ZNF43

Summary

ZNF43 (zinc finger protein 43, HGNC:13109) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 43 (P17038). May be involved in transcriptional regulation.

This gene belongs to the C2H2-type zinc finger gene family. The zinc finger proteins are involved in gene regulation and development, and are quite conserved throughout evolution. Like this gene product, a third of the zinc finger proteins containing C2H2 fingers also contain the KRAB domain, which has been found to be involved in protein-protein interactions.

Source: NCBI Gene 7594 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 25 total
• MANE Select transcript: NM_003423

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13109
Approved symbol	ZNF43
Name	zinc finger protein 43
Location	19p12
Locus type	gene with protein product
Status	Approved
Aliases	HTF6, KOX27
Ensembl gene	ENSG00000198521
Ensembl biotype	protein_coding
OMIM	603972
Entrez	7594

Gene structure

Transcript identifiers

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

ENST00000354959, ENST00000357491, ENST00000593551, ENST00000593886, ENST00000594012, ENST00000594312, ENST00000595461, ENST00000596899, ENST00000598288, ENST00000598381, ENST00000599414, ENST00000599906, ENST00000942356

RefSeq mRNA: 7 — MANE Select: NM_003423 NM_001256648, NM_001256649, NM_001256650, NM_001256651, NM_001256653, NM_001256654, NM_003423

CCDS: CCDS12413, CCDS59367, CCDS74321

Canonical transcript exons

ENST00000354959 — 4 exons

Exon	Start	End
ENSE00001418042	21804946	21809807
ENSE00003159524	21836036	21836182
ENSE00003494333	21817888	21817986
ENSE00003668336	21819095	21819221

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 89.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.4070 / max 491.2396, expressed in 1592 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180243	6.1565	1181
180237	5.9201	1384
180236	2.2064	925
180238	0.5093	235
180242	0.4685	281
180241	0.1462	53

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	89.83	gold quality
ganglionic eminence	UBERON:0004023	89.70	gold quality
ventricular zone	UBERON:0003053	89.03	gold quality
corpus callosum	UBERON:0002336	88.84	gold quality
adrenal tissue	UBERON:0018303	86.28	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.89	gold quality
bone marrow cell	CL:0002092	85.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.20	gold quality
endometrium	UBERON:0001295	84.02	gold quality
bone marrow	UBERON:0002371	83.55	gold quality
colonic epithelium	UBERON:0000397	82.97	gold quality
cortical plate	UBERON:0005343	81.46	gold quality
tonsil	UBERON:0002372	80.84	gold quality
islet of Langerhans	UBERON:0000006	80.53	gold quality
lymph node	UBERON:0000029	79.66	gold quality
sural nerve	UBERON:0015488	78.99	gold quality
cortex of kidney	UBERON:0001225	78.85	gold quality
rectum	UBERON:0001052	78.43	gold quality
testis	UBERON:0000473	78.09	gold quality
right testis	UBERON:0004534	77.82	gold quality
kidney	UBERON:0002113	77.44	gold quality
left testis	UBERON:0004533	77.19	gold quality
spleen	UBERON:0002106	77.10	gold quality
ovary	UBERON:0000992	76.91	gold quality
apex of heart	UBERON:0002098	76.79	gold quality
prostate gland	UBERON:0002367	76.50	gold quality
fallopian tube	UBERON:0003889	76.49	gold quality
metanephros cortex	UBERON:0010533	76.41	gold quality
smooth muscle tissue	UBERON:0001135	76.39	gold quality
urinary bladder	UBERON:0001255	76.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.88

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2564.1	ZNF43	More than 3 adjacent zinc fingers
MA2692.1	ZNF43	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

Upstream regulators (CollecTRI, top): E2F6

miRNA regulators (miRDB)

113 targeting ZNF43, 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-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-590-3P	99.96	74.34	6478
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-613	99.91	71.50	1710

Literature-anchored findings (GeneRIF, showing 1)

• Human embryo kidney cells that overexpressed AAK1 are adriamycin resistant (PMID:17178891)

Cross-species orthologs

0 orthologs

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 43 — P17038 (reviewed: P17038)

Alternative names: Zinc finger protein 39, Zinc finger protein HTF6, Zinc finger protein KOX27

All UniProt accessions (6): A0A087WSW2, P17038, M0QXI2, M0QYJ6, M0R0T7, M0R3D5

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. T- and B-cell lines.

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

Isoforms (2)

UniProt ID	Names	Canonical?
P17038-1	1	yes
P17038-2	2

RefSeq proteins (7): NP_001243577, NP_001243578, NP_001243579, NP_001243580, NP_001243582, NP_001243583, NP_003414* (*=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352, PF13912

UniProt features (33 total): zinc finger region 22, sequence conflict 6, sequence variant 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17038-F1	72.22	0.04

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 105 (showing top): PUJANA_CHEK2_PCC_NETWORK, MODULE_205, BLALOCK_ALZHEIMERS_DISEASE_UP, chr19p12, MODULE_123, SCHLOSSER_SERUM_RESPONSE_DN, MODULE_98, BECKER_TAMOXIFEN_RESISTANCE_DN, MODULE_198, STEIN_ESRRA_TARGETS_UP, MALONEY_RESPONSE_TO_17AAG_DN, PUJANA_XPRSS_INT_NETWORK, HAMAI_APOPTOSIS_VIA_TRAIL_UP, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (3): DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

396 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF43	CTSF	Q9UBX1	418
ZNF43	CXADR	P78310	400
ZNF43	LCP1	P13796	398
ZNF43	TACSTD2	P09758	395
ZNF43	CEACAM6	P40199	389
ZNF43	BST2	Q10589	371
ZNF43	POLR2F	P41584	368
ZNF43	Q6GMV1	Q6GMV1	358
ZNF43	KRABD2	Q6ZNG9	356
ZNF43	IDO1	P14902	353
ZNF43	CTRB1	P17538	347
ZNF43	C12orf42	Q96LP6	337
ZNF43	ZNG1F	Q4V339	314
ZNF43	ZNG1C	Q5JTY5	313
ZNF43	ZNF92	Q03936	309

IntAct

0 interactions, top by confidence:

BioGRID (4): ZNF43 (Affinity Capture-MS), ZNF43 (Co-fractionation), ZNF43 (Cross-Linking-MS (XL-MS)), ZNF43 (Affinity Capture-RNA)

ESM2 similar proteins: A2VDQ7, A6NK75, A6NN14, A6NNF4, A8MQ14, A8MTY0, A8MXY4, B7Z6K7, E9QAG8, O43345, O75290, O75373, O75437, P0CJ79, P10751, P17017, P17019, P17035, P17038, P18749, P35789, P51522, Q03923, Q03938, Q05481, Q14585, Q3SYV7, Q4V348, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6P5C7, Q6ZN08, Q6ZN57, Q6ZR52, Q86V71, Q86XN6, Q8IYB9, Q8N7Q3

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

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

5413 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:21807892:A:C	F715L	0.991
19:21807892:A:T	F715L	0.991
19:21807894:A:G	F715L	0.991
19:21807976:A:C	F687L	0.991
19:21807976:A:T	F687L	0.991
19:21807978:A:G	F687L	0.991
19:21807887:C:G	R717P	0.988
19:21808564:A:C	F491L	0.988
19:21808564:A:T	F491L	0.988
19:21808566:A:G	F491L	0.988
19:21807808:A:C	F743L	0.987
19:21807808:A:T	F743L	0.987
19:21807810:A:G	F743L	0.987
19:21808312:A:C	F575L	0.985
19:21808312:A:T	F575L	0.985
19:21808314:A:G	F575L	0.985
19:21807724:G:C	F771L	0.982
19:21807724:G:T	F771L	0.982
19:21807726:A:G	F771L	0.982
19:21808060:A:C	F659L	0.982
19:21808060:A:T	F659L	0.982
19:21808062:A:G	F659L	0.982
19:21808396:A:C	F547L	0.981
19:21808396:A:T	F547L	0.981
19:21808398:A:G	F547L	0.981
19:21807875:A:G	L721P	0.979
19:21808228:A:C	F603L	0.978
19:21808228:A:T	F603L	0.978
19:21808230:A:G	F603L	0.978
19:21808648:A:C	F463L	0.977

dbSNP variants (sampled 300 via entrez): RS1000014656 (19:21847163 C>G), RS1000042857 (19:21812992 T>C), RS1000048760 (19:21835336 T>A), RS1000138487 (19:21852438 T>C,G), RS1000147511 (19:21831244 T>C), RS1000153979 (19:21846879 T>C), RS1000155814 (19:21820282 T>A), RS1000216861 (19:21807121 G>A,T), RS1000236761 (19:21848487 G>A), RS1000268029 (19:21820584 AAAAAG>A), RS1000270525 (19:21847080 C>T), RS1000406173 (19:21842641 T>C), RS1000410562 (19:21813264 A>G,T), RS1000437453 (19:21842357 T>A), RS1000447829 (19:21852151 G>A)

Disease associations

OMIM: gene MIM:603972 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

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 expression, decreases expression	5
trichostatin A	decreases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, increases methylation	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
methylselenic acid	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
cobaltous chloride	increases expression	1
potassium chromate(VI)	increases expression	1
nickel sulfate	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
Sunitinib	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Niclosamide	decreases expression	1
Ozone	affects expression, increases abundance	1
Smoke	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Vanadates	decreases expression	1
Isotretinoin	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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