 G>A,C,T), RS1001928631 (19:12136194 T>C), RS1001950425 (19:12135857 G>A,T), RS1003177900 (19:12132468 C>A,G), RS1003283165 (19:12138969 A>G,T), RS1003518632 (19:12138469 C>A), RS1003846917 (19:12135356 G>C), RS1003951177 (19:12141920 G>C), RS1004003420 (19:12141632 T>C)

Disease associations

OMIM: gene MIM:194557 | 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

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	decreases expression	2
Valproic Acid	decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
sulforaphane	increases expression	1
resorcinol	decreases expression	1
CGP 52608	affects binding, increases reaction	1
clothianidin	increases expression	1
MT19c compound	increases expression	1
Benzo(a)pyrene	affects methylation	1
Copper	affects binding, decreases expression	1
Disulfiram	affects binding, decreases expression	1
Formaldehyde	decreases expression	1
Phenylmercuric Acetate	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Cadmium Chloride	increases expression	1
Acrylamide	increases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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