ZNF263

gene
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Also known as FPM315ZKSCAN12ZSCAN44

Summary

ZNF263 (zinc finger protein 263, HGNC:13056) is a protein-coding gene on chromosome 16p13.3, encoding Zinc finger protein 263 (O14978). Transcription factor that binds to the consensus sequence 5’-TCCTCCC-3’ and acts as a transcriptional repressor.

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in nucleus.

Source: NCBI Gene 10127 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 120 total
  • Transcription factor: yes — 12 downstream targets (CollecTRI)
  • MANE Select transcript: NM_005741

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13056
Approved symbolZNF263
Namezinc finger protein 263
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesFPM315, ZKSCAN12, ZSCAN44
Ensembl geneENSG00000006194
Ensembl biotypeprotein_coding
OMIM604191
Entrez10127

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000219069, ENST00000572748, ENST00000573578, ENST00000574253, ENST00000574674, ENST00000575332, ENST00000575823, ENST00000703449

RefSeq mRNA: 2 — MANE Select: NM_005741 NM_001411015, NM_005741

CCDS: CCDS10499, CCDS92094

Canonical transcript exons

ENST00000219069 — 6 exons

ExonStartEnd
ENSE0000083061832893933291460
ENSE0000264013032860233286149
ENSE0000265391332834913284205
ENSE0000399456132884543288570
ENSE0000399456232850593285239
ENSE0000399456532856813285754

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 91.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.5344 / max 56.0358, expressed in 1790 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
15241711.27851788
1524112.8462770
1524180.2559101

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370191.38gold quality
granulocyteCL:000009489.90gold quality
left ovaryUBERON:000211989.86gold quality
cortical plateUBERON:000534389.82gold quality
left uterine tubeUBERON:000130389.06gold quality
right ovaryUBERON:000211889.03gold quality
sural nerveUBERON:001548888.95gold quality
right uterine tubeUBERON:000130288.69gold quality
ventricular zoneUBERON:000305388.68gold quality
mucosa of stomachUBERON:000119988.50gold quality
ganglionic eminenceUBERON:000402388.41gold quality
body of stomachUBERON:000116188.40gold quality
right coronary arteryUBERON:000162588.34gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.27gold quality
popliteal arteryUBERON:000225088.22gold quality
tibial arteryUBERON:000761088.22gold quality
islet of LangerhansUBERON:000000688.05gold quality
pituitary glandUBERON:000000788.01gold quality
adenohypophysisUBERON:000219687.94gold quality
body of uterusUBERON:000985387.81gold quality
cerebellar hemisphereUBERON:000224587.60gold quality
descending thoracic aortaUBERON:000234587.55gold quality
cerebellar cortexUBERON:000212987.51gold quality
aortaUBERON:000094787.47gold quality
skin of legUBERON:000151187.39gold quality
ovaryUBERON:000099287.35gold quality
esophagogastric junction muscularis propriaUBERON:003584187.34gold quality
olfactory segment of nasal mucosaUBERON:000538687.28gold quality
muscle layer of sigmoid colonUBERON:003580587.24gold quality
stomachUBERON:000094587.21gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-75367yes82.66
E-MTAB-6142no80.10
E-ANND-3no4.25

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

12 targets.

TargetRegulation
ALOX5
ASXL1
COL11A2
FOXA1Repression
GAD1
NFKB
NT5E
RELN
RGS19
SART3
TPM1
ZFP42

JASPAR motifs

MotifNameFamily
MA0528.1ZNF263More than 3 adjacent zinc fingers
MA0528.2ZNF263More than 3 adjacent zinc fingers
MA0528.3ZNF263More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:19887448

Literature-anchored findings (GeneRIF, showing 8)

  • Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. (PMID:19887448)
  • The EGFR-ZNF263 signaling axis silences SIX3 in glioblastoma epigenetically. (PMID:32051553)
  • ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis. (PMID:32277030)
  • Circular RNA FOXP1 Induced by ZNF263 Upregulates U2AF2 Expression to Accelerate Renal Cell Carcinoma Tumorigenesis and Warburg Effect through Sponging miR-423-5p. (PMID:34514002)
  • Chromatin-associated OGT promotes the malignant progression of hepatocellular carcinoma by activating ZNF263. (PMID:37353617)
  • Zinc finger protein 263 upregulates interleukin 33 and suppresses autophagy to accelerate the malignant progression of non-small cell lung cancer. (PMID:37821764)
  • Transcription factor ZNF263 enhances EGFR-targeted therapeutic response and reduces residual disease in lung adenocarcinoma. (PMID:38335093)
  • Zinc finger protein 263 promotes colorectal cancer cell progression by activating STAT3 and enhancing chemoradiotherapy resistance. (PMID:39294234)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp263ENSMUSG00000022529
rattus_norvegicusZfp263ENSRNOG00000007678

Paralogs (30): ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZKSCAN3 (ENSG00000189298), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger protein 263O14978 (reviewed: O14978)

Alternative names: Zinc finger protein FPM315, Zinc finger protein with KRAB and SCAN domains 12

All UniProt accessions (7): O14978, B4DI05, D3DUC1, I3L0N0, I3L2X3, I3L393, I3NI39

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that binds to the consensus sequence 5’-TCCTCCC-3’ and acts as a transcriptional repressor. Binds to the promoter region of SIX3 and recruits other proteins involved in chromatin modification and transcriptional corepression, resulting in methylation of the promoter and transcriptional repression. Acts as a transcriptional repressor of HS3ST1 and HS3ST3A1 via binding to gene promoter regions.

Subunit / interactions. Interacts with a number of proteins involved in chromatin modification and transcriptional corepression including DNMT1, DNMT3A, HDAC2, PHF8, TRIM28/KAP1, SETDB1, EZH2, UHRF1, CBX3/HP1-gamma, and CBX5/HP1-alpha; recruits these proteins to the SIX3 promoter region, leading to SIX3 transcriptional repression. Interacts with MAPK3/ERK1 and MAPK1/ERK2.

Subcellular location. Nucleus.

Tissue specificity. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon and leukocyte.

Post-translational modifications. Ubiquitinated, leading to proteasomal degradation.

Miscellaneous. May be involved in the EGFR-mediated promotion of invasion and anchorage-independent growth in glioblastomas via silencing of SIX3. May act as a prognostic indicator in glioblastoma patients, with increased expression correlating with poor prognosis.

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

RefSeq proteins (2): NP_001397944, NP_005732* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF01352, PF02023, PF13465

UniProt features (30 total): zinc finger region 9, cross-link 7, sequence variant 4, region of interest 3, domain 2, modified residue 2, chain 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O14978-F161.190.09

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 (9): 166, 178, 17, 157, 285, 299, 376, 573, 582

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 107 (showing top): ENK_UV_RESPONSE_KERATINOCYTE_UP, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, BROWNE_HCMV_INFECTION_12HR_UP, PAX2_01, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_UP, GATA1_03, SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP, MODULE_204, MYB_Q5_01, RIZKI_TUMOR_INVASIVENESS_3D_UP, BROWNE_HCMV_INFECTION_14HR_UP, LAIHO_COLORECTAL_CANCER_SERRATED_DN, GENTILE_UV_LOW_DOSE_UP, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING

GO Biological Process (4): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (11): transcription cis-regulatory region binding (GO:0000976), RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), sequence-specific DNA binding (GO:0043565), 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:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II3
transcription by RNA polymerase II3
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
regulation of DNA-templated transcription2
negative regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
positive regulation of DNA-templated transcription1
transcription regulatory region nucleic acid binding1
sequence-specific double-stranded DNA binding1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
transcription cis-regulatory region binding1
transcription regulator activity1
transition metal ion binding1
DNA binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1536 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF263FOXA1P55317543
ZNF263RAD21O60216528
ZNF263STAT3P40763510
ZNF263SMC3Q9UQE7505
ZNF263JUNP05412486
ZNF263MEFVO15553479
ZNF263ZKSCAN2Q63HK3462
ZNF263FOXA2Q9Y261453
ZNF263TAL1P17542445
ZNF263SPI1P17947442
ZNF263HOXB13Q92826440
ZNF263TIGD7Q6NT04431
ZNF263GATBO75879429
ZNF263NFKB1P19838429
ZNF263L3MBTL4Q8NA19425

IntAct

61 interactions, top by confidence:

ABTypeScore
ZNF263TRIM41psi-mi:“MI:0915”(physical association)0.800
ZNF263SCAND1psi-mi:“MI:0915”(physical association)0.800
CLK2ZNF263psi-mi:“MI:0915”(physical association)0.560
ZNF263CLK3psi-mi:“MI:0915”(physical association)0.560
GPATCH2LZNF263psi-mi:“MI:0915”(physical association)0.560
ZNF263TCAF1psi-mi:“MI:0915”(physical association)0.560
ZNF263CLK2psi-mi:“MI:0915”(physical association)0.560
TCAF1ZNF263psi-mi:“MI:0915”(physical association)0.560
CLK3ZNF263psi-mi:“MI:0915”(physical association)0.560
ZNF263GPATCH2Lpsi-mi:“MI:0915”(physical association)0.560
ZNF263ZNF165psi-mi:“MI:0915”(physical association)0.560
ZNF263PPLpsi-mi:“MI:0915”(physical association)0.560
ZNF263JAKMIP2psi-mi:“MI:0915”(physical association)0.560
ZNF263ZSCAN22psi-mi:“MI:0915”(physical association)0.560
ZNF263LNX1psi-mi:“MI:0915”(physical association)0.560
SUFUZNF263psi-mi:“MI:0915”(physical association)0.550
ZNF263SUFUpsi-mi:“MI:0915”(physical association)0.550
ZNF263AHCYL1psi-mi:“MI:0914”(association)0.530
PCBD1ZNF263psi-mi:“MI:0915”(physical association)0.370
ZNF263ZSCAN1psi-mi:“MI:0915”(physical association)0.370
ZNF263EFEMP2psi-mi:“MI:0915”(physical association)0.370
ZNF263ZNF446psi-mi:“MI:0915”(physical association)0.370
ZNF263SPG21psi-mi:“MI:0915”(physical association)0.370

BioGRID (213): ZNF263 (Two-hybrid), ZNF263 (Two-hybrid), ZNF263 (Two-hybrid), GPATCH2L (Two-hybrid), ZNF263 (Affinity Capture-MS), ZNF263 (Affinity Capture-MS), EFEMP2 (Two-hybrid), ZNF446 (Two-hybrid), SPG21 (Two-hybrid), TRIM41 (Two-hybrid), SCAND1 (Two-hybrid), ZNF263 (Two-hybrid), NME7 (Two-hybrid), SUFU (Two-hybrid), PLEKHF2 (Two-hybrid)

ESM2 similar proteins: A1A5P9, A2AVR2, A6QPT6, B2KFW1, O14978, P17029, P17040, P17098, P25233, P70503, Q13342, Q14D33, Q3SYK4, Q3V3Q4, Q4KLI1, Q4R8H9, Q4V8E9, Q5PPP4, Q5R670, Q5R7U0, Q5VWK0, Q61066, Q63HK3, Q68CQ1, Q6PCZ4, Q7TS72, Q80ZG2, Q8BGS3, Q8CF60, Q8IWY8, Q8N660, Q8NDZ0, Q8TD17, Q921B4, Q923B3, Q96D09, Q96GC6, Q96JL9, Q96M43, Q99608

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance106
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

971 predictions. Top by Δscore:

VariantEffectΔscore
16:3300638:A:Tacceptor_gain1.0000
16:3284203:CAGGT:Cdonor_loss0.9900
16:3284204:AGG:Adonor_loss0.9900
16:3284206:GTGA:Gdonor_loss0.9900
16:3284207:T:Adonor_loss0.9900
16:3285223:GGCT:Gdonor_gain0.9900
16:3285224:GCTG:Gdonor_gain0.9900
16:3285234:A:Tdonor_gain0.9900
16:3285235:GAGGG:Gdonor_gain0.9900
16:3285237:GGG:Gdonor_gain0.9900
16:3285238:GGG:Gdonor_gain0.9900
16:3286021:A:AGacceptor_gain0.9900
16:3286022:G:GAacceptor_gain0.9900
16:3286123:A:Tdonor_gain0.9900
16:3289388:A:AGacceptor_gain0.9900
16:3289389:C:Gacceptor_gain0.9900
16:3289389:CCA:Cacceptor_loss0.9900
16:3289390:CA:Cacceptor_loss0.9900
16:3289391:A:ACacceptor_loss0.9900
16:3289391:A:AGacceptor_gain0.9900
16:3289392:G:GGacceptor_gain0.9900
16:3289392:GGA:Gacceptor_gain0.9900
16:3285763:G:Tdonor_gain0.9800
16:3289388:ACCAG:Aacceptor_gain0.9800
16:3300637:C:CTacceptor_gain0.9800
16:3284170:GA:Gdonor_gain0.9700
16:3289392:GGAGA:Gacceptor_gain0.9700
16:3285215:G:Tdonor_gain0.9600
16:3289391:AG:Aacceptor_gain0.9500
16:3289392:GG:Gacceptor_gain0.9500

AlphaMissense

4490 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:3289917:T:CF471L0.999
16:3289919:C:AF471L0.999
16:3289919:C:GF471L0.999
16:3290001:T:CF499L0.999
16:3290003:T:AF499L0.999
16:3290003:T:GF499L0.999
16:3290020:T:CL505P0.999
16:3290028:C:GH508D0.999
16:3290085:T:CF527L0.999
16:3290087:C:AF527L0.999
16:3290087:C:GF527L0.999
16:3290340:T:CF612L0.999
16:3290342:C:AF612L0.999
16:3290342:C:GF612L0.999
16:3290371:A:CQ622P0.999
16:3290424:T:CF640L0.999
16:3290426:C:AF640L0.999
16:3290426:C:GF640L0.999
16:3289833:T:CF443L0.998
16:3289835:C:AF443L0.998
16:3289835:C:GF443L0.998
16:3289867:G:CR454P0.998
16:3289936:T:CL477P0.998
16:3289944:C:GH480D0.998
16:3289946:C:AH480Q0.998
16:3289946:C:GH480Q0.998
16:3289958:C:AH484Q0.998
16:3289958:C:GH484Q0.998
16:3290002:T:CF499S0.998
16:3290030:C:AH508Q0.998

dbSNP variants (sampled 300 via entrez): RS1000184372 (16:3292719 G>A,T), RS1000360526 (16:3287300 C>T), RS1000455546 (16:3287204 G>A,C), RS1000743295 (16:3294549 T>C), RS1000762091 (16:3294088 G>C,T), RS1000792025 (16:3288170 T>C,G), RS1000921371 (16:3293956 C>T), RS1001357154 (16:3293052 G>A), RS1001378029 (16:3283208 T>C), RS1001487363 (16:3287571 C>G), RS1001521469 (16:3287851 T>C), RS1001576701 (16:3288633 G>A,T), RS1001627804 (16:3283232 A>T), RS1001633526 (16:3294214 C>T), RS1001750157 (16:3282856 G>A)

Disease associations

OMIM: gene MIM:604191 | 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

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

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionincreases expression2
Aflatoxin B1decreases methylation, increases expression2
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
bisphenol Faffects cotreatment, decreases expression1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
geraniolincreases expression1
sodium arseniteincreases expression1
tamibarotenedecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
K 7174increases expression1
PCI 5002affects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Cadmiumincreases abundance, increases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Diazinonincreases methylation1
Fluorouracilaffects expression1
Indomethacinaffects cotreatment, decreases expression1
Leadaffects expression1
Plant Extractsaffects cotreatment, increases expression1
Silverincreases expression1
Smokedecreases expression1
Dronabinoldecreases expression1
Thiramincreases expression1
Tretinoindecreases expression1
Valproic Acidincreases expression1
Zincaffects cotreatment, increases expression1

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_A8F6SEES3-1V human ZNF263, clone1Embryonic stem cellMale
CVCL_A8F7SEES3-1V human ZNF263, clone2Embryonic stem cellMale
CVCL_A8F8SEES3-1V human ZNF263, clone3Embryonic stem cellMale
CVCL_D9W2Ubigene HEK293 ZNF263 KOTransformed 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.