ZNF10

Summary

ZNF10 (zinc finger protein 10, HGNC:12879) is a protein-coding gene on chromosome 12q24.33, encoding Zinc finger protein 10 (P21506). May be involved in transcriptional regulation.

The protein encoded by this gene contains a C2H2 zinc finger, and has been shown to function as a transcriptional repressor. The Kruppel-associated box (KRAB) domain of this protein is found to be responsible for its transcriptional repression activity. RING finger containing protein TIF1 was reported to interact with the KRAB domain, and may serve as a mediator for the repression activity of this protein.

Source: NCBI Gene 7556 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 33 total — 1 likely-pathogenic
• MANE Select transcript: NM_015394

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12879
Approved symbol	ZNF10
Name	zinc finger protein 10
Location	12q24.33
Locus type	gene with protein product
Status	Approved
Aliases	KOX1
Ensembl gene	ENSG00000256223
Ensembl biotype	protein_coding
OMIM	194538
Entrez	7556

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 21 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000248211, ENST00000402932, ENST00000426665, ENST00000536704, ENST00000536877, ENST00000537119, ENST00000538918, ENST00000540609, ENST00000540927, ENST00000543271, ENST00000869334, ENST00000869335, ENST00000869336, ENST00000869337, ENST00000869338, ENST00000869339, ENST00000869340, ENST00000915347, ENST00000915348, ENST00000915349, ENST00000915350, ENST00000962635, ENST00000962636, ENST00000962637, ENST00000962638

RefSeq mRNA: 1 — MANE Select: NM_015394 NM_015394

CCDS: CCDS9283

Canonical transcript exons

ENST00000248211 — 5 exons

Exon	Start	End
ENSE00001287780	133155503	133159465
ENSE00002310325	133130627	133130754
ENSE00003472870	133144434	133144525
ENSE00003617170	133151028	133151154
ENSE00003688266	133151809	133151904

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 93.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.2660 / max 222.0225, expressed in 1568 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128859	7.5686	1464
128858	1.6973	850

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	93.51	gold quality
pituitary gland	UBERON:0000007	92.90	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.53	gold quality
right lobe of thyroid gland	UBERON:0001119	89.44	gold quality
left lobe of thyroid gland	UBERON:0001120	89.42	gold quality
thyroid gland	UBERON:0002046	88.56	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.89	gold quality
left ovary	UBERON:0002119	87.70	gold quality
right uterine tube	UBERON:0001302	87.60	gold quality
right ovary	UBERON:0002118	86.92	gold quality
body of pancreas	UBERON:0001150	86.74	gold quality
mucosa of stomach	UBERON:0001199	86.67	gold quality
secondary oocyte	CL:0000655	86.45	gold quality
popliteal artery	UBERON:0002250	85.95	gold quality
tibial artery	UBERON:0007610	85.95	gold quality
body of uterus	UBERON:0009853	85.49	gold quality
cortical plate	UBERON:0005343	85.46	gold quality
left uterine tube	UBERON:0001303	85.40	gold quality
aorta	UBERON:0000947	85.10	gold quality
endocervix	UBERON:0000458	85.00	gold quality
ovary	UBERON:0000992	84.96	gold quality
metanephros cortex	UBERON:0010533	84.92	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.70	gold quality
thoracic aorta	UBERON:0001515	84.26	gold quality
right coronary artery	UBERON:0001625	84.25	gold quality
ascending aorta	UBERON:0001496	84.23	gold quality
descending thoracic aorta	UBERON:0002345	84.13	gold quality
muscle layer of sigmoid colon	UBERON:0035805	83.55	gold quality
body of stomach	UBERON:0001161	83.16	gold quality
calcaneal tendon	UBERON:0003701	83.09	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.67

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
CD74

miRNA regulators (miRDB)

107 targeting ZNF10, 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-340-5P	100.00	72.50	4437
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-548AW	99.99	72.57	3559
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-493-5P	99.96	72.47	2382
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-338-5P	99.92	72.34	2951

Literature-anchored findings (GeneRIF, showing 3)

• Data indicate that Xenopus laevis XFIN-AB displayed reduced potency in repression compared to human ZNF10 KRAB-AB. (PMID:24498343)
• results indicate that ZNF10 could be involved in a potent intrinsic antiretroviral defense (PMID:26096782)
• The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. (PMID:35162997)

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), 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)

Protein

Protein identifiers

Zinc finger protein 10 — P21506 (reviewed: P21506)

Alternative names: Zinc finger protein KOX1

All UniProt accessions (5): P21506, F5GZ75, F5H0R3, F5H311, F8WD46

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subunit / interactions. Interacts (via the KRAB domain) with TRIM28 (via the RBCC domain).

Subcellular location. Nucleus.

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

RefSeq proteins (1): NP_056209* (*=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, PF13465

UniProt features (17 total): zinc finger region 11, sequence conflict 3, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P21506-F1	63.45	0.17

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 71 (showing top): MORF_ZNF10, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, BROWNE_HCMV_INFECTION_10HR_UP, MORF_DCC, chr12q24, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, PDGF_UP.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, E2F5_TARGET_GENES, PAX3_TARGET_GENES, PCGF1_TARGET_GENES, SKIL_TARGET_GENES, ZIM3_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944)

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), transcription cis-regulatory region binding (GO:0000976), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), protein-containing complex (GO:0032991)

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
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	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
transition metal ion binding	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
cellular_component	1

Protein interactions and networks

STRING

384 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF10	TRIM28	Q13263	930
ZNF10	SETDB1	Q15047	734
ZNF10	TRIM24	O15164	596
ZNF10	TRIM33	Q9UPN9	595
ZNF10	RNF215	Q9Y6U7	584
ZNF10	TMPRSS12	Q86WS5	544
ZNF10	GTF3C3	Q9Y5Q9	487
ZNF10	ERGIC2	Q96RQ1	473
ZNF10	ZZZ3	Q8IYH5	446
ZNF10	KMT5B	Q4FZB7	424
ZNF10	KMT5C	Q86Y97	424
ZNF10	TRAT1	Q6PIZ9	396
ZNF10	ZNF438	Q7Z4V0	392
ZNF10	KAT8	Q9H7Z6	383
ZNF10	PRR22	Q8IZ63	367

IntAct

13 interactions, top by confidence:

A	B	Type	Score
ZNF10	CARD10	psi-mi:“MI:0915”(physical association)	0.560
ZNF10	TRIM28	psi-mi:“MI:0915”(physical association)	0.550
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF10	Trim24	psi-mi:“MI:0915”(physical association)	0.370
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
ZNF10	NES	psi-mi:“MI:0914”(association)	0.350
ZNF10	NDEL1	psi-mi:“MI:0915”(physical association)	0.000
FMR1	ZNF10	psi-mi:“MI:0915”(physical association)	0.000
NDEL1	ZNF10	psi-mi:“MI:0915”(physical association)	0.000
ZNF10	CARD10	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (29): TRIM28 (Two-hybrid), TRIM24 (Two-hybrid), ZNF10 (Two-hybrid), TRIM28 (Reconstituted Complex), TRIM28 (Co-purification), ZNF10 (Affinity Capture-Western), USP34 (Affinity Capture-MS), NES (Affinity Capture-MS), SETD2 (Affinity Capture-MS), HDAC6 (Affinity Capture-MS), PACSIN2 (Affinity Capture-MS), SRY (Reconstituted Complex), Sry (Reconstituted Complex), TRIM28 (Reconstituted Complex), ZNF10 (Affinity Capture-Western)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	20
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
563980	GRCh37/hg19 12q24.33(chr12:130973400-133777902)x3	Likely pathogenic

SpliceAI

1195 predictions. Top by Δscore:

Variant	Effect	Δscore
12:133144432:A:AG	acceptor_gain	1.0000
12:133144433:G:GG	acceptor_gain	1.0000
12:133144433:GC:G	acceptor_gain	1.0000
12:133144433:GCT:G	acceptor_gain	1.0000
12:133144433:GCTT:G	acceptor_gain	1.0000
12:133144433:GCTTT:G	acceptor_gain	1.0000
12:133144496:GATGC:G	donor_gain	1.0000
12:133144524:GG:G	donor_gain	1.0000
12:133144525:GG:G	donor_gain	1.0000
12:133151021:GTTGT:G	acceptor_loss	1.0000
12:133151022:TTGTA:T	acceptor_loss	1.0000
12:133151023:TGTA:T	acceptor_loss	1.0000
12:133151025:TA:T	acceptor_loss	1.0000
12:133151025:TAGAC:T	acceptor_loss	1.0000
12:133151026:A:AG	acceptor_gain	1.0000
12:133151026:A:AT	acceptor_loss	1.0000
12:133151026:A:C	acceptor_loss	1.0000
12:133151027:G:GA	acceptor_gain	1.0000
12:133151027:GAC:G	acceptor_gain	1.0000
12:133151027:GACA:G	acceptor_gain	1.0000
12:133151027:GACAC:G	acceptor_gain	1.0000
12:133151153:GG:G	donor_gain	1.0000
12:133151153:GGGTA:G	donor_loss	1.0000
12:133151154:GG:G	donor_gain	1.0000
12:133151155:G:GA	donor_loss	1.0000
12:133151155:G:GC	donor_loss	1.0000
12:133151155:G:GG	donor_gain	1.0000
12:133151156:TAAGA:T	donor_loss	1.0000
12:133151798:A:AG	acceptor_gain	1.0000
12:133151798:ACT:A	acceptor_gain	1.0000

AlphaMissense

3829 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:133156654:T:C	F470L	0.999
12:133156656:C:A	F470L	0.999
12:133156656:C:G	F470L	0.999
12:133156738:T:C	F498L	0.998
12:133156740:C:A	F498L	0.998
12:133156740:C:G	F498L	0.998
12:133156757:T:C	L504P	0.998
12:133156234:T:C	F330L	0.997
12:133156236:C:A	F330L	0.997
12:133156236:C:G	F330L	0.997
12:133156402:T:C	F386L	0.997
12:133156404:C:A	F386L	0.997
12:133156404:C:G	F386L	0.997
12:133156505:T:C	L420P	0.997
12:133156570:T:C	F442L	0.997
12:133156572:T:A	F442L	0.997
12:133156572:T:G	F442L	0.997
12:133156597:C:G	H451D	0.997
12:133156599:T:A	H451Q	0.997
12:133156599:T:G	H451Q	0.997
12:133156673:T:C	L476P	0.997
12:133156685:A:C	Q480P	0.997
12:133156577:G:C	R444P	0.996
12:133156589:T:C	L448P	0.996
12:133156150:T:C	F302L	0.995
12:133156152:C:A	F302L	0.995
12:133156152:C:G	F302L	0.995
12:133156421:T:C	L392P	0.995
12:133156527:C:A	H427Q	0.995
12:133156527:C:G	H427Q	0.995

dbSNP variants (sampled 300 via entrez): RS1000047427 (12:133131470 ATACTGT>A), RS1000080748 (12:133130706 T>G), RS1000134559 (12:133130550 A>C), RS1000192111 (12:133149077 A>AGTT), RS1000228124 (12:133149280 C>T), RS1000333066 (12:133149237 G>A), RS1000391025 (12:133143047 T>A,C), RS1000457215 (12:133155602 A>G,T), RS1000508647 (12:133150593 A>G), RS1000737462 (12:133157183 A>G), RS1000806953 (12:133155250 T>C), RS1000966761 (12:133137844 C>G), RS1001020478 (12:133143795 C>T), RS1001082659 (12:133132034 A>G), RS1001146516 (12:133137036 TC>T)

Disease associations

OMIM: gene MIM:194538 | 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
GCST010002_179	Refractive error	1.000000e-12

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
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
trichostatin A	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
cupric oxide	increases expression	1
hydroquinone	decreases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cadmium	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Mercury	decreases expression	1
Methotrexate	increases expression	1
Plant Oils	increases expression	1
Thiram	increases expression	1
Urethane	increases expression	1
Valproic Acid	decreases expression	1
Vitamin E	decreases expression	1
Antirheumatic Agents	increases expression	1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TZ34	HAP1 ZNF10 (-)	Cancer cell line	Male
CVCL_XW00	HEK293 eGFP-ZNF10	Transformed cell line	Female

Clinical trials (associated diseases)

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