ZNF516

gene
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Also known as HsT287KIAA0222

Summary

ZNF516 (zinc finger protein 516, HGNC:28990) is a protein-coding gene on chromosome 18q23, encoding Zinc finger protein 516 (Q92618). Transcriptional regulator that binds to the promoter and activates the transcription of genes promoting brown adipose tissue (BAT) differentiation.

Zinc-finger proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. This gene encodes a zinc-finger protein, and belongs to the krueppel C2H2-type zinc-finger protein family. It may be involved in transcriptional regulation.

Source: NCBI Gene 9658 — RefSeq curated summary.

At a glance

  • GWAS associations: 20
  • Clinical variants (ClinVar): 246 total
  • MANE Select transcript: NM_014643

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28990
Approved symbolZNF516
Namezinc finger protein 516
Location18q23
Locus typegene with protein product
StatusApproved
AliasesHsT287, KIAA0222
Ensembl geneENSG00000101493
Ensembl biotypeprotein_coding
OMIM615114
Entrez9658

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 13 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000443185, ENST00000532857, ENST00000542818, ENST00000543743, ENST00000617840, ENST00000871208, ENST00000871209, ENST00000871210, ENST00000915360, ENST00000915361, ENST00000915362, ENST00000957637, ENST00000957638, ENST00000957639

RefSeq mRNA: 1 — MANE Select: NM_014643 NM_014643

CCDS: CCDS74234

Canonical transcript exons

ENST00000443185 — 7 exons

ExonStartEnd
ENSE000014091247649514476495242
ENSE000014112347646302876463141
ENSE000016479137637885576380303
ENSE000016632707635768276362557
ENSE000035181627637052876370595
ENSE000035965407637146776371571
ENSE000036684477644124576443211

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 94.63.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.7054 / max 279.0276, expressed in 1454 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
1724772.48551046
1724751.2682630
1724560.8854460
1724780.5852343
1724760.2233106
1724790.197070
1724570.03096
1724800.02984

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225594.63gold quality
endocervixUBERON:000045894.04gold quality
left testisUBERON:000453392.48gold quality
body of uterusUBERON:000985392.23gold quality
right testisUBERON:000453492.15gold quality
testisUBERON:000047391.03gold quality
left ovaryUBERON:000211991.01gold quality
right uterine tubeUBERON:000130290.82gold quality
endometriumUBERON:000129590.47gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047390.09gold quality
ectocervixUBERON:001224990.05gold quality
right ovaryUBERON:000211889.84gold quality
monocyteCL:000057689.64gold quality
mononuclear cellCL:000084289.40gold quality
left uterine tubeUBERON:000130389.27gold quality
uterusUBERON:000099589.00gold quality
leukocyteCL:000073888.93gold quality
seminal vesicleUBERON:000099888.65gold quality
bloodUBERON:000017888.52gold quality
ovaryUBERON:000099288.44gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.40gold quality
olfactory segment of nasal mucosaUBERON:000538688.10gold quality
deciduaUBERON:000245087.92gold quality
myometriumUBERON:000129687.78gold quality
adenohypophysisUBERON:000219687.37gold quality
tibial nerveUBERON:000132386.39gold quality
lower esophagus mucosaUBERON:003583486.06gold quality
female reproductive systemUBERON:000047485.80gold quality
pituitary glandUBERON:000000785.74gold quality
sural nerveUBERON:001548885.62gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

304 targeting ZNF516, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692A100.0074.406850
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-196A-5P100.0068.16684
HSA-MIR-196B-5P100.0068.16681
HSA-MIR-4533100.0069.482758
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-8485100.0077.574731
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4455100.0065.481587
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-188-3P100.0068.761240
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4692100.0067.322066
HSA-MIR-4673100.0066.641490
HSA-MIR-5193100.0067.261744
HSA-MIR-548AW99.9972.573559
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-607799.9968.042299

Literature-anchored findings (GeneRIF, showing 4)

  • one interacting gene pair (RBMS3 versus ZNF516) which, even after Bonferroni correction for multiple testing, showed consistently significant effects on hip bone mineral density. (PMID:23045156)
  • ZNF516 promoter methylation was the best biomarker, with both sensitivity and specificity of 90% (AUC = 0.92), results subsequently corroborated in a Prevalence cohort. (PMID:24241165)
  • ZNF516 represses EGFR transcription through the interaction with the CtBP/LSD1/CoREST complex. (PMID:28947780)
  • MiR-371-5p regulates trophoblast cell proliferation, migration, and invasion by directly targeting ZNF516. (PMID:38761180)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp516ENSMUSG00000058881
rattus_norvegicusZfp516ENSRNOG00000016258

Paralogs (14): HIVEP2 (ENSG00000010818), HIVEP1 (ENSG00000095951), SALL4 (ENSG00000101115), SALL1 (ENSG00000103449), BCL11A (ENSG00000119866), ZNF831 (ENSG00000124203), RREB1 (ENSG00000124782), HIVEP3 (ENSG00000127124), BCL11B (ENSG00000127152), ZNF219 (ENSG00000165804), SALL2 (ENSG00000165821), ZNF217 (ENSG00000171940), ZNF536 (ENSG00000198597), SALL3 (ENSG00000256463)

Protein

Protein identifiers

Zinc finger protein 516Q92618 (reviewed: Q92618)

All UniProt accessions (4): Q92618, A0A087WUJ4, F5H2K2, H0YH41

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional regulator that binds to the promoter and activates the transcription of genes promoting brown adipose tissue (BAT) differentiation. Among brown adipose tissue-specific genes, binds the proximal region of the promoter of the UCP1 gene to activate its transcription and thereby regulate thermogenesis. May also play a role in the cellular response to replication stress.

Subunit / interactions. Interacts with PRDM16; the interaction is direct and may play a role in the transcription of brown adipose tissue-specific genes. Interacts with PWWP2B. Interacts with HDAC1; this interaction is enhanced in the presence of PWWP2B.

Subcellular location. Nucleus.

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

RefSeq proteins (1): NP_055458* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR051967Krueppel_C2H2-ZFFamily

Pfam: PF00096

UniProt features (35 total): compositionally biased region 11, zinc finger region 10, region of interest 7, cross-link 4, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92618-F151.850.04

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): 643, 681, 1043, 1062

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 212 (showing top): GOBP_RESPONSE_TO_COLD, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, TOMLINS_PROSTATE_CANCER_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN, GOBP_BROWN_FAT_CELL_DIFFERENTIATION, MODULE_123, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, GOBP_FAT_CELL_DIFFERENTIATION, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP, GOBP_TEMPERATURE_HOMEOSTASIS, GOBP_ADIPOSE_TISSUE_DEVELOPMENT

GO Biological Process (7): regulation of DNA-templated transcription (GO:0006355), response to cold (GO:0009409), positive regulation of DNA-templated transcription (GO:0045893), brown fat cell differentiation (GO:0050873), adipose tissue development (GO:0060612), positive regulation of cold-induced thermogenesis (GO:0120162), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), cis-regulatory region sequence-specific DNA binding (GO:0000987), zinc ion binding (GO:0008270), DNA-binding transcription factor binding (GO:0140297), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA-templated transcription2
regulation of DNA-templated transcription2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of gene expression1
regulation of RNA biosynthetic process1
response to stress1
response to temperature stimulus1
positive regulation of RNA biosynthetic process1
fat cell differentiation1
animal organ development1
connective tissue development1
positive regulation of multicellular organismal process1
cold-induced thermogenesis1
regulation of cold-induced thermogenesis1
transcription by RNA polymerase II1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transcription cis-regulatory region binding1
transition metal ion binding1
transcription factor binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

732 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF516RCOR1Q9UKL0888
ZNF516PRDM16Q9HAZ2826
ZNF516CTBP1Q13363803
ZNF516CTBP2P56545684
ZNF516KLF3P57682648
ZNF516KDM1AO60341643
ZNF516ZNF217O75362637
ZNF516MBOAT2Q6ZWT7636
ZNF516NRIP1P48552614
ZNF516CBX2Q14781546
ZNF516MEX3CQ5U5Q3539
ZNF516ZMYM2Q9UBW7535
ZNF516ZMYM3Q14202515
ZNF516ZFPM1Q8IX07497
ZNF516SLC66A2Q8N2U9488

IntAct

75 interactions, top by confidence:

ABTypeScore
ZNF516CTBP1psi-mi:“MI:0915”(physical association)0.880
ZNF516HDAC1psi-mi:“MI:0915”(physical association)0.880
S100BS100A4psi-mi:“MI:0914”(association)0.870
HDAC1CDK2AP1psi-mi:“MI:0914”(association)0.840
CTBP1ZEB2psi-mi:“MI:0914”(association)0.800
CTBP1KDM1Apsi-mi:“MI:0914”(association)0.790
HDAC1TNRC18psi-mi:“MI:0914”(association)0.790
MED23MED19psi-mi:“MI:2364”(proximity)0.770
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
CTBP1CBX4psi-mi:“MI:0914”(association)0.700
ZNF516CTBP2psi-mi:“MI:0915”(physical association)0.660
ZNF516HDAC2psi-mi:“MI:0915”(physical association)0.660
ZNF516RCOR1psi-mi:“MI:0915”(physical association)0.660
ZBTB18HSPA8psi-mi:“MI:0914”(association)0.640
DCAF7PFDN6psi-mi:“MI:2364”(proximity)0.570
ZNF516KDM1Apsi-mi:“MI:0914”(association)0.560
ZNF516KDM1Apsi-mi:“MI:0915”(physical association)0.560
ZBTB42MID1psi-mi:“MI:0914”(association)0.530

BioGRID (79): ZNF516 (Affinity Capture-MS), ZNF516 (Proximity Label-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Affinity Capture-RNA), ZNF516 (Proximity Label-MS), ZNF516 (Affinity Capture-MS), ZNF516 (Proximity Label-MS), ZNF516 (Proximity Label-MS), ZNF516 (Proximity Label-MS)

ESM2 similar proteins: A0A2Z4LIS9, A6QPM6, A7X8B3, A7X8B5, A7X8B7, A7X8C4, A7X8C7, A7X8C9, A7XW16, A7XW20, A7XW25, O08664, O15054, O43151, O70218, O89113, P09066, P14652, P17542, P19419, P19622, P22091, P23683, P49640, P70061, P78412, P82976, P97503, Q00587, Q04890, Q05916, Q05917, Q12950, Q15270, Q17QW1, Q3U133, Q5JPB2, Q5NCY0, Q6ZW13, Q80WY3

Diamond homologs: A1L2U9, A2A884, A2ANX9, B0X0K1, B0X9H6, B0XS89, B1WAZ8, B1WBU4, E9PZZ1, E9Q6W4, G5EBU4, O15090, O60315, O62836, O73694, O75362, O77459, P08048, P10925, P15822, P17010, P17012, P20662, P26635, P28166, P28575, P28698, P31509, P31629, P36197, P52739, P53243, P60319, P78871, P80944, Q00453, Q00900, Q01800, Q02026, Q02027

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 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
Negative Regulation of CDH1 Gene Transcription820.5×1e-06
Regulation of PTEN gene transcription519.0×8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance211
Likely benign16
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3172 predictions. Top by Δscore:

VariantEffectΔscore
18:76443210:ACCT:Aacceptor_loss1.0000
18:76443218:C:CTacceptor_gain1.0000
18:76454219:A:Cacceptor_gain1.0000
18:76370316:AGAC:Adonor_gain0.9900
18:76370596:C:CCacceptor_gain0.9900
18:76371619:G:Cacceptor_gain0.9900
18:76371625:G:Cacceptor_gain0.9900
18:76371625:G:GCacceptor_gain0.9900
18:76371634:C:CTacceptor_gain0.9900
18:76371642:C:CTacceptor_gain0.9900
18:76371643:G:Tacceptor_gain0.9900
18:76380299:TCCCC:Tacceptor_gain0.9900
18:76380300:CCCC:Cacceptor_gain0.9900
18:76380300:CCCCC:Cacceptor_gain0.9900
18:76380301:CCC:Cacceptor_gain0.9900
18:76380301:CCCC:Cacceptor_gain0.9900
18:76380302:CC:Cacceptor_gain0.9900
18:76380302:CCC:Cacceptor_gain0.9900
18:76380303:CC:Cacceptor_gain0.9900
18:76380304:C:CCacceptor_gain0.9900
18:76380304:C:Gacceptor_loss0.9900
18:76443207:AGCAC:Aacceptor_gain0.9900
18:76443208:GCAC:Gacceptor_gain0.9900
18:76443209:CAC:Cacceptor_gain0.9900
18:76443209:CACC:Cacceptor_gain0.9900
18:76443210:AC:Aacceptor_gain0.9900
18:76443211:CC:Cacceptor_gain0.9900
18:76443212:C:CCacceptor_gain0.9900
18:76443219:A:Tacceptor_gain0.9900
18:76454218:C:CTacceptor_gain0.9900

AlphaMissense

7603 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:76441483:G:CF524L1.000
18:76441483:G:TF524L1.000
18:76441485:A:GF524L1.000
18:76442173:G:CH294Q1.000
18:76442173:G:TH294Q1.000
18:76442175:G:CH294D1.000
18:76442200:G:CF285L1.000
18:76442200:G:TF285L1.000
18:76442201:A:GF285S1.000
18:76442202:A:GF285L1.000
18:76442223:A:GC278R1.000
18:76442815:G:CH80Q1.000
18:76442815:G:TH80Q1.000
18:76442817:G:CH80D1.000
18:76442825:A:GL77P1.000
18:76442865:A:GC64R1.000
18:76442887:G:CH56Q1.000
18:76442887:G:TH56Q1.000
18:76442894:C:GR54P1.000
18:76442895:G:TR54S1.000
18:76442899:G:CH52Q1.000
18:76442899:G:TH52Q1.000
18:76442901:G:CH52D1.000
18:76442901:G:TH52N1.000
18:76442926:G:CF43L1.000
18:76442926:G:TF43L1.000
18:76442928:A:GF43L1.000
18:76441456:G:CH533Q0.999
18:76441456:G:TH533Q0.999
18:76441458:G:CH533D0.999

dbSNP variants (sampled 300 via entrez): RS1000006694 (18:76468673 G>C), RS1000033709 (18:76378176 C>T), RS1000033933 (18:76468273 A>G), RS1000062357 (18:76399046 C>G), RS1000104321 (18:76408147 G>A), RS1000134828 (18:76357966 T>C,G), RS1000140998 (18:76465392 G>GA), RS1000149698 (18:76451748 G>A), RS1000213952 (18:76439408 G>A,C), RS1000222000 (18:76429787 C>A,T), RS1000225494 (18:76450164 T>C), RS1000270973 (18:76431733 CCTTG>C), RS1000274487 (18:76439368 T>C), RS1000275184 (18:76396201 G>C), RS1000288116 (18:76391632 T>C)

Disease associations

OMIM: gene MIM:615114 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

20 associations (top):

StudyTraitp-value
GCST000785_7Longevity1.000000e-06
GCST001713_28Dental caries4.000000e-06
GCST001871_1Renal transplant outcome4.000000e-08
GCST002688_4Very long-chain saturated fatty acid levels (fatty acid 22:0)6.000000e-06
GCST004608_128Granulocyte percentage of myeloid white cells5.000000e-15
GCST004609_89Monocyte percentage of white cells3.000000e-18
GCST005580_107Intraocular pressure1.000000e-11
GCST006073_52Tenofovir clearance in HIV infection4.000000e-06
GCST006394_81Intraocular pressure4.000000e-08
GCST006412_126Intraocular pressure2.000000e-08
GCST006626_9Pulse pressure1.000000e-12
GCST010002_143Refractive error3.000000e-08
GCST012490_295Femur bone mineral density x serum urate levels interaction7.000000e-10
GCST012490_449Femur bone mineral density x serum urate levels interaction2.000000e-10
GCST90002393_624Monocyte count1.000000e-15
GCST90002394_426Monocyte percentage of white cells5.000000e-46
GCST90002398_96Neutrophil count9.000000e-19
GCST90002399_259Neutrophil percentage of white cells9.000000e-13
GCST90002404_198Red cell distribution width2.000000e-10
GCST90002407_170White blood cell count2.000000e-13

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0005199renal transplant outcome measurement
EFO:0006796very long-chain saturated fatty acid measurement
EFO:0007997granulocyte percentage of myeloid white cells
EFO:0007989monocyte percentage of leukocytes
EFO:0004695intraocular pressure measurement
EFO:0005763pulse pressure measurement
EFO:0004531urate measurement
EFO:0005091monocyte count
EFO:0004833neutrophil count
EFO:0007990neutrophil percentage of leukocytes
EFO:0009188Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, affects methylation, decreases methylation3
Air Pollutantsaffects expression, increases abundance, increases expression2
Smokedecreases expression, increases abundance, increases expression2
Valproic Acidincreases expression, increases methylation2
FR900359affects phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
trichostatin Aincreases expression1
sodium arseniteaffects methylation1
potassium chromate(VI)decreases expression1
aflatoxin B2decreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
di-n-butylphosphoric acidaffects expression1
monomethylarsonous acidincreases expression1
Arsenic Trioxideincreases expression1
Leflunomideincreases expression1
Arsenicaffects methylation1
Caffeineincreases phosphorylation1
Doxorubicindecreases expression1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression1
Ozoneaffects expression, increases abundance1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Cyclosporinedecreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfateincreases expression1
Lactic Acidincreases expression1

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.