ZNF343

Summary

ZNF343 (zinc finger protein 343, HGNC:16017) is a protein-coding gene on chromosome 20p13, encoding Zinc finger protein 343 (Q6P1L6). May be involved in transcriptional regulation.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 79175 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 116 total
• MANE Select transcript: NM_024325

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16017
Approved symbol	ZNF343
Name	zinc finger protein 343
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	MGC10715
Ensembl gene	ENSG00000088876
Ensembl biotype	protein_coding
Entrez	79175

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 22 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000278772, ENST00000358413, ENST00000381253, ENST00000421216, ENST00000445484, ENST00000465019, ENST00000612935, ENST00000617391, ENST00000674000, ENST00000911235, ENST00000911236, ENST00000911237, ENST00000911238, ENST00000911239, ENST00000911240, ENST00000911241, ENST00000911242, ENST00000928350, ENST00000928351, ENST00000928352, ENST00000952204, ENST00000952205, ENST00000952206, ENST00000952207

RefSeq mRNA: 11 — MANE Select: NM_024325 NM_001282495, NM_001282496, NM_001282497, NM_001282498, NM_001282499, NM_001321800, NM_001321801, NM_001321802, NM_001321803, NM_001321805, NM_024325

CCDS: CCDS13028, CCDS74692, CCDS74693, CCDS74694

Canonical transcript exons

ENST00000278772 — 6 exons

Exon	Start	End
ENSE00001487976	2508881	2508915
ENSE00003466077	2481817	2484656
ENSE00003475814	2493778	2494044
ENSE00003641561	2500656	2500742
ENSE00003645952	2493519	2493577
ENSE00003787668	2492699	2492825

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 87.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.3031 / max 114.8289, expressed in 1676 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186096	5.3031	1676

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	87.17	gold quality
secondary oocyte	CL:0000655	86.70	gold quality
calcaneal tendon	UBERON:0003701	85.25	gold quality
mucosa of stomach	UBERON:0001199	82.97	gold quality
popliteal artery	UBERON:0002250	82.16	gold quality
tibial artery	UBERON:0007610	82.16	gold quality
gastrocnemius	UBERON:0001388	81.71	gold quality
muscle of leg	UBERON:0001383	81.33	gold quality
lower esophagus muscularis layer	UBERON:0035833	81.26	gold quality
lower esophagus	UBERON:0013473	81.23	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	81.15	gold quality
aorta	UBERON:0000947	81.10	gold quality
muscle layer of sigmoid colon	UBERON:0035805	80.96	gold quality
body of uterus	UBERON:0009853	80.94	gold quality
tendon	UBERON:0000043	80.68	gold quality
tibial nerve	UBERON:0001323	80.20	gold quality
ascending aorta	UBERON:0001496	80.17	gold quality
thoracic aorta	UBERON:0001515	80.13	gold quality
left coronary artery	UBERON:0001626	80.13	gold quality
descending thoracic aorta	UBERON:0002345	80.11	gold quality
left ovary	UBERON:0002119	80.06	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.04	gold quality
smooth muscle tissue	UBERON:0001135	79.85	gold quality
stromal cell of endometrium	CL:0002255	79.79	gold quality
ectocervix	UBERON:0012249	79.70	gold quality
skin of leg	UBERON:0001511	79.55	gold quality
left uterine tube	UBERON:0001303	79.54	gold quality
right ovary	UBERON:0002118	79.51	gold quality
right coronary artery	UBERON:0001625	79.42	gold quality
skin of abdomen	UBERON:0001416	79.27	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.25
E-MTAB-6058	no	58.07

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1711.1	ZNF343	More than 3 adjacent zinc fingers
MA1711.2	ZNF343	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28273063

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

52 targeting ZNF343, 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-6870-5P	99.99	68.55	2115
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-452-3P	99.01	66.25	1241
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-7113-3P	98.75	65.71	1120
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-4490	98.51	68.47	943

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), 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), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 343 — Q6P1L6 (reviewed: Q6P1L6)

All UniProt accessions (5): Q6P1L6, A0A087WZQ2, A0A0A0MSR0, A0A0A0MT63, A0A669KB96

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.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6P1L6-1	1	yes
Q6P1L6-2	2
Q6P1L6-3	3

RefSeq proteins (11): NP_001269424, NP_001269425, NP_001269426, NP_001269427, NP_001269428, NP_001308729, NP_001308730, NP_001308731, NP_001308732, NP_001308734, NP_077301* (*=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
IPR048414	PDRM9-like_Znf-C2H2	Domain
IPR050589	Ikaros_C2H2-ZF	Family

Pfam: PF00096, PF01352, PF21225

UniProt features (21 total): zinc finger region 12, splice variant 3, chain 1, domain 1, region of interest 1, cross-link 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P1L6-F1	67.58	0.42

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): 435

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 55 (showing top): MODULE_48, MODULE_95, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MODULE_49, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, FIGUEROA_AML_METHYLATION_CLUSTER_6_UP, PEDRIOLI_MIR31_TARGETS_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MODULE_163, IL15_UP.V1_UP, IL2_UP.V1_UP, KRAS.600.LUNG.BREAST_UP.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CREB3L4_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (9): 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), sequence-specific double-stranded DNA binding (GO:1990837), transcription cis-regulatory region binding (GO:0000976), DNA binding (GO:0003677), protein binding (GO:0005515), 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
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	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
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
nucleic acid binding	1
binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

610 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF343	TMC3	Q7Z5M5	506
ZNF343	SUMF2	Q8NBJ7	433
ZNF343	STK35	Q8TDR2	404
ZNF343	C3orf52	Q5BVD1	400
ZNF343	CLVS2	Q5SYC1	392
ZNF343	DENND10	Q8TCE6	380
ZNF343	INTS14	Q96SY0	371
ZNF343	TBC1D20	Q96BZ9	369
ZNF343	SMIM26	A0A096LP01	368
ZNF343	FAM110A	Q9BQ89	365
ZNF343	RNASE11	Q8TAA1	359
ZNF343	SLC22A24	Q8N4F4	358
ZNF343	SOX30	O94993	355
ZNF343	GTF3C3	Q9Y5Q9	333
ZNF343	AP5S1	Q9NUS5	324

IntAct

68 interactions, top by confidence:

A	B	Type	Score
ZNF343	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
UBQLN1	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
TEPSIN	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF835	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
PAX9	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
KLC4	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF319	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	NME7	psi-mi:“MI:0915”(physical association)	0.560
SDCBP	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	FAM90A1	psi-mi:“MI:0915”(physical association)	0.560
USP20	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	NUDT22	psi-mi:“MI:0915”(physical association)	0.560
BFSP2	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	NEK6	psi-mi:“MI:0915”(physical association)	0.560
STK16	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ACTN3	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	TEPSIN	psi-mi:“MI:0915”(physical association)	0.560
RAD51D	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	ZNF835	psi-mi:“MI:0915”(physical association)	0.560
JRK	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
RUNX1T1	ZNF343	psi-mi:“MI:0915”(physical association)	0.560
ZNF343	CCDC125	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (25): ZNF343 (Two-hybrid), ZNF343 (Affinity Capture-RNA), ZNF343 (Two-hybrid), STK16 (Two-hybrid), NEK6 (Two-hybrid), ZNF835 (Two-hybrid), USP20 (Two-hybrid), KLC4 (Two-hybrid), SDCBP (Two-hybrid), NME7 (Two-hybrid), TRIM41 (Two-hybrid), NUDT22 (Two-hybrid), NXF1 (Two-hybrid), ZNF319 (Two-hybrid), ENTHD2 (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: A2VDP4, A3KN32, A3KN36, A6NM28, A6QLU5, A6QPT6, A7MBI1, B4DU55, E9PYI1, G3X9G7, O60765, O75290, O75467, O94892, O95780, P10072, P15622, P17030, P17032, P17098, P21506, P51508, P51786, P52736, P52738, Q06730, Q06732, Q08DG8, Q14929, Q16587, Q29RZ4, Q2M218, Q2TL60, Q49AA0, Q4R8H9, Q4V8A8, Q571J5, Q5CZA5, Q5HYK9, Q5MCW4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	91
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

940 predictions. Top by Δscore:

Variant	Effect	Δscore
20:2492693:CCTTA:C	donor_loss	1.0000
20:2492694:CTTA:C	donor_loss	1.0000
20:2492695:TTA:T	donor_loss	1.0000
20:2492696:TACC:T	donor_loss	1.0000
20:2492697:A:AC	donor_gain	1.0000
20:2492697:A:AG	donor_loss	1.0000
20:2492697:AC:A	donor_gain	1.0000
20:2492698:C:CC	donor_gain	1.0000
20:2492698:CC:C	donor_gain	1.0000
20:2492698:CCCA:C	donor_gain	1.0000
20:2492714:T:TA	donor_gain	1.0000
20:2492826:CTAC:C	acceptor_loss	1.0000
20:2493518:CCA:C	donor_gain	1.0000
20:2493573:CAAGC:C	acceptor_gain	1.0000
20:2508941:T:TA	donor_gain	1.0000
20:2492698:CCCAA:C	donor_gain	0.9900
20:2492826:C:CC	acceptor_gain	0.9900
20:2493512:AACTC:A	donor_loss	0.9900
20:2493513:ACTC:A	donor_loss	0.9900
20:2493513:ACTCA:A	donor_loss	0.9900
20:2493514:CT:C	donor_loss	0.9900
20:2493515:TCA:T	donor_loss	0.9900
20:2493516:C:CG	donor_loss	0.9900
20:2493517:A:AC	donor_gain	0.9900
20:2493518:C:A	donor_loss	0.9900
20:2493518:C:CA	donor_loss	0.9900
20:2493518:C:CC	donor_gain	0.9900
20:2493518:CCACT:C	donor_gain	0.9900
20:2493576:GCC:G	acceptor_loss	0.9900
20:2493576:GCCTA:G	acceptor_loss	0.9900

AlphaMissense

3951 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:2484043:A:C	F306L	0.998
20:2484043:A:T	F306L	0.998
20:2484045:A:G	F306L	0.998
20:2483455:A:C	F502L	0.997
20:2483455:A:T	F502L	0.997
20:2483457:A:G	F502L	0.997
20:2483623:A:C	F446L	0.997
20:2483623:A:T	F446L	0.997
20:2483625:A:G	F446L	0.997
20:2483707:A:C	F418L	0.997
20:2483707:A:T	F418L	0.997
20:2483709:A:G	F418L	0.997
20:2483287:A:C	F558L	0.996
20:2483287:A:T	F558L	0.996
20:2483289:A:G	F558L	0.996
20:2483371:A:C	F530L	0.996
20:2483371:A:T	F530L	0.996
20:2483373:A:G	F530L	0.996
20:2483539:A:C	F474L	0.996
20:2483539:A:T	F474L	0.996
20:2483541:A:G	F474L	0.996
20:2483203:A:C	F586L	0.995
20:2483203:A:T	F586L	0.995
20:2483205:A:G	F586L	0.995
20:2483791:A:C	F390L	0.995
20:2483791:A:T	F390L	0.995
20:2483793:A:G	F390L	0.995
20:2483690:A:G	L424P	0.994
20:2483875:A:C	F362L	0.994
20:2483875:A:T	F362L	0.994

dbSNP variants (sampled 300 via entrez): RS1000062112 (20:2511696 A>G), RS1000188723 (20:2501390 G>C), RS1000269316 (20:2485284 C>A), RS1000367334 (20:2496957 G>A), RS1000388501 (20:2498698 A>G), RS1000440618 (20:2491856 AT>A,ATT), RS1000451603 (20:2500765 G>A), RS1000471851 (20:2491573 GA>G,GAA), RS1000507913 (20:2486696 G>A), RS1000523010 (20:2500610 G>A,T), RS1000541843 (20:2490196 C>A,T), RS1000578676 (20:2484964 C>T), RS1000727602 (20:2495026 T>C), RS1000777396 (20:2493420 T>C), RS1000795462 (20:2496621 T>C)

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

2 associations (top):

Study	Trait	p-value
GCST003139_20	Glomerular filtration rate in chronic kidney disease	2.000000e-06
GCST004723_14	Conotruncal heart defects (maternal effects)	7.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs4815273	ZNF343	3	0.00	1	hydrochlorothiazide
rs6083538	ZNF343		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, decreases expression	3
Arsenic	affects methylation, decreases methylation	2
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression, increases expression	1
arsenite	increases methylation	1
nickel sulfate	decreases expression	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Leflunomide	increases expression	1
Amphotericin B	increases expression	1
Benzo(a)pyrene	increases methylation	1
Catechin	affects cotreatment, decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Methyl Methanesulfonate	increases expression	1
Phthalic Acids	decreases methylation	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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