ZNF264

gene
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Also known as KIAA0412

Summary

ZNF264 (zinc finger protein 264, HGNC:13057) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 264 (O43296). May be involved in transcriptional regulation.

This gene encodes a zinc finger protein and belongs to the krueppel C2H2-type zinc-finger protein family. Zinc finger proteins are often localized in the nucleus, bind nucleic acids, and regulate transcription.

Source: NCBI Gene 9422 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 115 total
  • Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_003417

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13057
Approved symbolZNF264
Namezinc finger protein 264
Location19q13.43
Locus typegene with protein product
StatusApproved
AliasesKIAA0412
Ensembl geneENSG00000083844
Ensembl biotypeprotein_coding
OMIM604668
Entrez9422

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000263095, ENST00000594126, ENST00000597447, ENST00000599653, ENST00000600531

RefSeq mRNA: 1 — MANE Select: NM_003417 NM_003417

CCDS: CCDS33127

Canonical transcript exons

ENST00000263095 — 4 exons

ExonStartEnd
ENSE000013063085721135457222846
ENSE000013225915719150057191946
ENSE000024459595720539757205492
ENSE000024706175719387557194001

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 90.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.4549 / max 63.1018, expressed in 1744 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1777419.59021735
1777400.8647608

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233690.55gold quality
nippleUBERON:000203090.00gold quality
caput epididymisUBERON:000435888.12gold quality
bronchial epithelial cellCL:000232887.72gold quality
visceral pleuraUBERON:000240187.00gold quality
parietal pleuraUBERON:000240086.94gold quality
corpus epididymisUBERON:000435986.92gold quality
calcaneal tendonUBERON:000370186.20gold quality
pleuraUBERON:000097786.17gold quality
sural nerveUBERON:001548884.55gold quality
cauda epididymisUBERON:000436084.11gold quality
epithelium of bronchusUBERON:000203184.08gold quality
bronchusUBERON:000218584.01gold quality
mammalian vulvaUBERON:000099783.97gold quality
endothelial cellCL:000011583.68gold quality
renal medullaUBERON:000036283.62gold quality
corpus callosumUBERON:000233683.59gold quality
urethraUBERON:000005783.46gold quality
inferior vagus X ganglionUBERON:000536383.46gold quality
postcentral gyrusUBERON:000258183.33gold quality
adult organismUBERON:000702383.18gold quality
adrenal tissueUBERON:001830383.15gold quality
parietal lobeUBERON:000187283.11gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.08gold quality
superior surface of tongueUBERON:000737183.04gold quality
pylorusUBERON:000116682.88gold quality
lower lobe of lungUBERON:000894982.80gold quality
medial globus pallidusUBERON:000247782.61gold quality
tendonUBERON:000004382.59gold quality
seminal vesicleUBERON:000099882.28gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.94
E-MTAB-7303no111.21
E-MTAB-6142no18.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

351 targeting ZNF264, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-8485100.0077.574731
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3163100.0077.238605
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-5692A100.0074.406850
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4262100.0073.263931
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4533100.0069.482758
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3134100.0066.43777
HSA-MIR-4455100.0065.481587
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-453499.9966.581907
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-453199.9969.703181
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-450099.9972.722367

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
drosophila_melanogasterCG2712FBGN0024975
drosophila_melanogasterPhsFBGN0036522
drosophila_melanogasterCG3281FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), 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), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 264O43296 (reviewed: O43296)

All UniProt accessions (5): O43296, M0QXF3, M0QZJ4, M0QZT5, M0R146

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Relatively highly expressed in kidney, thymus, testis, ovary, brain, lung, placenta, and prostate, and relatively low expression in heart, liver, skeletal muscle, pancreas, spleen, and small intestine.

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

RefSeq proteins (1): NP_003408* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050758Znf_C2H2-typeFamily

Pfam: PF00096, PF01352

UniProt features (27 total): zinc finger region 13, region of interest 3, compositionally biased region 3, modified residue 3, sequence variant 2, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O43296-F166.720.10

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 (4): 80, 343, 511, 425

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway
R-HSA-9843940Regulation of endogenous retroelements by KRAB-ZFP proteins

MSigDB gene sets: 175 (showing top): MODULE_255, BROWNE_HCMV_INFECTION_8HR_UP, MODULE_317, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, MORF_ZNF10, BLALOCK_ALZHEIMERS_DISEASE_UP, MODULE_123, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, MORF_EPHA7, MORF_RAB3A, MORF_BMPR2, MORF_WNT1, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, MORF_IL9

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-2 pathways:

CategoryPathways
RNA Polymerase II Transcription1
Regulation of endogenous retroelements1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

742 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF264USP29Q9HBJ7449
ZNF264ZNF704Q6ZNC4399
ZNF264LYSMD1Q96S90348
ZNF264SLC67A1Q96BI1305
ZNF264C2CD2Q9Y426305
ZNF264ANKIB1Q9P2G1300
ZNF264ZC3H12CQ9C0D7295
ZNF264CAMSAP2Q08AD1288
ZNF264C2CD4CQ8TF44288
ZNF264INTS2Q9H0H0287
ZNF264MRPS12O15235277
ZNF264KIAA1549LQ6ZVL6276
ZNF264TMEM101Q96IK0274
ZNF264BTF3L4Q96K17271
ZNF264N4BP2L2Q92802267

IntAct

55 interactions, top by confidence:

ABTypeScore
ZNF264TRIM41psi-mi:“MI:0915”(physical association)0.740
ZNF264CEP70psi-mi:“MI:0915”(physical association)0.600
ZNF264ZNF175psi-mi:“MI:0915”(physical association)0.560
ZNF264KRTAP10-6psi-mi:“MI:0915”(physical association)0.560
ZNF264MCCpsi-mi:“MI:0915”(physical association)0.560
ZNF264KRTAP2-4psi-mi:“MI:0915”(physical association)0.560
GOLGA6L9ZNF264psi-mi:“MI:0915”(physical association)0.560
ZNF264KRTAP10-8psi-mi:“MI:0915”(physical association)0.560
ZNF264ZNF526psi-mi:“MI:0915”(physical association)0.560
IPO8ZNF264psi-mi:“MI:0915”(physical association)0.560
ZNF264KRTAP10-7psi-mi:“MI:0915”(physical association)0.560
ZNF264PICK1psi-mi:“MI:0915”(physical association)0.560
ZNF264MDFIpsi-mi:“MI:0915”(physical association)0.560
ZNF264DVL3psi-mi:“MI:0915”(physical association)0.560
ZNF264psi-mi:“MI:0915”(physical association)0.560
TRIM28ZNF320psi-mi:“MI:0914”(association)0.530
KRTAP10-1ZNF264psi-mi:“MI:0915”(physical association)0.370
ZNF264TRIM24psi-mi:“MI:0914”(association)0.350
CBX5ZNF568psi-mi:“MI:0914”(association)0.350
ZNF264CEP70psi-mi:“MI:0915”(physical association)0.000
ZNF264ZNF175psi-mi:“MI:0915”(physical association)0.000
ZNF264KRTAP10-6psi-mi:“MI:0915”(physical association)0.000
ZNF264MCCpsi-mi:“MI:0915”(physical association)0.000
ZNF264KRTAP2-4psi-mi:“MI:0915”(physical association)0.000
ZNF264GOLGA6L9psi-mi:“MI:0915”(physical association)0.000
ZNF264psi-mi:“MI:0915”(physical association)0.000
ZNF264KRTAP10-8psi-mi:“MI:0915”(physical association)0.000

BioGRID (60): ZNF264 (Two-hybrid), ZNF264 (Two-hybrid), ZNF264 (Two-hybrid), NDEL1 (Two-hybrid), TRIM41 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-1 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-3 (Two-hybrid), ZYG11A (Affinity Capture-MS), CENPB (Affinity Capture-MS), TRIM24 (Affinity Capture-MS), GOPC (Affinity Capture-MS), ZNF805 (Affinity Capture-MS), TRIM41 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, A6QLU5, B2RUI1, D3ZVT0, O14709, O43296, O75123, P10072, P15621, P17020, P17097, P51814, P85977, Q08ER8, Q0VGE8, Q14590, Q32KN0, Q3KQV3, Q4V8A8, Q5CZA5, Q5RBX0, Q5RCD9, Q5VIY5, Q61116, Q61967, Q6GQR8, Q6P9A3, Q6ZMS4, Q7TSH9, Q7TSI0, Q7Z3I7, Q86UD4, Q86WZ6, Q8BFS8, Q8IZ26, Q8N9F8, Q8TAF7

Diamond homologs: A6NDX5, A6NN14, A6QLU5, A7MBI1, A8MQ14, B4DU55, B4DX44, O43296, O60765, O75290, O75346, O75437, O95780, P10072, P10078, P17014, P17030, P17032, P17097, P17098, P51523, P51814, P52736, P52738, P52742, Q05481, Q06730, Q06732, Q14586, Q14929, Q15928, Q16587, Q29RZ4, Q2KI58, Q3KNS6, Q3V080, Q3ZCX4, Q49AA0, Q4R6C2, Q4V8A8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 20 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:

PathwayPartnersFoldFDR
Keratinization517.4×4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance97
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1011 predictions. Top by Δscore:

VariantEffectΔscore
19:57193874:GGT:Gacceptor_gain1.0000
19:57193874:GGTGT:Gacceptor_gain1.0000
19:57193962:G:GTdonor_gain1.0000
19:57194000:GG:Gdonor_gain1.0000
19:57194000:GGGTA:Gdonor_loss1.0000
19:57194001:GG:Gdonor_gain1.0000
19:57194002:G:Cdonor_loss1.0000
19:57194002:G:GGdonor_gain1.0000
19:57194003:T:Gdonor_loss1.0000
19:57191944:CAGG:Cdonor_loss0.9900
19:57191945:AGG:Adonor_loss0.9900
19:57191946:GGTG:Gdonor_loss0.9900
19:57191947:GTG:Gdonor_loss0.9900
19:57191948:T:Adonor_loss0.9900
19:57193871:CCAG:Cacceptor_loss0.9900
19:57193873:A:AGacceptor_gain0.9900
19:57193873:AG:Aacceptor_gain0.9900
19:57193873:AGGT:Aacceptor_gain0.9900
19:57193873:AGGTG:Aacceptor_loss0.9900
19:57193874:G:GAacceptor_gain0.9900
19:57193874:GG:Gacceptor_gain0.9900
19:57193874:GGTG:Gacceptor_gain0.9900
19:57192548:G:GGdonor_gain0.9800
19:57192554:A:Tdonor_gain0.9800
19:57193864:T:TAacceptor_gain0.9800
19:57191949:GAGTG:Gdonor_loss0.9700
19:57193968:A:AGdonor_gain0.9700
19:57194000:GGGT:Gdonor_gain0.9600
19:57194001:GGT:Gdonor_gain0.9600
19:57205846:C:Gdonor_gain0.9600

AlphaMissense

4149 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:57212487:T:CF464L0.999
19:57212489:T:AF464L0.999
19:57212489:T:GF464L0.999
19:57212506:T:CL470P0.999
19:57212655:T:CF520L0.999
19:57212657:T:AF520L0.999
19:57212657:T:GF520L0.999
19:57212739:T:CF548L0.999
19:57212741:C:AF548L0.999
19:57212741:C:GF548L0.999
19:57211899:T:CF268L0.998
19:57211901:C:AF268L0.998
19:57211901:C:GF268L0.998
19:57211983:T:CF296L0.998
19:57211985:C:AF296L0.998
19:57211985:C:GF296L0.998
19:57212319:T:CF408L0.998
19:57212321:C:AF408L0.998
19:57212321:C:GF408L0.998
19:57212403:T:CF436L0.998
19:57212405:C:AF436L0.998
19:57212405:C:GF436L0.998
19:57212512:G:CR472P0.998
19:57212516:C:AH473Q0.998
19:57212516:C:GH473Q0.998
19:57212571:T:CF492L0.998
19:57212573:C:AF492L0.998
19:57212573:C:GF492L0.998
19:57212674:T:CL526P0.998
19:57212680:G:CR528P0.998

dbSNP variants (sampled 300 via entrez): RS1000200469 (19:57190972 G>C,T), RS1000206519 (19:57195919 A>G), RS1000223729 (19:57203983 G>A), RS1000328406 (19:57195987 A>T), RS1000411689 (19:57201397 C>T), RS1000436330 (19:57201361 C>A), RS1000468149 (19:57190627 C>G), RS1000477650 (19:57222867 C>G), RS1000610861 (19:57206451 C>G,T), RS1000799265 (19:57218256 G>A,C), RS1000849887 (19:57218596 A>G), RS1000890220 (19:57201667 C>A), RS1000915614 (19:57196975 C>T), RS1001186434 (19:57212416 C>G,T), RS1001191587 (19:57200373 A>G)

Disease associations

OMIM: gene MIM:604668 | 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):

StudyTraitp-value
GCST001144_10Dupuytren’s disease7.000000e-14
GCST004858_25Dupuytren’s disease2.000000e-17
GCST008823_1Body mass index2.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004229Dupuytren Contracture
EFO:0004340body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects cotreatment, decreases expression, increases abundance, increases expression2
Benzo(a)pyreneincreases methylation, affects methylation2
Tetrachlorodibenzodioxinincreases expression, affects expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
testosterone enanthateaffects expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
bisphenol Aaffects cotreatment, increases methylation1
geraniolincreases expression1
terbufosincreases methylation1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
bazedoxifeneincreases expression1
ICG 001increases expression1
abrineincreases expression1
jinfukangdecreases expression, affects cotreatment1
NSC 689534affects binding, increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Cisplatinaffects cotreatment, decreases expression1
Copperincreases expression, affects binding1
Doxorubicindecreases expression1
Fonofosincreases methylation1
Ethyl Methanesulfonateincreases expression1
Formaldehydedecreases expression1
Gallic Acidincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_HD17HEK293 eGFP-ZNF264Transformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.