ZNF529

Summary

ZNF529 (zinc finger protein 529, HGNC:29328) is a protein-coding gene on chromosome 19q13.12, encoding Zinc finger protein 529 (Q6P280). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 57711 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 78 total
• MANE Select transcript: NM_020951

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29328
Approved symbol	ZNF529
Name	zinc finger protein 529
Location	19q13.12
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1615
Ensembl gene	ENSG00000186020
Ensembl biotype	protein_coding
Entrez	57711

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000334116, ENST00000452073, ENST00000585960, ENST00000585983, ENST00000586115, ENST00000586458, ENST00000587286, ENST00000590656, ENST00000591340, ENST00000867184, ENST00000867185, ENST00000867186, ENST00000867187, ENST00000933095

RefSeq mRNA: 6 — MANE Select: NM_020951 NM_001145649, NM_001145650, NM_001321351, NM_001352272, NM_001352273, NM_020951

CCDS: CCDS54256, CCDS82335

Canonical transcript exons

ENST00000591340 — 5 exons

Exon	Start	End
ENSE00002749174	36573140	36573292
ENSE00002890383	36543613	36548322
ENSE00003466838	36554670	36554796
ENSE00003497591	36572333	36572392
ENSE00003623172	36556104	36556197

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 91.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.7339 / max 265.8441, expressed in 1776 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180682	9.7435	1744
180685	3.5542	1010
180684	0.2057	99
180683	0.1227	28
180686	0.1078	39

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	91.64	gold quality
germinal epithelium of ovary	UBERON:0001304	90.12	gold quality
Brodmann (1909) area 23	UBERON:0013554	89.43	gold quality
oocyte	CL:0000023	89.26	gold quality
cortical plate	UBERON:0005343	88.72	gold quality
secondary oocyte	CL:0000655	88.58	gold quality
buccal mucosa cell	CL:0002336	87.12	silver quality
skin of hip	UBERON:0001554	86.87	gold quality
pigmented layer of retina	UBERON:0001782	85.83	gold quality
upper leg skin	UBERON:0004262	85.79	gold quality
right uterine tube	UBERON:0001302	85.76	gold quality
cerebellar hemisphere	UBERON:0002245	85.61	gold quality
cerebellar cortex	UBERON:0002129	85.54	gold quality
adrenal tissue	UBERON:0018303	85.40	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.38	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.84	gold quality
cerebellum	UBERON:0002037	84.77	gold quality
primary visual cortex	UBERON:0002436	84.65	gold quality
caput epididymis	UBERON:0004358	84.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.00	gold quality
calcaneal tendon	UBERON:0003701	84.00	gold quality
corpus callosum	UBERON:0002336	83.91	gold quality
entorhinal cortex	UBERON:0002728	83.89	gold quality
parietal pleura	UBERON:0002400	83.75	gold quality
tibia	UBERON:0000979	83.69	gold quality
spinal cord	UBERON:0002240	83.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.30	gold quality
nucleus accumbens	UBERON:0001882	83.30	gold quality
cauda epididymis	UBERON:0004360	83.17	gold quality
ganglionic eminence	UBERON:0004023	82.88	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	11.29
E-ANND-3	yes	4.82
E-GEOD-75367	no	254.31

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

170 targeting ZNF529, 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-5011-5P	100.00	83.46	5820
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4789-5P	99.98	70.76	2721

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), 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), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 529 — Q6P280 (reviewed: Q6P280)

All UniProt accessions (7): A0A0C4DFR4, Q6P280, K7EKM0, K7EL49, K7ELR0, K7ES80, K7ESA1

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

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

RefSeq proteins (6): NP_001139121, NP_001139122, NP_001308280, NP_001339201, NP_001339202, NP_066002* (*=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

Pfam: PF00096, PF01352

UniProt features (19 total): zinc finger region 12, cross-link 2, sequence conflict 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P280-F1	58.59	0.16

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 (2): 87, 268

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 125 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GCM_GSPT1, GCM_ZNF198, GCM_BCL2L1, GCM_SUFU, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, GCM_NF2, MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6, GCM_RBM8A, NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP, BROWNE_HCMV_INFECTION_48HR_UP, GCM_RAN, GCM_MLL

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 transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), sequence-specific DNA binding (GO:0043565), 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
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

538 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF529	RSPH14	Q9UHP6	580
ZNF529	SNX14	Q9Y5W7	578
ZNF529	PNRC2	Q9NPJ4	502
ZNF529	GARIN5A	Q6IPT2	477
ZNF529	SLC6A13	Q9NSD5	470
ZNF529	NLE1	Q9NVX2	466
ZNF529	KHDC4	Q7Z7F0	450
ZNF529	LGALS4	P56470	407
ZNF529	SRPRB	Q9Y5M8	406
ZNF529	MRPS12	O15235	396
ZNF529	CLIP4	Q8N3C7	380
ZNF529	WDR44	Q5JSH3	377
ZNF529	GPLD1	P80108	373
ZNF529	FOXC1	Q12948	372
ZNF529	LIPC	P11150	368

IntAct

3 interactions, top by confidence:

A	B	Type	Score
MYL2	ZNF529	psi-mi:“MI:0915”(physical association)	0.490

BioGRID (9): ZNF529 (Biochemical Activity), ZNF529 (Two-hybrid), ZNF529 (Affinity Capture-MS), ZNF529 (Protein-peptide), ZNF529 (Affinity Capture-MS), ZNF529 (Affinity Capture-MS), ZNF529 (Cross-Linking-MS (XL-MS)), ZNF529 (Proximity Label-MS), ZNF529 (Affinity Capture-RNA)

ESM2 similar proteins: A0JPL0, A6NK53, E7ETH6, E9Q8G5, O14628, P21506, P51508, Q09FC8, Q13360, Q2M218, Q2M3X9, Q2VY69, Q3KQV3, Q3SY52, Q4R882, Q5HY98, Q5REN4, Q5RES8, Q68DI1, Q6NX49, Q6P280, Q6PG37, Q6V9R5, Q6ZMW2, Q7Z340, Q86XU0, Q8IYI8, Q8N587, Q8N720, Q8N859, Q8NB42, Q8NDW4, Q8NEK5, Q8WXB4, Q96MR9, Q96MU6, Q96NG8, Q96NJ3, Q96SR6, Q9BR84

Diamond homologs: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	69
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

920 predictions. Top by Δscore:

Variant	Effect	Δscore
19:36554665:TTTA:T	donor_loss	1.0000
19:36554666:TTACC:T	donor_loss	1.0000
19:36554667:TA:T	donor_loss	1.0000
19:36554668:A:AC	donor_gain	1.0000
19:36554668:A:C	donor_loss	1.0000
19:36554668:AC:A	donor_gain	1.0000
19:36554669:C:CC	donor_gain	1.0000
19:36554669:CC:C	donor_gain	1.0000
19:36554672:A:AC	donor_gain	0.9900
19:36554709:C:A	donor_gain	0.9900
19:36554792:AGTTC:A	acceptor_gain	0.9900
19:36554793:GTTC:G	acceptor_gain	0.9900
19:36554794:TTC:T	acceptor_gain	0.9900
19:36554795:TC:T	acceptor_gain	0.9900
19:36554796:CC:C	acceptor_gain	0.9900
19:36554797:C:CC	acceptor_gain	0.9900
19:36554797:CTGAA:C	acceptor_loss	0.9900
19:36554798:T:A	acceptor_loss	0.9900
19:36572393:C:CC	acceptor_gain	0.9900
19:36572403:A:T	acceptor_gain	0.9900
19:36548319:AAATC:A	acceptor_loss	0.9800
19:36548322:TC:T	acceptor_loss	0.9800
19:36548323:C:CA	acceptor_loss	0.9800
19:36548324:T:A	acceptor_loss	0.9800
19:36551868:T:C	donor_gain	0.9800
19:36554708:T:TA	donor_gain	0.9800
19:36556102:A:AC	donor_gain	0.9800
19:36556103:C:CC	donor_gain	0.9800
19:36572402:C:CT	acceptor_gain	0.9800
19:36548323:C:CC	acceptor_gain	0.9700

AlphaMissense

3802 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:36547265:A:C	F431L	0.998
19:36547265:A:T	F431L	0.998
19:36547267:A:G	F431L	0.998
19:36547517:A:C	F347L	0.998
19:36547517:A:T	F347L	0.998
19:36547519:A:G	F347L	0.998
19:36547601:G:C	F319L	0.998
19:36547601:G:T	F319L	0.998
19:36547603:A:G	F319L	0.998
19:36547097:A:C	F487L	0.997
19:36547097:A:T	F487L	0.997
19:36547099:A:G	F487L	0.997
19:36547332:A:G	L409P	0.997
19:36547349:A:C	F403L	0.997
19:36547349:A:T	F403L	0.997
19:36547351:A:G	F403L	0.997
19:36547433:A:C	F375L	0.997
19:36547433:A:T	F375L	0.997
19:36547435:A:G	F375L	0.997
19:36547584:A:G	L325P	0.997
19:36547408:G:C	H384D	0.996
19:36547500:A:G	L353P	0.996
19:36547572:T:G	Q329P	0.996
19:36554762:A:G	F48S	0.996
19:36547154:A:C	H468Q	0.995
19:36547154:A:T	H468Q	0.995
19:36547322:A:C	H412Q	0.995
19:36547322:A:T	H412Q	0.995
19:36547324:G:C	H412D	0.995
19:36547336:A:G	S408P	0.995

dbSNP variants (sampled 300 via entrez): RS1000027576 (19:36583680 GA>G,GAA), RS1000059156 (19:36595215 A>C,G), RS1000156644 (19:36589737 G>C), RS1000165260 (19:36602441 T>A,C), RS1000184058 (19:36555034 T>C), RS1000184853 (19:36606121 T>G), RS1000237346 (19:36605881 T>C), RS1000263490 (19:36548747 G>A), RS1000334977 (19:36581828 G>A), RS1000364544 (19:36570486 A>G), RS1000367485 (19:36598944 C>G,T), RS1000500302 (19:36591490 C>T), RS1000543165 (19:36553165 G>A), RS1000606742 (19:36555657 T>C), RS1000687488 (19:36561033 T>C,G)

Disease associations

OMIM: gene `` | 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
GCST011347_60	Low density lipoprotein cholesterol levels	1.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression	6
trichostatin A	affects cotreatment, decreases expression, increases expression	3
mercuric bromide	decreases expression, affects cotreatment	2
Air Pollutants	increases abundance, increases expression, decreases expression	2
Benzo(a)pyrene	affects methylation, decreases methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
aflatoxin B2	increases methylation	1
resorcinol	increases expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
Temozolomide	increases expression	1
Leflunomide	increases expression	1
Catechin	affects cotreatment, increases expression	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Naled	affects expression	1
Urethane	affects expression	1
Cyclosporine	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XW59	HEK293 eGFP-ZNF529	Transformed cell line	Female

Clinical trials (associated diseases)

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