ZNF460

Summary

ZNF460 (zinc finger protein 460, HGNC:21628) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 460 (Q14592). May be involved in transcriptional regulation.

Zinc finger proteins, such as ZNF272, interact with nucleic acids and have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form 1 family of zinc finger proteins. See ZFP93 (MIM 604749) for additional information on zinc finger proteins.

Source: NCBI Gene 10794 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_006635

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21628
Approved symbol	ZNF460
Name	zinc finger protein 460
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	HZF8
Ensembl gene	ENSG00000197714
Ensembl biotype	protein_coding
OMIM	604755
Entrez	10794

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000360338, ENST00000537645, ENST00000599602, ENST00000950772

RefSeq mRNA: 2 — MANE Select: NM_006635 NM_001330622, NM_006635

CCDS: CCDS12949, CCDS82404

Canonical transcript exons

ENST00000360338 — 3 exons

Exon	Start	End
ENSE00001405062	57280485	57280836
ENSE00001418334	57290699	57294069
ENSE00003694151	57284551	57284677

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 91.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.9130 / max 350.1447, expressed in 1812 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177753	12.9453	1776
177751	11.7271	1779
177750	1.7848	1073
177755	1.2265	680
177754	0.8813	547
177759	0.6810	404
177756	0.2640	119
177757	0.2254	87
177758	0.1076	32
177752	0.0700	24

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	91.44	gold quality
colonic epithelium	UBERON:0000397	91.43	gold quality
calcaneal tendon	UBERON:0003701	91.38	gold quality
sural nerve	UBERON:0015488	90.94	gold quality
tendon	UBERON:0000043	89.87	gold quality
tendon of biceps brachii	UBERON:0008188	89.39	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.35	gold quality
bone marrow cell	CL:0002092	81.07	gold quality
medial globus pallidus	UBERON:0002477	78.44	gold quality
buccal mucosa cell	CL:0002336	77.86	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.80	gold quality
cortical plate	UBERON:0005343	75.43	gold quality
ventricular zone	UBERON:0003053	74.32	gold quality
corpus callosum	UBERON:0002336	73.17	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.10	gold quality
stromal cell of endometrium	CL:0002255	71.23	gold quality
ganglionic eminence	UBERON:0004023	71.09	gold quality
tonsil	UBERON:0002372	70.94	gold quality
globus pallidus	UBERON:0001875	70.52	gold quality
monocyte	CL:0000576	70.44	gold quality
mononuclear cell	CL:0000842	70.25	gold quality
leukocyte	CL:0000738	69.96	gold quality
islet of Langerhans	UBERON:0000006	69.89	gold quality
secondary oocyte	CL:0000655	68.23	gold quality
muscle of leg	UBERON:0001383	67.07	gold quality
gastrocnemius	UBERON:0001388	66.74	gold quality
left ovary	UBERON:0002119	65.15	gold quality
adrenal gland	UBERON:0002369	64.69	gold quality
omental fat pad	UBERON:0010414	64.38	gold quality
peritoneum	UBERON:0002358	64.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.18

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1596.1	ZNF460	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28473536

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

93 targeting ZNF460, 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-5193	100.00	67.26	1744
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
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-539-5P	99.93	70.30	2855
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-7-1-3P	99.91	71.53	4384

Literature-anchored findings (GeneRIF, showing 4)

• Molecular cloning and tissue distribution of ZNF460. (PMID:15004467)
• Circular RNA mitochondrial translation optimization 1 homologue (CircMTO1) induced by zinc finger protein 460 (ZNF460) promotes oral squamous cell carcinoma progression through the microRNA miR-320a / alpha thalassemia/mental retardation, X-linked (ATRX) axis. (PMID:34738503)
• ZNF460 mediates epithelial-mesenchymal transition to promote gastric cancer progression by transactivating APOC1 expression. (PMID:36563923)
• ZNF460-regulated COMMD7 Promotes Acute Myeloid Leukemia Proliferation Via the NF-kappaB Signaling Pathway. (PMID:37057209)

Cross-species orthologs

0 orthologs

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 460 — Q14592 (reviewed: Q14592)

Alternative names: Zinc finger protein 272, Zinc finger protein HZF8

All UniProt accessions (2): Q14592, M0R0J6

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitously expressed at low levels. Highest levels are found in pancreas and liver.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q14592-1	1	yes
Q14592-2	2

RefSeq proteins (2): NP_001317551, NP_006626* (*=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
IPR050331	Zinc_finger_PRDM4/PRDM1/PRDM14	Family

Pfam: PF00096, PF01352

UniProt features (30 total): cross-link 15, zinc finger region 11, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14592-F1	66.89	0.33

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 (15): 117, 194, 203, 207, 209, 250, 278, 287, 300, 305, 306, 362, 371, 446, 455

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 69 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP, PDGF_UP.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, ELF2_TARGET_GENES, FOXN3_TARGET_GENES, GLI3_TARGET_GENES, ID1_TARGET_GENES, KAT5_TARGET_GENES, NKX2_2_TARGET_GENES, ZBTB12_TARGET_GENES, ZFHX3_TARGET_GENES, ZNF10_TARGET_GENES, ZNF175_TARGET_GENES

GO Biological Process (2): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (7): 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), sequence-specific double-stranded DNA binding (GO:1990837), 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
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	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
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

442 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF460	SERINC1	Q9NRX5	543
ZNF460	DTWD2	Q8NBA8	447
ZNF460	CNOT6L	Q96LI5	447
ZNF460	VAPA	Q9P0L0	400
ZNF460	NUDT13	Q86X67	400
ZNF460	KLHL15	Q96M94	393
ZNF460	PLEKHJ1	Q9NW61	376
ZNF460	SLC35E4	Q6ICL7	371
ZNF460	ZMYND19	Q96E35	348
ZNF460	LMNTD1	Q8N9Z9	324
ZNF460	PPP1R35	Q8TAP8	323
ZNF460	K7EJK4	K7EJK4	321
ZNF460	SCAMP4	Q969E2	307
ZNF460	RBM12B	Q8IXT5	305
ZNF460	TMEM101	Q96IK0	305

IntAct

78 interactions, top by confidence:

A	B	Type	Score
ZNF460	TRIM41	psi-mi:“MI:0915”(physical association)	0.670
GPR156	PLD2	psi-mi:“MI:0914”(association)	0.640
IPO8	TRIM28	psi-mi:“MI:0914”(association)	0.640
SDC2	PDPK1	psi-mi:“MI:0914”(association)	0.640
ZNF250	ZNF460	psi-mi:“MI:0915”(physical association)	0.560
FGF12	ZNF460	psi-mi:“MI:0915”(physical association)	0.560
DEUP1	ZNF460	psi-mi:“MI:0915”(physical association)	0.560
ZNF460	ZNF250	psi-mi:“MI:0915”(physical association)	0.560
ZNF460	FGF12	psi-mi:“MI:0915”(physical association)	0.560
ZNF460	DEUP1	psi-mi:“MI:0915”(physical association)	0.560
ZNF460	ZNF330	psi-mi:“MI:0915”(physical association)	0.560
LMO1	ZNF460	psi-mi:“MI:0915”(physical association)	0.560
ZNF460	DMWD	psi-mi:“MI:0915”(physical association)	0.560
ZNF460	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
VWCE	ZNF316	psi-mi:“MI:0914”(association)	0.530
DCAF8	DCAF8L1	psi-mi:“MI:0914”(association)	0.530
PRICKLE3	SIAH2	psi-mi:“MI:0914”(association)	0.530
RPF1	ZNF324	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530

BioGRID (173): ZNF460 (Two-hybrid), ZNF250 (Two-hybrid), CCDC67 (Two-hybrid), ZNF460 (Affinity Capture-RNA), ZNF460 (Affinity Capture-RNA), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS)

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: 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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 67 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
Regulation of endogenous retroelements by KRAB-ZFP proteins	6	13.6×	8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

225 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57284676:GG:G	donor_gain	1.0000
19:57284677:GG:G	donor_gain	1.0000
19:57284678:G:C	donor_loss	1.0000
19:57284679:T:G	donor_loss	1.0000
19:57290694:TTCA:T	acceptor_loss	1.0000
19:57290695:TCAG:T	acceptor_loss	1.0000
19:57290696:CAG:C	acceptor_loss	1.0000
19:57280836:GGT:G	donor_loss	0.9900
19:57280837:G:GG	donor_gain	0.9900
19:57284547:TCAG:T	acceptor_loss	0.9900
19:57284548:CA:C	acceptor_loss	0.9900
19:57284549:A:AC	acceptor_loss	0.9900
19:57284550:G:T	acceptor_loss	0.9900
19:57284550:GGA:G	acceptor_gain	0.9900
19:57284678:G:GG	donor_gain	0.9900
19:57290697:A:AG	acceptor_gain	0.9900
19:57290698:G:GA	acceptor_gain	0.9900
19:57290698:GGT:G	acceptor_gain	0.9900
19:57280833:GCAG:G	donor_gain	0.9800
19:57284540:T:TA	acceptor_gain	0.9800
19:57284549:A:AG	acceptor_gain	0.9800
19:57284549:AG:A	acceptor_gain	0.9800
19:57284550:G:GG	acceptor_gain	0.9800
19:57284550:GG:G	acceptor_gain	0.9800
19:57284550:GGAGT:G	acceptor_gain	0.9800
19:57290683:ATTGT:A	acceptor_gain	0.9800
19:57290687:T:TA	acceptor_gain	0.9800
19:57290695:TCAGG:T	acceptor_gain	0.9800
19:57290696:CAGG:C	acceptor_gain	0.9800
19:57290697:AG:A	acceptor_gain	0.9800

AlphaMissense

3750 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57291406:T:C	F289L	0.999
19:57291408:T:A	F289L	0.999
19:57291408:T:G	F289L	0.999
19:57291658:T:C	F373L	0.999
19:57291660:C:A	F373L	0.999
19:57291660:C:G	F373L	0.999
19:57291742:T:C	F401L	0.999
19:57291744:T:A	F401L	0.999
19:57291744:T:G	F401L	0.999
19:57291761:T:C	L407P	0.999
19:57291910:T:C	F457L	0.999
19:57291912:T:A	F457L	0.999
19:57291912:T:G	F457L	0.999
19:57291994:T:C	F485L	0.999
19:57291996:C:A	F485L	0.999
19:57291996:C:G	F485L	0.999
19:57291238:T:C	F233L	0.998
19:57291240:C:A	F233L	0.998
19:57291240:C:G	F233L	0.998
19:57291322:T:C	F261L	0.998
19:57291324:C:A	F261L	0.998
19:57291324:C:G	F261L	0.998
19:57291608:G:C	R356P	0.998
19:57291826:T:C	F429L	0.998
19:57291828:T:A	F429L	0.998
19:57291828:T:G	F429L	0.998
19:57291245:G:C	R235P	0.997
19:57291490:T:C	F317L	0.997
19:57291492:T:A	F317L	0.997
19:57291492:T:G	F317L	0.997

dbSNP variants (sampled 300 via entrez): RS1000115705 (19:57283261 C>T), RS1000184005 (19:57287956 T>C), RS1000336512 (19:57281029 G>C), RS1001224352 (19:57284107 A>G), RS1001302417 (19:57279600 T>G), RS1001445360 (19:57289618 C>T), RS1001534395 (19:57293107 G>A), RS1001693583 (19:57287853 G>A), RS1001753460 (19:57282588 G>A), RS1001894980 (19:57289209 A>G), RS1002125047 (19:57280256 C>G), RS1002226675 (19:57285440 T>C), RS1002279119 (19:57285099 A>G), RS1002279828 (19:57278884 G>A), RS1002309322 (19:57279087 G>A)

Disease associations

OMIM: gene MIM:604755 | 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
GCST006979_687	Heel bone mineral density	3.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	3
Cadmium Chloride	increases abundance, increases expression	3
sodium arsenite	increases abundance, increases expression	2
Cisplatin	affects cotreatment, decreases expression	2
Estradiol	increases expression	2
Tobacco Smoke Pollution	increases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
titanium dioxide	decreases methylation	1
trichostatin A	decreases expression	1
perfluorooctanoic acid	increases expression	1
manganese chloride	decreases expression, increases abundance	1
resorcinol	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
corosolic acid	decreases expression	1
bisphenol B	increases expression	1
abrine	increases expression	1
bisphenol Z	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Cadmium	increases expression, increases abundance	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Manganese	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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