ZNF329

Summary

ZNF329 (zinc finger protein 329, HGNC:14209) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 329 (Q86UD4). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-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 79673 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 96 total
• MANE Select transcript: NM_024620

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14209
Approved symbol	ZNF329
Name	zinc finger protein 329
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12586
Ensembl gene	ENSG00000181894
Ensembl biotype	protein_coding
Entrez	79673

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 15 protein_coding, 1 nonsense_mediated_decay

ENST00000358067, ENST00000500161, ENST00000597186, ENST00000598312, ENST00000601887, ENST00000858110, ENST00000858111, ENST00000858112, ENST00000933728, ENST00000933729, ENST00000933730, ENST00000933731, ENST00000941681, ENST00000941682, ENST00000941683, ENST00000941684

RefSeq mRNA: 1 — MANE Select: NM_024620 NM_024620

CCDS: CCDS12972

Canonical transcript exons

ENST00000598312 — 4 exons

Exon	Start	End
ENSE00001249988	58142557	58142661
ENSE00002210169	58143105	58143198
ENSE00003004495	58126248	58129511
ENSE00003023331	58150752	58150789

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 90.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.4155 / max 65.0649, expressed in 1655 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182934	4.2161	1547
182936	0.9427	608
182935	0.9158	563
182937	0.3408	178

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	90.85	gold quality
cortical plate	UBERON:0005343	86.00	gold quality
parietal pleura	UBERON:0002400	84.22	gold quality
ventricular zone	UBERON:0003053	83.95	gold quality
secondary oocyte	CL:0000655	83.85	gold quality
visceral pleura	UBERON:0002401	83.05	gold quality
ganglionic eminence	UBERON:0004023	82.97	gold quality
pleura	UBERON:0000977	82.91	gold quality
amniotic fluid	UBERON:0000173	82.81	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.76	gold quality
islet of Langerhans	UBERON:0000006	81.20	gold quality
germinal epithelium of ovary	UBERON:0001304	80.97	gold quality
prefrontal cortex	UBERON:0000451	79.99	gold quality
embryo	UBERON:0000922	79.47	gold quality
renal glomerulus	UBERON:0000074	79.31	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.08	gold quality
pigmented layer of retina	UBERON:0001782	78.81	gold quality
stromal cell of endometrium	CL:0002255	78.80	gold quality
seminal vesicle	UBERON:0000998	78.43	gold quality
metanephric glomerulus	UBERON:0004736	78.32	gold quality
nephron tubule	UBERON:0001231	78.26	gold quality
primary visual cortex	UBERON:0002436	77.99	gold quality
Brodmann (1909) area 23	UBERON:0013554	77.89	gold quality
metanephros	UBERON:0000081	77.81	gold quality
frontal cortex	UBERON:0001870	77.65	gold quality
neocortex	UBERON:0001950	77.55	gold quality
cerebellar cortex	UBERON:0002129	77.53	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	77.53	gold quality
cerebellum	UBERON:0002037	77.49	gold quality
cerebellar hemisphere	UBERON:0002245	77.45	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

88 targeting ZNF329, 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-513A-5P	100.00	69.77	2465
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-3681-3P	99.88	70.46	2254

Literature-anchored findings (GeneRIF, showing 1)

• TYROBP influences a batch of genes that are related to Alzheimer’s disease; ZNF329 and RB1 significantly regulate those ‘mesenchymal’ gene expression signature genes for brain tumors. By merely leveraging gene expression data, Context Based Dependency Network (CBDN) can efficiently infer the existence of gene-gene interactions as well as their regulatory directions. (PMID:27556418)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp329	ENSMUSG00000057894
rattus_norvegicus	Zfp329	ENSRNOG00000019376
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), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 329 — Q86UD4 (reviewed: Q86UD4)

All UniProt accessions (2): Q86UD4, M0R136

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 (1): NP_078896* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050589	Ikaros_C2H2-ZF	Family

Pfam: PF00096

UniProt features (17 total): zinc finger region 12, sequence variant 2, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86UD4-F1	65.62	0.33

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 (1): 50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, CCTGTGA_MIR513, ACEVEDO_LIVER_CANCER_UP, HAMAI_APOPTOSIS_VIA_TRAIL_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY, GSE5503_MLN_DC_VS_PLN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GLI1_TARGET_GENES, NCOA2_TARGET_GENES, SUPT16H_TARGET_GENES, ZNF563_TARGET_GENES, ZNF618_TARGET_GENES

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
cis-regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

482 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF329	FAM90A1	Q86YD7	396
ZNF329	K7EJK4	K7EJK4	392
ZNF329	PGGHG	Q32M88	380
ZNF329	TMUB2	Q71RG4	367
ZNF329	PLS1	Q14651	364
ZNF329	ERICH1	Q86X53	336
ZNF329	R3HDM2	Q9Y2K5	336
ZNF329	STK32C	Q86UX6	326
ZNF329	RCCD1	A6NED2	324
ZNF329	PIMREG	Q9BSJ6	313
ZNF329	CCDC87	Q9NVE4	305
ZNF329	GXYLT1	Q4G148	305
ZNF329	HYAL4	Q2M3T9	290
ZNF329	CCDC3	Q9BQI4	290
ZNF329	GTF2E2	P29084	271

IntAct

89 interactions, top by confidence:

A	B	Type	Score
CEP70	ZNF329	psi-mi:“MI:0915”(physical association)	0.780
ZNF329	CEP70	psi-mi:“MI:0915”(physical association)	0.780
ZNF329	TRIM41	psi-mi:“MI:0915”(physical association)	0.670
TRIM41	ZNF329	psi-mi:“MI:0915”(physical association)	0.670
ZNF329	MTUS2	psi-mi:“MI:0915”(physical association)	0.670
MTUS2	ZNF329	psi-mi:“MI:0915”(physical association)	0.670
MEOX2	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
ZNF329	TRIM37	psi-mi:“MI:0915”(physical association)	0.560
ZNF329	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
KRT40	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
ZNF329	OPTN	psi-mi:“MI:0915”(physical association)	0.560
ZNF329		psi-mi:“MI:0915”(physical association)	0.560
ZNF329	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
ZNF329	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
OPTN	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-5	ZNF329	psi-mi:“MI:0915”(physical association)	0.560
ZNF329	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
ZNF329	KRT40	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (33): ZNF329 (Two-hybrid), ZNF329 (Two-hybrid), ZNF329 (Two-hybrid), ZNF329 (Two-hybrid), CEP70 (Two-hybrid), TRIM41 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-1 (Two-hybrid), KRTAP10-5 (Two-hybrid), ZNF329 (Affinity Capture-MS), ZNF329 (Affinity Capture-RNA), ZNF329 (Affinity Capture-MS), ZNF329 (Two-hybrid), ZNF329 (Two-hybrid)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

Diamond homologs: Q63HK3, Q6GQR8, Q86UD4, Q6NX49

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

771 predictions. Top by Δscore:

Variant	Effect	Δscore
19:58129507:CCAAA:C	acceptor_gain	1.0000
19:58129508:CAAA:C	acceptor_gain	1.0000
19:58129508:CAAAC:C	acceptor_gain	1.0000
19:58129512:C:CC	acceptor_gain	1.0000
19:58142662:C:CC	acceptor_gain	1.0000
19:58150698:T:TA	donor_gain	1.0000
19:58150699:C:A	donor_gain	1.0000
19:58150747:CTTA:C	donor_loss	1.0000
19:58150748:TTAC:T	donor_loss	1.0000
19:58150749:TACGG:T	donor_loss	1.0000
19:58150750:A:AC	donor_gain	1.0000
19:58150750:ACGG:A	donor_loss	1.0000
19:58150751:C:CC	donor_gain	1.0000
19:58129509:AAA:A	acceptor_gain	0.9900
19:58129510:AA:A	acceptor_gain	0.9900
19:58129510:AACT:A	acceptor_loss	0.9900
19:58129511:ACTG:A	acceptor_loss	0.9900
19:58142657:CATCT:C	acceptor_gain	0.9900
19:58142660:CT:C	acceptor_gain	0.9900
19:58150744:GCACT:G	donor_loss	0.9900
19:58150745:CACT:C	donor_loss	0.9900
19:58150746:ACTTA:A	donor_loss	0.9900
19:58150751:CG:C	donor_gain	0.9900
19:58150751:CGG:C	donor_gain	0.9900
19:58150751:CGGT:C	donor_gain	0.9900
19:58142674:C:T	acceptor_gain	0.9800
19:58150682:TCC:T	donor_gain	0.9800
19:58150751:CGGTT:C	donor_gain	0.9800
19:58129515:C:CT	acceptor_gain	0.9600
19:58142549:GTACT:G	donor_loss	0.9600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000072658 (19:58129818 C>A,T), RS1000096615 (19:58142883 T>C), RS1000114630 (19:58148056 C>A,T), RS1000218401 (19:58153344 A>T), RS1000317060 (19:58150030 A>T), RS1000657762 (19:58138960 T>A), RS1000715931 (19:58128453 C>A,G,T), RS1000723571 (19:58149395 A>G), RS1000769216 (19:58133349 G>A,T), RS1000821996 (19:58133626 T>C), RS1001101376 (19:58144037 C>A,T), RS1001353542 (19:58144946 T>A), RS1001373826 (19:58131565 A>G), RS1001484830 (19:58131290 A>G), RS1001593396 (19:58148794 A>G,T)

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

3 associations (top):

Study	Trait	p-value
GCST010204_115	Low density lipoprotein cholesterol levels	3.000000e-23
GCST010243_195	Apolipoprotein B levels	6.000000e-27
GCST010245_204	LDL cholesterol levels	1.000000e-27

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004615	apolipoprotein B measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance	3
Benzo(a)pyrene	affects methylation, decreases methylation, increases mutagenesis	3
bisphenol A	decreases expression, decreases methylation, increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases expression	2
Cyclosporine	decreases expression, increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
geraniol	increases expression	1
beta-lapachone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
abrine	increases expression	1
Arsenic	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Endosulfan	increases expression	1
Formaldehyde	decreases expression	1
Gallic Acid	decreases expression	1
Aflatoxin B1	decreases methylation	1
Sodium Selenite	decreases expression	1

Clinical trials (associated diseases)

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