ZNF512

gene
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Also known as KIAA1805

Summary

ZNF512 (zinc finger protein 512, HGNC:29380) is a protein-coding gene on chromosome 2p23.3, encoding Zinc finger protein 512 (Q96ME7). Sequence-specific DNA-binding protein that recognizes repetitive and non-consecutive TTC sequences in pericentric repeat and initiates heterochromatin formation through interaction with SUV39H1/2 methyltransferases which catalyze histone H3K9 methylation.

This gene encodes a protein containing four putative zinc finger motifs. Zinc finger motifs may bind to proteins or nucleic acids. Zinc finger-containing proteins are involved in a variety of processes, including regulation of transcription. Alternative splicing results in multiple transcript variants for this gene.

Source: NCBI Gene 84450 — RefSeq curated summary.

At a glance

  • GWAS associations: 11
  • Clinical variants (ClinVar): 67 total
  • MANE Select transcript: NM_032434

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29380
Approved symbolZNF512
Namezinc finger protein 512
Location2p23.3
Locus typegene with protein product
StatusApproved
AliasesKIAA1805
Ensembl geneENSG00000243943
Ensembl biotypeprotein_coding
OMIM620921
Entrez84450

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000355467, ENST00000379717, ENST00000413371, ENST00000416005, ENST00000461705, ENST00000488055, ENST00000494548, ENST00000556601, ENST00000879762, ENST00000879763, ENST00000937483, ENST00000937484, ENST00000948674

RefSeq mRNA: 6 — MANE Select: NM_032434 NM_001271286, NM_001271287, NM_001271288, NM_001271289, NM_001271318, NM_032434

CCDS: CCDS1758, CCDS59428, CCDS59429

Canonical transcript exons

ENST00000355467 — 14 exons

ExonStartEnd
ENSE000009630182760069127600815
ENSE000034630122760784527608039
ENSE000035025382759806727598254
ENSE000035098462761626227616324
ENSE000035111022760135627601442
ENSE000035140252760246327602561
ENSE000035149642761747327617571
ENSE000035737812761516827615269
ENSE000036378632758365827583716
ENSE000036502362760314027603307
ENSE000037151792759958327599678
ENSE000037332272759997027600053
ENSE000038413852762115327623217
ENSE000038428732758304227583142

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 95.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.1890 / max 1516.1399, expressed in 1778 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1938016.13531776
193790.7257409
193810.3120118
193820.01592

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534395.79gold quality
ganglionic eminenceUBERON:000402394.73gold quality
ventricular zoneUBERON:000305393.60gold quality
ileal mucosaUBERON:000033193.39gold quality
left ovaryUBERON:000211992.94gold quality
tibialis anteriorUBERON:000138592.65silver quality
right ovaryUBERON:000211892.61gold quality
ovaryUBERON:000099292.30gold quality
body of uterusUBERON:000985392.00gold quality
endocervixUBERON:000045891.90gold quality
calcaneal tendonUBERON:000370191.74gold quality
cauda epididymisUBERON:000436091.49gold quality
pancreatic ductal cellCL:000207991.47gold quality
smooth muscle tissueUBERON:000113591.46gold quality
corpus epididymisUBERON:000435991.32gold quality
popliteal arteryUBERON:000225090.77gold quality
tibial arteryUBERON:000761090.77gold quality
sural nerveUBERON:001548890.73gold quality
cardiac muscle of right atriumUBERON:000337990.66silver quality
caput epididymisUBERON:000435890.66gold quality
islet of LangerhansUBERON:000000690.57gold quality
right uterine tubeUBERON:000130290.52gold quality
right coronary arteryUBERON:000162590.49gold quality
adenohypophysisUBERON:000219690.22gold quality
aortaUBERON:000094790.12gold quality
tibial nerveUBERON:000132390.11gold quality
muscle layer of sigmoid colonUBERON:003580590.09gold quality
lymph nodeUBERON:000002989.93gold quality
thyroid glandUBERON:000204689.92gold quality
left uterine tubeUBERON:000130389.86gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-100618yes542.85
E-ANND-3yes3.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting ZNF512, 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-6740-5P100.0065.64932
HSA-MIR-340-5P100.0072.504437
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-4533100.0069.482758
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-450099.9972.722367
HSA-MIR-607799.9968.042299
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-569699.9872.364487
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-9-3P99.9670.882068

Literature-anchored findings (GeneRIF, showing 2)

  • MFSD2B, CCL20 and STAT1, or STARD7 and ZNF512 genes may be risk or protect factors in prognosis of ADC; HTR2B, DPP4, and TGFBRAP1 genes may be risk factors in prognosis of SQC. (PMID:27301951)
  • risk (C) allele of the SNP (rs2275294) in the ZNF512B gene, cervical flexor muscle power and body weight index might have clinical potential for amyotrophic lateral sclerosis prognostication (PMID:30567526)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_rerioznf512ENSDARG00000041910
mus_musculusZfp512ENSMUSG00000062761
rattus_norvegicusZfp512ENSRNOG00000039815
drosophila_melanogasterVajk3FBGN0028544
drosophila_melanogasterVajk2FBGN0032538
drosophila_melanogasternahodaFBGN0034797
drosophila_melanogasterVajk4FBGN0050101
caenorhabditis_elegansWBGENE00007479

Paralogs (2): GGN (ENSG00000179168), ZNF512B (ENSG00000196700)

Protein

Protein identifiers

Zinc finger protein 512Q96ME7 (reviewed: Q96ME7)

All UniProt accessions (2): Q96ME7, G3XAG1

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific DNA-binding protein that recognizes repetitive and non-consecutive TTC sequences in pericentric repeat and initiates heterochromatin formation through interaction with SUV39H1/2 methyltransferases which catalyze histone H3K9 methylation.

Subunit / interactions. Interacts with SUV39H1 and SUV39H2; this interaction initiates heterochromatin formation.

Subcellular location. Chromosome. Nucleus.

Domain organisation. Has an atypical organization of its zinc-fingers, with long linkers separating them, providing flexibility for recognizing non-consecutive 3-nucleotide triplets targeted by each zinc finger.

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

Isoforms (3)

UniProt IDNamesCanonical?
Q96ME7-11yes
Q96ME7-22
Q96ME7-33

RefSeq proteins (6): NP_001258215, NP_001258216, NP_001258217, NP_001258218, NP_001258247, NP_115810* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR048403ZNF512_znf-C2H2Domain
IPR048408ZNF512_C2HCDomain
IPR052274Krueppel_C2H2_Zn-fingerFamily

Pfam: PF00096, PF21276, PF21367

UniProt features (27 total): compositionally biased region 5, zinc finger region 4, cross-link 4, splice variant 3, helix 3, region of interest 3, strand 2, chain 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2CTDSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96ME7-F162.760.02

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): 18, 84, 227, 333

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 102 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GCM_GSPT1, GGGTGGRR_PAX4_03, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, GCM_NUMA1, LASTOWSKA_COAMPLIFIED_WITH_MYCN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MAF_Q6, GCM_NF2, GOBP_CHROMATIN_REMODELING, GOBP_HETEROCHROMATIN_ORGANIZATION, AGCTCCT_MIR28, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, NKX3A_01, GCM_RBM8A

GO Biological Process (2): constitutive heterochromatin formation (GO:0140719), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), pericentric heterochromatin (GO:0005721)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
heterochromatin formation1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
nucleic acid binding1
transcription cis-regulatory region binding1
regulation of DNA-templated transcription1
transcription regulator activity1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
chromosome, centromeric region1
heterochromatin1

Protein interactions and networks

STRING

1070 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF512SPATA31H1Q68DN1766
ZNF512CCDC121Q6ZUS5729
ZNF512ZNF362Q5T0B9651
ZNF512SDAD1Q9NVU7623
ZNF512KRTCAP3Q53RY4605
ZNF512FNDC4Q9H6D8594
ZNF512NRBP1Q9UHY1581
ZNF512GPN1Q9HCN4578
ZNF512C4orf17Q53FE4578
ZNF512ZNF451Q9Y4E5570
ZNF512GCKRQ14397541
ZNF512NIPBLQ6KC79520
ZNF512IFT172Q9UG01519
ZNF512RRP15Q9Y3B9519
ZNF512SPDYE11P0DTA3479

IntAct

210 interactions, top by confidence:

ABTypeScore
HDAC2KDM1Apsi-mi:“MI:0914”(association)0.890
TUBG1TUBG1psi-mi:“MI:2364”(proximity)0.760
RPL14RRP8psi-mi:“MI:0914”(association)0.640
NOP53RRP8psi-mi:“MI:0914”(association)0.640
NOL12RRP8psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
KANK2ZNF512psi-mi:“MI:0915”(physical association)0.560
RPL28MAGEB2psi-mi:“MI:0914”(association)0.560
BCORCBX4psi-mi:“MI:0914”(association)0.530
ZNF512ZNF724psi-mi:“MI:0914”(association)0.530
RBM34NVLpsi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
RSBN1SETD1Apsi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
RPL8RRP8psi-mi:“MI:0914”(association)0.530
RPF1ZNF324psi-mi:“MI:0914”(association)0.530
MED27POLR2Dpsi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
ZNF71DKC1psi-mi:“MI:0914”(association)0.530
MKI67ZC3H11Apsi-mi:“MI:0914”(association)0.480

BioGRID (344): ZNF512 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Proximity Label-MS), ZNF512 (Proximity Label-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF512 (Proximity Label-MS), ZNF273 (Affinity Capture-MS), ZNF724P (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8GR68, A0JPQ7, A4FV61, F7AQ22, O62666, O62674, O62676, O62678, O75151, O75152, P49140, P53349, P97432, Q13233, Q14596, Q15047, Q1LY51, Q3ZC82, Q4R6F6, Q53F19, Q5F3Z9, Q5R6F3, Q5SUE8, Q5XJV7, Q5ZJJ1, Q60698, Q60974, Q62925, Q69Z61, Q69Z99, Q6AI12, Q6NXK2, Q6PJT7, Q6ZNC4, Q7TMD5, Q80VG1, Q80XA6, Q86XL3, Q8BG81, Q8BJ05

Diamond homologs: A4FV61, Q5R6F3, Q69Z99, Q95JV5, Q96KM6, Q96ME7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 206 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
Peptide chain elongation2724.6×1e-28
Viral mRNA Translation2724.6×1e-28
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA2724.4×1e-28
Selenocysteine synthesis2723.4×3e-28
Eukaryotic Translation Termination2723.4×3e-28
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)2722.9×4e-28
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA2722.9×4e-28
Formation of a pool of free 40S subunits2721.8×1e-27

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation2827.7×3e-30
ribosomal large subunit biogenesis716.6×4e-05
translation2915.9×4e-24
ribosomal small subunit biogenesis1113.4×1e-07
rRNA processing1612.1×9e-11
regulation of alternative mRNA splicing, via spliceosome67.8×9e-03
nucleosome assembly86.0×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2271 predictions. Top by Δscore:

VariantEffectΔscore
2:27583140:GCC:Gdonor_gain1.0000
2:27583143:G:GGdonor_gain1.0000
2:27598065:A:AGacceptor_gain1.0000
2:27598066:G:GGacceptor_gain1.0000
2:27599568:T:TAacceptor_gain1.0000
2:27599571:A:AGacceptor_gain1.0000
2:27599571:AT:Aacceptor_gain1.0000
2:27599571:ATG:Aacceptor_gain1.0000
2:27599572:T:Gacceptor_gain1.0000
2:27599572:T:TAacceptor_gain1.0000
2:27599573:G:Aacceptor_gain1.0000
2:27599576:A:AGacceptor_gain1.0000
2:27599577:C:Gacceptor_gain1.0000
2:27599579:TCAG:Tacceptor_loss1.0000
2:27599581:A:AGacceptor_gain1.0000
2:27599581:AG:Aacceptor_gain1.0000
2:27599581:AGG:Aacceptor_gain1.0000
2:27599582:G:GAacceptor_gain1.0000
2:27599582:GG:Gacceptor_gain1.0000
2:27599582:GGG:Gacceptor_gain1.0000
2:27599582:GGGT:Gacceptor_gain1.0000
2:27599582:GGGTC:Gacceptor_gain1.0000
2:27599678:GGTAA:Gdonor_loss1.0000
2:27599679:G:GGdonor_gain1.0000
2:27599679:GT:Gdonor_loss1.0000
2:27599684:G:GTdonor_gain1.0000
2:27600689:A:AGacceptor_gain1.0000
2:27600690:G:GGacceptor_gain1.0000
2:27600690:GGCA:Gacceptor_gain1.0000
2:27600811:AGCAG:Adonor_loss1.0000

AlphaMissense

3726 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:27600744:T:CC171R1.000
2:27600787:T:CL185S1.000
2:27615169:T:CL378S1.000
2:27615174:T:CY380H1.000
2:27615174:T:GY380D1.000
2:27615222:T:AW396R1.000
2:27615222:T:CW396R1.000
2:27615258:T:AC408S1.000
2:27615258:T:CC408R1.000
2:27615259:G:CC408S1.000
2:27615260:T:GC408W1.000
2:27616265:T:AC413S1.000
2:27616265:T:CC413R1.000
2:27616266:G:AC413Y1.000
2:27616266:G:CC413S1.000
2:27616296:T:CL423P1.000
2:27616308:T:CL427P1.000
2:27616316:T:CC430R1.000
2:27616317:G:AC430Y1.000
2:27616318:T:GC430W1.000
2:27617500:T:AC442S1.000
2:27617500:T:CC442R1.000
2:27617501:G:CC442S1.000
2:27617502:T:GC442W1.000
2:27617509:T:AC445S1.000
2:27617509:T:CC445R1.000
2:27617510:G:AC445Y1.000
2:27617510:G:CC445S1.000
2:27617511:T:GC445W1.000
2:27617521:T:CF449L1.000

dbSNP variants (sampled 300 via entrez): RS1000131716 (2:27585386 A>C,G), RS1000218101 (2:27620190 AATT>A), RS1000298168 (2:27619410 A>AT), RS1000315913 (2:27617738 T>C), RS1000410750 (2:27617067 C>A), RS1000461368 (2:27585852 T>A), RS1000608739 (2:27596656 T>C), RS1000665125 (2:27593070 A>G), RS1000703363 (2:27609972 C>T), RS1000765950 (2:27603432 G>A), RS1000857703 (2:27623440 T>C), RS1000914084 (2:27599469 T>G), RS1000957859 (2:27587278 T>C), RS1001058531 (2:27606383 GAC>G), RS1001064670 (2:27584019 C>T)

Disease associations

OMIM: gene MIM:620921 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

StudyTraitp-value
GCST001006_4Waist Circumference - Triglycerides (WC-TG)5.000000e-09
GCST001841_15Palmitoleic acid (16:1n-7) levels1.000000e-09
GCST001905_4Hypertriglyceridemia2.000000e-13
GCST003858_1Oral cavity cancer4.000000e-08
GCST005308_2Nonalcoholic fatty liver disease1.000000e-06
GCST008103_38Bipolar disorder1.000000e-07
GCST008985_2Triglycerides7.000000e-12
GCST008985_3Triglycerides7.000000e-07
GCST010060_6Cholesterol3.000000e-08
GCST011320_40Type 2 diabetes or prostate cancer (pleiotropy)1.000000e-08
GCST90000025_804Appendicular lean mass5.000000e-13

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0000195metabolic syndrome
EFO:0004530triglyceride measurement
EFO:0004574total cholesterol measurement
EFO:0004980appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, decreases methylation6
GSK-J4decreases expression1
TAK-243increases sumoylation1
methylmercuric chloridedecreases expression1
trichostatin Adecreases expression1
beta-lapachonedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cupric oxideincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, 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 aciddecreases expression1
Leflunomidedecreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Ethanoldecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Cisplatinincreases expression, affects cotreatment1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Rotenonedecreases expression1
Smokeincreases abundance, increases expression1
Urethanedecreases expression1
Cyclosporinedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_HA03K562 eGFP-ZNF512Cancer cell lineFemale

Clinical trials (associated diseases)

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