ZNF439

Summary

ZNF439 (zinc finger protein 439, HGNC:20873) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 439 (Q8NDP4). 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 90594 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_001348719

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20873
Approved symbol	ZNF439
Name	zinc finger protein 439
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp571K0837
Ensembl gene	ENSG00000171291
Ensembl biotype	protein_coding
Entrez	90594

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000304030, ENST00000442091, ENST00000455282, ENST00000592495, ENST00000592534, ENST00000682736

RefSeq mRNA: 9 — MANE Select: NM_001348719 NM_001348718, NM_001348719, NM_001348720, NM_001348721, NM_001348722, NM_001348723, NM_001348724, NM_001348725, NM_152262

CCDS: CCDS12268, CCDS86705, CCDS92520

Canonical transcript exons

ENST00000682736 — 4 exons

Exon	Start	End
ENSE00003525611	11866537	11866597
ENSE00003918598	11866205	11866331
ENSE00003921219	11848726	11848930
ENSE00003921352	11867306	11869486

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 85.99.

FANTOM5 (CAGE): breadth broad, TPM avg 4.6393 / max 118.5534, expressed in 910 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173969	4.6393	910

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	85.99	gold quality
ventricular zone	UBERON:0003053	85.64	gold quality
ganglionic eminence	UBERON:0004023	85.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.44	gold quality
cerebellar hemisphere	UBERON:0002245	82.98	gold quality
cerebellar cortex	UBERON:0002129	82.90	gold quality
calcaneal tendon	UBERON:0003701	82.21	gold quality
right hemisphere of cerebellum	UBERON:0014890	82.13	gold quality
cerebellum	UBERON:0002037	81.68	gold quality
adenohypophysis	UBERON:0002196	80.50	gold quality
left ovary	UBERON:0002119	79.67	gold quality
metanephros cortex	UBERON:0010533	79.62	gold quality
granulocyte	CL:0000094	79.44	gold quality
right ovary	UBERON:0002118	79.44	gold quality
spleen	UBERON:0002106	79.31	gold quality
pituitary gland	UBERON:0000007	79.12	gold quality
right lobe of thyroid gland	UBERON:0001119	78.48	gold quality
left lobe of thyroid gland	UBERON:0001120	78.47	gold quality
small intestine Peyer’s patch	UBERON:0003454	78.34	gold quality
tendon	UBERON:0000043	78.03	gold quality
tibial artery	UBERON:0007610	77.98	gold quality
popliteal artery	UBERON:0002250	77.97	gold quality
thyroid gland	UBERON:0002046	77.72	gold quality
mucosa of transverse colon	UBERON:0004991	77.26	gold quality
ovary	UBERON:0000992	77.25	gold quality
right lung	UBERON:0002167	77.25	gold quality
right coronary artery	UBERON:0001625	77.20	gold quality
adrenal tissue	UBERON:0018303	77.18	gold quality
skin of abdomen	UBERON:0001416	77.13	gold quality
tibial nerve	UBERON:0001323	77.10	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

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp78	ENSMUSG00000055150
rattus_norvegicus		ENSRNOG00000083797
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), 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), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 439 — Q8NDP4 (reviewed: Q8NDP4)

All UniProt accessions (4): A0A0C4DG37, A0A804HI69, C9JMA7, Q8NDP4

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 (9): NP_001335647, NP_001335648, NP_001335649, NP_001335650, NP_001335651, NP_001335652, NP_001335653, NP_001335654, NP_689475 (=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 (15 total): zinc finger region 11, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NDP4-F1	69.51	0.25

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 55 (showing top): PEREZ_TP63_TARGETS, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MARTENS_TRETINOIN_RESPONSE_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CBX7_TARGET_GENES, FOXN3_TARGET_GENES, NFKBIA_TARGET_GENES, MIR6867_5P, MIR4262, MIR6809_3P, MIR181A_5P_MIR181B_5P, MIR181D_5P, MIR181C_5P

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), protein binding (GO:0005515), 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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

316 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF439	OR6S1	Q8NH40	583
ZNF439	CWF19L2	Q2TBE0	445
ZNF439	NUDT22	Q9BRQ3	416
ZNF439	DENND11	A4D1U4	400
ZNF439	VSTM2B	A6NLU5	377
ZNF439	FAM53A	Q6NSI3	374
ZNF439	RPS7	P23821	357
ZNF439	DUS3L	Q96G46	355
ZNF439	CTDSPL2	Q05D32	349
ZNF439	CCDC181	Q5TID7	348
ZNF439	TMEM205	Q6UW68	348
ZNF439	BEND4	Q6ZU67	323
ZNF439	USP54	Q70EL1	308
ZNF439	HTR3E	A5X5Y0	300
ZNF439	COMMD5	Q9GZQ3	299

IntAct

91 interactions, top by confidence:

A	B	Type	Score
ZNF439	MDFI	psi-mi:“MI:0915”(physical association)	0.830
MDFI	ZNF439	psi-mi:“MI:0915”(physical association)	0.830
GMNN	ZNF439	psi-mi:“MI:0915”(physical association)	0.780
ZNF439	GMNN	psi-mi:“MI:0915”(physical association)	0.780
KRTAP5-9	ZNF439	psi-mi:“MI:0915”(physical association)	0.720
ZNF439	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.720
ZNF439	KRT40	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-8	ZNF439	psi-mi:“MI:0915”(physical association)	0.720
ZNF439	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.720
KRT40	ZNF439	psi-mi:“MI:0915”(physical association)	0.720
MTUS2	ZNF439	psi-mi:“MI:0915”(physical association)	0.670
ZNF439	MTUS2	psi-mi:“MI:0915”(physical association)	0.670
CCNDBP1	ZNF439	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-5	ZNF439	psi-mi:“MI:0915”(physical association)	0.560
ZNF439	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (40): ZNF439 (Two-hybrid), ZNF439 (Two-hybrid), ZNF439 (Two-hybrid), ZNF439 (Two-hybrid), ZNF439 (Two-hybrid), ZNF439 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-1 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-3 (Two-hybrid), NOTCH2NL (Two-hybrid), ZNF439 (Two-hybrid)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 25 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:

Pathway	Partners	Fold	FDR
Keratinization	9	29.5×	2e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	14
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

105 predictions. Top by Δscore:

Variant	Effect	Δscore
19:11866329:TAGG:T	donor_loss	1.0000
19:11866331:GGTA:G	donor_loss	1.0000
19:11866332:GTA:G	donor_loss	1.0000
19:11867295:A:AG	acceptor_gain	1.0000
19:11867296:T:G	acceptor_gain	1.0000
19:11867300:T:TA	acceptor_gain	1.0000
19:11867303:CA:C	acceptor_loss	1.0000
19:11867304:A:AG	acceptor_gain	1.0000
19:11867304:AG:A	acceptor_gain	1.0000
19:11867305:G:A	acceptor_loss	1.0000
19:11867305:G:GT	acceptor_gain	1.0000
19:11867305:GG:G	acceptor_gain	1.0000
19:11867305:GGA:G	acceptor_gain	1.0000
19:11867305:GGAGT:G	acceptor_gain	1.0000
19:11866292:G:T	donor_gain	0.9900
19:11866332:G:GG	donor_gain	0.9900
19:11866333:T:G	donor_loss	0.9900
19:11866532:TTTA:T	acceptor_loss	0.9900
19:11866533:TTAGG:T	acceptor_loss	0.9900
19:11866534:TAG:T	acceptor_loss	0.9900
19:11866535:A:AG	acceptor_gain	0.9900
19:11866535:AGG:A	acceptor_loss	0.9900
19:11866536:G:GC	acceptor_loss	0.9900
19:11866536:G:GG	acceptor_gain	0.9900
19:11866593:TTCAG:T	donor_loss	0.9900
19:11866594:TCAG:T	donor_loss	0.9900
19:11866595:CAGG:C	donor_loss	0.9900
19:11866596:AGGTA:A	donor_loss	0.9900
19:11866597:GGTAA:G	donor_loss	0.9900
19:11866598:GT:G	donor_loss	0.9900

AlphaMissense

3376 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:11868240:T:C	F391L	0.987
19:11868242:C:A	F391L	0.987
19:11868242:C:G	F391L	0.987
19:11868408:T:C	F447L	0.985
19:11868410:C:A	F447L	0.985
19:11868410:C:G	F447L	0.985
19:11868156:T:C	F363L	0.982
19:11868158:T:A	F363L	0.982
19:11868158:T:G	F363L	0.982
19:11868324:T:C	F419L	0.979
19:11868326:C:A	F419L	0.979
19:11868326:C:G	F419L	0.979
19:11867820:T:C	F251L	0.976
19:11867822:T:A	F251L	0.976
19:11867822:T:G	F251L	0.976
19:11868492:T:C	F475L	0.974
19:11868494:C:A	F475L	0.974
19:11868494:C:G	F475L	0.974
19:11867904:T:C	F279L	0.971
19:11867906:C:A	F279L	0.971
19:11867906:C:G	F279L	0.971
19:11868330:T:C	S421P	0.969
19:11868414:T:C	S449P	0.967
19:11868241:T:C	F391S	0.958
19:11866238:T:C	F28L	0.955
19:11866240:C:A	F28L	0.955
19:11866240:C:G	F28L	0.955
19:11868281:C:A	H404Q	0.955
19:11868281:C:G	H404Q	0.955
19:11867736:T:C	F223L	0.953

dbSNP variants (sampled 300 via entrez): RS1000075737 (19:11860587 A>C), RS1000086154 (19:11864541 C>G), RS1000186843 (19:11849077 G>T), RS1000554986 (19:11847607 G>A), RS1001017853 (19:11849776 T>A), RS1001069775 (19:11849509 C>G,T), RS1001291508 (19:11869624 CT>C,CTT,CTTTTT), RS1001297620 (19:11854721 G>A), RS1001629376 (19:11857664 G>T), RS1001731737 (19:11851920 T>A), RS1001805399 (19:11852143 G>A), RS1001903943 (19:11855976 C>T), RS1001922850 (19:11854114 C>T), RS1002010841 (19:11847350 C>T), RS1002065448 (19:11850664 A>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
GCST011358_11	Academic attainment (English)	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0011015	educational attainment

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, decreases expression, affects cotreatment	3
trichostatin A	affects cotreatment, decreases expression	2
bisphenol S	affects cotreatment, decreases methylation, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
GSK-J4	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
CGP 52608	increases reaction, affects binding	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
belinostat	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
licochalcone B	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Hydralazine	increases expression, affects cotreatment	1
Indomethacin	affects cotreatment, increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Plant Extracts	increases expression, affects cotreatment	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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