ZNF860

Summary

ZNF860 (zinc finger protein 860, HGNC:34513) is a protein-coding gene on chromosome 3p24.1, encoding Zinc finger protein 860 (A6NHJ4). 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 344787 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• MANE Select transcript: NM_001137674

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34513
Approved symbol	ZNF860
Name	zinc finger protein 860
Location	3p24.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000197385
Ensembl biotype	protein_coding
Entrez	344787

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000360311, ENST00000489408, ENST00000912157, ENST00000912158

RefSeq mRNA: 1 — MANE Select: NM_001137674 NM_001137674

CCDS: CCDS46784

Canonical transcript exons

ENST00000360311 — 2 exons

Exon	Start	End
ENSE00001402366	31988660	31991723
ENSE00001740301	31981750	31981902

Expression profiles

Bgee: expression breadth ubiquitous, 121 present calls, max score 74.75.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0893 / max 117.9256, expressed in 580 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
35867	2.0893	580

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.75	gold quality
cortical plate	UBERON:0005343	73.28	gold quality
lymph node	UBERON:0000029	71.43	gold quality
islet of Langerhans	UBERON:0000006	68.90	gold quality
calcaneal tendon	UBERON:0003701	68.71	gold quality
tonsil	UBERON:0002372	68.01	gold quality
endometrium	UBERON:0001295	67.90	gold quality
lower esophagus mucosa	UBERON:0035834	67.39	gold quality
esophagus mucosa	UBERON:0002469	66.87	gold quality
placenta	UBERON:0001987	66.21	gold quality
vermiform appendix	UBERON:0001154	65.72	gold quality
quadriceps femoris	UBERON:0001377	65.49	gold quality
urinary bladder	UBERON:0001255	65.05	gold quality
thymus	UBERON:0002370	64.75	silver quality
cerebellar vermis	UBERON:0004720	64.61	gold quality
rectum	UBERON:0001052	63.49	gold quality
smooth muscle tissue	UBERON:0001135	63.37	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	62.72	gold quality
minor salivary gland	UBERON:0001830	62.59	gold quality
saliva-secreting gland	UBERON:0001044	62.17	gold quality
prostate gland	UBERON:0002367	61.93	gold quality
metanephros cortex	UBERON:0010533	61.54	gold quality
spleen	UBERON:0002106	61.05	gold quality
pituitary gland	UBERON:0000007	61.04	gold quality
adenohypophysis	UBERON:0002196	61.03	gold quality
cortex of kidney	UBERON:0001225	60.79	gold quality
adult mammalian kidney	UBERON:0000082	60.36	gold quality
bone marrow cell	CL:0002092	60.27	silver quality
kidney	UBERON:0002113	60.26	gold quality
fallopian tube	UBERON:0003889	59.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.42

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

48 targeting ZNF860, 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-3134	100.00	66.43	777
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-548J-3P	99.94	72.61	4881
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-335-3P	99.93	73.36	4958
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-4728-3P	99.47	68.94	981
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-155-5P	99.35	70.16	1509
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-580-5P	99.28	70.94	1776
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-3978	99.24	68.39	2201

Literature-anchored findings (GeneRIF, showing 1)

• The gastric cancer (GC) tissues had significantly upregulated ZNF860 expression. High ZNF860 RNA expression was independently associated with shorter recurrence-free survival in patients with early GC. Six genes (OSBPL10, FAM208A, TOPBP1, SPTY2D1, NAB1, and CMTM6) were positively co-expressed with ZNF860, suggesting that ZNF860 probably acts as a transcription enhancer in GC. (PMID:30767193)

Cross-species orthologs

0 orthologs

Paralogs (11): ZNF761 (ENSG00000160336), ZNF701 (ENSG00000167562), ZNF816 (ENSG00000180257), ZNF766 (ENSG00000196214), ZNF765 (ENSG00000196417), ZNF813 (ENSG00000198346), ZNF525 (ENSG00000203326), ZNF468 (ENSG00000204604), ZNF888 (ENSG00000213793), ZNF578 (ENSG00000258405), (ENSG00000269825)

Protein

Protein identifiers

Zinc finger protein 860 — A6NHJ4 (reviewed: A6NHJ4)

All UniProt accessions (1): A6NHJ4

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 (1): NP_001131146* (*=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 (19 total): zinc finger region 14, sequence conflict 2, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NHJ4-F1	63.66	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 (1): 220

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 36 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, BARX1_TARGET_GENES, CREB3L4_TARGET_GENES, GREB1_TARGET_GENES, HMG20B_TARGET_GENES, HOXB4_TARGET_GENES, HOXC6_TARGET_GENES, ZNF2_TARGET_GENES, ZNF513_TARGET_GENES, MIR5582_3P, MIR4698, MIR2115_3P, MIR580_5P, MIR3978

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

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF860	OR4F6	Q8NGB9	621
ZNF860	LRRC58	Q96CX6	541
ZNF860	OSBPL10	Q9BXB5	507
ZNF860	MAMLD1	Q13495	473
ZNF860	OR52E4	Q8NGH9	432
ZNF860	CAND2	O75155	392
ZNF860	MED8	Q96G25	387
ZNF860	TOPAZ1	Q8N9V7	375
ZNF860	RBM44	Q6ZP01	375
ZNF860	SPTY2D1	Q68D10	375
ZNF860	KIAA1328	Q86T90	370
ZNF860	TAFA4	Q96LR4	370
ZNF860	LPGAT1	Q92604	369
ZNF860	MOB3C	Q70IA8	366
ZNF860	ACAD10	Q6JQN1	349

IntAct

7 interactions, top by confidence:

A	B	Type	Score
ZNF860	CEP70	psi-mi:“MI:0915”(physical association)	0.560
ZNF860	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.560
ZNF860	CEP70	psi-mi:“MI:0915”(physical association)	0.000
ZNF860	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.000
CEP70	ZNF860	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): ZNF860 (Affinity Capture-RNA), ZNF860 (Affinity Capture-RNA), ZNF860 (Two-hybrid), KRTAP10-9 (Two-hybrid)

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, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

98 predictions. Top by Δscore:

Variant	Effect	Δscore
3:31981850:G:T	donor_gain	0.9900
3:31981900:CAGG:C	donor_loss	0.9900
3:31981901:AGGT:A	donor_loss	0.9900
3:31981903:GTA:G	donor_loss	0.9900
3:31983081:GCCA:G	donor_gain	0.9900
3:31983087:T:A	donor_gain	0.9800
3:31981903:G:GG	donor_gain	0.9700
3:31981849:G:GT	donor_gain	0.9600
3:31983084:A:AG	donor_gain	0.9600
3:31983085:G:GG	donor_gain	0.9600
3:31981893:A:AG	donor_gain	0.9400
3:31981880:G:T	donor_gain	0.9300
3:31988658:A:AG	acceptor_gain	0.8400
3:31988659:G:GG	acceptor_gain	0.8400
3:31988659:GTCA:G	acceptor_gain	0.8400
3:31988659:GT:G	acceptor_gain	0.8300
3:31988658:A:T	acceptor_gain	0.8100
3:31988654:CATCA:C	acceptor_gain	0.8000
3:31988655:ATCAG:A	acceptor_gain	0.7900
3:31988656:TCAGT:T	acceptor_gain	0.7900
3:31988657:CAG:C	acceptor_gain	0.7900
3:31988659:GTC:G	acceptor_gain	0.7800
3:31988653:T:G	acceptor_gain	0.7700
3:31988659:G:T	acceptor_gain	0.7700
3:31988652:A:AG	acceptor_gain	0.7600
3:31986236:T:G	acceptor_gain	0.7500
3:31981894:T:G	donor_gain	0.7400
3:31981900:CAG:C	donor_gain	0.7400
3:31988658:A:AC	acceptor_loss	0.6900
3:31988659:G:A	acceptor_loss	0.6900

AlphaMissense

4262 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:31990214:T:C	F379L	0.996
3:31990216:T:A	F379L	0.996
3:31990216:T:G	F379L	0.996
3:31990466:T:C	F463L	0.995
3:31990468:C:A	F463L	0.995
3:31990468:C:G	F463L	0.995
3:31990130:T:C	F351L	0.994
3:31990132:C:A	F351L	0.994
3:31990132:C:G	F351L	0.994
3:31990046:T:C	F323L	0.993
3:31990048:T:A	F323L	0.993
3:31990048:T:G	F323L	0.993
3:31990416:G:C	R446P	0.993
3:31990550:T:C	F491L	0.993
3:31990552:C:A	F491L	0.993
3:31990552:C:G	F491L	0.993
3:31990137:G:C	R353P	0.986
3:31990493:C:G	H472D	0.986
3:31990634:T:C	F519L	0.985
3:31990636:T:A	F519L	0.985
3:31990636:T:G	F519L	0.985
3:31989962:T:C	F295L	0.984
3:31989964:T:A	F295L	0.984
3:31989964:T:G	F295L	0.984
3:31990159:C:A	H360Q	0.982
3:31990159:C:G	H360Q	0.982
3:31990485:T:C	L469P	0.981
3:31990493:C:A	H472N	0.980
3:31990725:G:C	R549P	0.980
3:31990389:G:C	R437P	0.979

dbSNP variants (sampled 300 via entrez): RS1000035986 (3:32000455 A>G), RS1000156100 (3:31994646 T>C,G), RS1000298873 (3:31986028 T>C), RS1000374836 (3:31980699 G>A), RS1000405524 (3:32000778 C>A,T), RS1000412357 (3:31980557 C>A), RS1000504620 (3:32000525 A>G), RS1000505626 (3:31982711 A>G), RS1000736976 (3:32005620 A>G,T), RS1000830435 (3:32005794 A>G), RS1000902423 (3:31988606 C>G,T), RS1001103977 (3:31992734 C>G), RS1001118391 (3:31994517 G>A), RS1001119364 (3:32006851 C>T), RS1001344196 (3:32003949 G>A,C)

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

3 associations (top):

Study	Trait	p-value
GCST002312_8	Periodontal disease-related phenotype (Socransky)	6.000000e-06
GCST004946_13	Schizophrenia	3.000000e-08
GCST012174_1	Diabetic retinopathy in type 2 diabetes	7.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	2
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
ethyl-p-hydroxybenzoate	increases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
licochalcone B	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Temozolomide	decreases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Smoke	increases expression	1
Urethane	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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