ZNF429

Summary

ZNF429 (zinc finger protein 429, HGNC:20817) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 429 (Q86V71). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor 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 353088 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 103 total
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 4 cancer types
• MANE Select transcript: NM_001001415

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20817
Approved symbol	ZNF429
Name	zinc finger protein 429
Location	19p12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000197013
Ensembl biotype	protein_coding
OMIM	621242
Entrez	353088

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding_CDS_not_defined, 4 protein_coding

ENST00000358491, ENST00000594022, ENST00000594385, ENST00000596126, ENST00000596237, ENST00000597078, ENST00000597556, ENST00000598747, ENST00000967842

RefSeq mRNA: 6 — MANE Select: NM_001001415 NM_001001415, NM_001346912, NM_001346913, NM_001346914, NM_001346915, NM_001346916

CCDS: CCDS42537

Canonical transcript exons

ENST00000358491 — 4 exons

Exon	Start	End
ENSE00001423830	21536280	21540668
ENSE00003201912	21505602	21505774
ENSE00003471539	21530589	21530684
ENSE00003630617	21529658	21529784

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 89.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.7248 / max 151.8242, expressed in 1558 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174893	6.5935	1556
174894	0.1313	21

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	89.84	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.11	gold quality
spinal cord	UBERON:0002240	86.85	gold quality
islet of Langerhans	UBERON:0000006	86.70	gold quality
medial globus pallidus	UBERON:0002477	84.86	gold quality
adrenal tissue	UBERON:0018303	84.62	gold quality
hypothalamus	UBERON:0001898	84.21	gold quality
right adrenal gland cortex	UBERON:0035827	84.10	gold quality
right adrenal gland	UBERON:0001233	84.09	gold quality
cortical plate	UBERON:0005343	84.03	gold quality
cerebellar hemisphere	UBERON:0002245	84.02	gold quality
cerebellar cortex	UBERON:0002129	83.87	gold quality
amygdala	UBERON:0001876	83.86	gold quality
left adrenal gland cortex	UBERON:0035825	83.67	gold quality
left adrenal gland	UBERON:0001234	83.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	83.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.03	gold quality
pancreas	UBERON:0001264	82.88	gold quality
anterior cingulate cortex	UBERON:0009835	82.84	gold quality
body of pancreas	UBERON:0001150	82.80	gold quality
adrenal gland	UBERON:0002369	82.78	gold quality
cerebellum	UBERON:0002037	82.53	gold quality
putamen	UBERON:0001874	82.16	gold quality
ventricular zone	UBERON:0003053	82.16	gold quality
adenohypophysis	UBERON:0002196	82.11	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.02	gold quality
ganglionic eminence	UBERON:0004023	81.81	gold quality
caudate nucleus	UBERON:0001873	81.69	gold quality
adrenal cortex	UBERON:0001235	81.65	gold quality
calcaneal tendon	UBERON:0003701	81.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting ZNF429, 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-504-3P	99.30	67.18	1745
HSA-MIR-10395-3P	98.10	66.70	1726
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-1972	97.67	67.38	1172
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-122-5P	97.23	64.92	1024
HSA-MIR-6879-3P	93.93	64.00	759

Cross-species orthologs

22 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp273	ENSMUSG00000030446
mus_musculus	Zfp455	ENSMUSG00000051037
mus_musculus	Zfp85	ENSMUSG00000058331
mus_musculus	Zfp708	ENSMUSG00000058883
mus_musculus	Rsl1	ENSMUSG00000058900
mus_musculus	Zfp874b	ENSMUSG00000059839
mus_musculus	Zfp874a	ENSMUSG00000069206
mus_musculus	Zfp58	ENSMUSG00000071291
mus_musculus	Rslcan18	ENSMUSG00000074824
mus_musculus	Zfp429	ENSMUSG00000078994
mus_musculus	Zfp456	ENSMUSG00000078995
mus_musculus	Zfp493	ENSMUSG00000090659
mus_musculus	Zfp87	ENSMUSG00000097333
rattus_norvegicus	LOC102547287	ENSRNOG00000016462
rattus_norvegicus	Zfp58	ENSRNOG00000017963
rattus_norvegicus	Zfp455	ENSRNOG00000031576
rattus_norvegicus	Zfp455l1	ENSRNOG00000042308
rattus_norvegicus	Zfp273l-ps1	ENSRNOG00000046353
rattus_norvegicus	Zfp708	ENSRNOG00000049662
rattus_norvegicus	Rsl1	ENSRNOG00000057159
rattus_norvegicus		ENSRNOG00000066838
rattus_norvegicus		ENSRNOG00000085686

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 429 — Q86V71 (reviewed: Q86V71)

All UniProt accessions (3): Q86V71, M0QYC4, M0QZ47

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

RefSeq proteins (6): NP_001001415, NP_001333841, NP_001333842, NP_001333843, NP_001333844, NP_001333845 (=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
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352

UniProt features (30 total): zinc finger region 18, sequence conflict 7, chain 1, domain 1, region of interest 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86V71-F1	72.50	0.11

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): 605

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 28 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, chr19p12, TGGAAA_NFAT_Q4_01, YOSHIMURA_MAPK8_TARGETS_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, KATSANOU_ELAVL1_TARGETS_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, ZWANG_DOWN_BY_2ND_EGF_PULSE, NFE2L2.V2, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

GO Biological Process (3): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), 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 transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
negative regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

368 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF429	ICA1L	Q8NDH6	498
ZNF429	CYP20A1	Q6UW02	497
ZNF429	GK5	Q6ZS86	493
ZNF429	CYB5D2	Q8WUJ1	416
ZNF429	ANAPC16	Q96DE5	398
ZNF429	CIAO1	O76071	375
ZNF429	ZNG1E	Q5RIA9	358
ZNF429	ZNG1F	Q4V339	355
ZNF429	ZNG1C	Q5JTY5	354
ZNF429	C17orf75	Q9HAS0	346
ZNF429	DCAF10	Q5QP82	345
ZNF429	RAB3IP	Q96QF0	319
ZNF429	FBLIM1	Q8WUP2	306
ZNF429	SSH1	Q8WYL5	299
ZNF429	S4R434	S4R434	293

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ECE1	ZNF429	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (1): ZNF429 (Affinity Capture-RNA)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 4 cancer types — BLCA, CHOL, HCC, PRAD.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	87
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

956 predictions. Top by Δscore:

Variant	Effect	Δscore
19:21529639:T:A	acceptor_gain	1.0000
19:21529656:AGG:A	acceptor_gain	1.0000
19:21529657:GGG:G	acceptor_gain	1.0000
19:21529780:CCTGG:C	donor_loss	1.0000
19:21529784:GGTGA:G	donor_loss	1.0000
19:21529785:G:GA	donor_loss	1.0000
19:21529786:T:A	donor_loss	1.0000
19:21530682:CAGG:C	donor_loss	1.0000
19:21530684:GG:G	donor_loss	1.0000
19:21530686:T:G	donor_loss	1.0000
19:21536278:A:AG	acceptor_gain	1.0000
19:21536278:AGTT:A	acceptor_gain	1.0000
19:21536279:G:GG	acceptor_gain	1.0000
19:21536279:GTT:G	acceptor_gain	1.0000
19:21536279:GTTG:G	acceptor_gain	1.0000
19:21536279:GTTGT:G	acceptor_gain	1.0000
19:21529636:T:TA	acceptor_gain	0.9900
19:21529646:T:TA	acceptor_gain	0.9900
19:21529650:T:TA	acceptor_gain	0.9900
19:21529654:TCAGG:T	acceptor_loss	0.9900
19:21529655:CA:C	acceptor_loss	0.9900
19:21529656:A:AG	acceptor_gain	0.9900
19:21529656:A:C	acceptor_loss	0.9900
19:21529656:AG:A	acceptor_gain	0.9900
19:21529657:G:GA	acceptor_gain	0.9900
19:21529657:GG:G	acceptor_gain	0.9900
19:21529657:GGGA:G	acceptor_gain	0.9900
19:21529657:GGGAC:G	acceptor_gain	0.9900
19:21529783:GG:G	donor_gain	0.9900
19:21529784:GG:G	donor_gain	0.9900

AlphaMissense

4470 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:21537689:T:C	F546L	0.996
19:21537691:T:A	F546L	0.996
19:21537691:T:G	F546L	0.996
19:21537773:T:C	F574L	0.996
19:21537775:T:A	F574L	0.996
19:21537775:T:G	F574L	0.996
19:21537857:T:C	F602L	0.992
19:21537859:T:A	F602L	0.992
19:21537859:T:G	F602L	0.992
19:21536849:T:C	F266L	0.987
19:21536851:T:A	F266L	0.987
19:21536851:T:G	F266L	0.987
19:21537605:T:C	F518L	0.986
19:21537607:T:A	F518L	0.986
19:21537607:T:G	F518L	0.986
19:21537941:T:C	F630L	0.986
19:21537943:T:A	F630L	0.986
19:21537943:T:G	F630L	0.986
19:21537521:T:C	F490L	0.985
19:21537523:T:A	F490L	0.985
19:21537523:T:G	F490L	0.985
19:21537101:T:C	F350L	0.982
19:21537103:T:A	F350L	0.982
19:21537103:T:G	F350L	0.982
19:21537864:G:C	R604P	0.981
19:21537017:T:C	F322L	0.980
19:21537019:T:A	F322L	0.980
19:21537019:T:G	F322L	0.980
19:21537696:G:C	R548P	0.980
19:21537792:T:C	L580P	0.980

dbSNP variants (sampled 300 via entrez): RS1000058279 (19:21514546 G>A), RS1000159261 (19:21539166 T>A), RS1000211023 (19:21539387 T>C), RS1000248485 (19:21511301 A>G), RS1000368055 (19:21526096 G>C,T), RS1000460288 (19:21538320 AG>A), RS1000564455 (19:21510724 G>A), RS1000691416 (19:21505238 C>T), RS1000879390 (19:21527457 T>C), RS1000935058 (19:21510478 G>T), RS1000992640 (19:21522064 C>G,T), RS1001090785 (19:21515688 A>G), RS1001122226 (19:21515948 G>C), RS1001140655 (19:21521173 T>C), RS1001398310 (19:21509978 T>C)

Disease associations

OMIM: gene MIM:621242 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000326_3	Pain	2.000000e-10
GCST003209_2	Colorectal or endometrial cancer	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004230	endometrial neoplasm

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
sulforaphane	affects binding	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases methylation	1
Vanadates	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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