ZNF346

gene
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Also known as JAZZfp346

Summary

ZNF346 (zinc finger protein 346, HGNC:16403) is a protein-coding gene on chromosome 5q35.2, encoding Zinc finger protein 346 (Q9UL40). Binds with low affinity to dsDNA and ssRNA, and with high affinity to dsRNA, with no detectable sequence specificity.

The protein encoded by this gene is a nucleolar, zinc finger protein that preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids, rather than DNA alone. Mutational studies indicate that the zinc finger domains are not only essential for dsRNA binding, but are also required for its nucleolar localization. The encoded protein may be involved in cell growth and survival. It plays a role in protecting neurons by inhibiting cell cycle re-entry via stimulation of p21 gene expression. Alternative splicing of this gene results in multiple transcript variants.

Source: NCBI Gene 23567 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 46 total
  • MANE Select transcript: NM_012279

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16403
Approved symbolZNF346
Namezinc finger protein 346
Location5q35.2
Locus typegene with protein product
StatusApproved
AliasesJAZ, Zfp346
Ensembl geneENSG00000113761
Ensembl biotypeprotein_coding
OMIM605308
Entrez23567

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 27 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay

ENST00000358149, ENST00000503039, ENST00000503425, ENST00000504600, ENST00000506693, ENST00000508155, ENST00000510933, ENST00000511834, ENST00000512315, ENST00000513587, ENST00000883438, ENST00000883439, ENST00000883440, ENST00000883441, ENST00000883442, ENST00000883443, ENST00000883444, ENST00000883445, ENST00000883446, ENST00000883447, ENST00000883448, ENST00000883449, ENST00000921160, ENST00000921161, ENST00000921162, ENST00000921163, ENST00000921164, ENST00000921165, ENST00000947036, ENST00000947037, ENST00000947038

RefSeq mRNA: 10 — MANE Select: NM_012279 NM_001308213, NM_001308214, NM_001308215, NM_001308216, NM_001308218, NM_001308219, NM_001308221, NM_001308223, NM_001363713, NM_012279

CCDS: CCDS4409, CCDS78094, CCDS83052, CCDS83053, CCDS83054, CCDS87353

Canonical transcript exons

ENST00000358149 — 7 exons

ExonStartEnd
ENSE00001095546177041778177041870
ENSE00001095551177044389177044533
ENSE00001412343177022696177022913
ENSE00001426578177064512177067985
ENSE00003501605177041126177041229
ENSE00003575048177062058177062151
ENSE00003617799177050751177050936

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 90.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.2069 / max 270.4276, expressed in 1811 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
6044321.51341811
604440.6934438

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207990.13gold quality
buccal mucosa cellCL:000233689.76gold quality
cortical plateUBERON:000534389.46gold quality
ventricular zoneUBERON:000305389.09gold quality
sural nerveUBERON:001548889.04gold quality
ganglionic eminenceUBERON:000402388.95gold quality
tendon of biceps brachiiUBERON:000818887.25gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.55gold quality
calcaneal tendonUBERON:000370186.48gold quality
tendonUBERON:000004385.66gold quality
hindlimb stylopod muscleUBERON:000425285.02gold quality
tibialis anteriorUBERON:000138584.86silver quality
adrenal tissueUBERON:001830384.54gold quality
epithelial cell of pancreasCL:000008384.44silver quality
right hemisphere of cerebellumUBERON:001489083.95gold quality
cerebellar hemisphereUBERON:000224583.90gold quality
cerebellar cortexUBERON:000212983.87gold quality
cerebellumUBERON:000203783.78gold quality
colonic epitheliumUBERON:000039783.62gold quality
prefrontal cortexUBERON:000045183.61gold quality
left ovaryUBERON:000211983.44gold quality
right ovaryUBERON:000211883.21gold quality
oocyteCL:000002382.92gold quality
left lobe of thyroid glandUBERON:000112082.69gold quality
smooth muscle tissueUBERON:000113582.66gold quality
thyroid glandUBERON:000204682.59gold quality
bloodUBERON:000017882.53gold quality
tonsilUBERON:000237282.34gold quality
islet of LangerhansUBERON:000000682.32gold quality
bone marrow cellCL:000209282.18gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.40

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

124 targeting ZNF346, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4481100.0066.421669
HSA-MIR-428299.9975.366408
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-185-3P99.9567.011743
HSA-MIR-808299.9567.271170
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-329-3P99.9166.561234
HSA-MIR-362-3P99.9166.381267
HSA-MIR-568299.8972.561005
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-95-5P99.8972.173973
HSA-MIR-427199.8868.322244
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-444799.8567.812900

Literature-anchored findings (GeneRIF, showing 4)

  • JAZ is exported by exportin-5 but translocates back into nuclei by a facilitated diffusion mechanism (PMID:15254228)
  • JAZ directly binds E2F1 in vitro in a dsRNA-independent manner, and JAZ’s dsRNA binding ZF domains, which are necessary for localizing JAZ to the nucleus, are required for repression of transcriptional activity in vivo. (PMID:21715977)
  • This detection method can be readily extended to multiplex detection of miRNAs with only one ALP-conjugated JAZ probe due to its nonsequence-specific binding character (PMID:28208259)
  • ZNF385A and ZNF346 Serve as Prognostic Biomarkers Associated with an Inflamed Immunosuppressive Tumor Microenvironment in Hepatocellular Carcinoma. (PMID:36834567)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioznf346ENSDARG00000060695
mus_musculusZfp346ENSMUSG00000021481
rattus_norvegicusZfp346ENSRNOG00000016867
drosophila_melanogasterCG1231FBGN0035134
drosophila_melanogasterdbfFBGN0287630

Paralogs (9): ZNF385B (ENSG00000144331), ZMAT2 (ENSG00000146007), ZNF385D (ENSG00000151789), ZNF385A (ENSG00000161642), ZMAT4 (ENSG00000165061), ZMAT1 (ENSG00000166432), KRCC1 (ENSG00000172086), ZMAT3 (ENSG00000172667), ZNF385C (ENSG00000187595)

Protein

Protein identifiers

Zinc finger protein 346Q9UL40 (reviewed: Q9UL40)

Alternative names: Just another zinc finger protein

All UniProt accessions (6): Q9UL40, B7Z4J8, B7Z4N4, B7Z6B6, B7Z6Q2, D6RJ07

UniProt curated annotations — full annotation on UniProt →

Function. Binds with low affinity to dsDNA and ssRNA, and with high affinity to dsRNA, with no detectable sequence specificity. May bind to specific miRNA hairpins.

Subunit / interactions. Forms a heteromeric complex with XPO5 and ILF3. Found in a nuclear export complex with XPO5, RAN, ILF3, ZNF346 and double-stranded RNA. Interacts with XPO5. Interacts with ILF3 in an RNA-independent manner.

Subcellular location. Nucleus. Nucleolus. Cytoplasm.

Domain organisation. The zinc-finger domains are required for binding to dsRNA, and also for nuclear localization.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UL40-11yes
Q9UL40-22
Q9UL40-33

RefSeq proteins (10): NP_001295142, NP_001295143, NP_001295144, NP_001295145, NP_001295147, NP_001295148, NP_001295150, NP_001295152, NP_001350642, NP_036411* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003604Matrin/U1-like-C_Znf_C2H2Domain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR051868ZN346_ZMAT4Family

Pfam: PF12874

UniProt features (29 total): binding site 8, zinc finger region 4, cross-link 2, splice variant 2, turn 2, strand 2, helix 2, region of interest 2, compositionally biased region 2, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2MKDSOLUTION NMR
2MKNSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UL40-F167.170.10

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 78; 91; 97; 136; 139; 152; 158; 75

Post-translational modifications (3): 1, 114, 170

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 89 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MAYBURD_RESPONSE_TO_L663536_UP, PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN, GOCC_NUCLEOLUS, GOMF_MIRNA_BINDING, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GOMF_REGULATORY_RNA_BINDING, BANP_TARGET_GENES, DYRK1A_TARGET_GENES, FEV_TARGET_GENES, HOXB4_TARGET_GENES, ID2_TARGET_GENES, IRF5_TARGET_GENES, NFE2L1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (8): RNA binding (GO:0003723), double-stranded RNA binding (GO:0003725), zinc ion binding (GO:0008270), enzyme binding (GO:0019899), miRNA binding (GO:0035198), nucleic acid binding (GO:0003676), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
nuclear lumen2
cellular anatomical structure2
nucleic acid binding1
RNA binding1
transition metal ion binding1
protein binding1
regulatory RNA binding1
cation binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

980 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF346MYCP01106986
ZNF346ICE2Q659A1947
ZNF346MT-CO1P00395899
ZNF346SKP1P34991841
ZNF346HBS1LQ9Y450822
ZNF346CUL1Q13616750
ZNF346A0A087WZY1A0A087WZY1720
ZNF346EIF2AK2P19525715
ZNF346PRH1P02810715
ZNF346SFRP4Q6FHJ7696
ZNF346ETF1P46055695
ZNF346ICE1Q9Y2F5667
ZNF346LOXP28300575
ZNF346RBX1P62877572
ZNF346MYBL2P10244571

IntAct

128 interactions, top by confidence:

ABTypeScore
ZNF346TARBP2psi-mi:“MI:0915”(physical association)0.720
TARBP2ZNF346psi-mi:“MI:0915”(physical association)0.720
ZNF346EIF2AK2psi-mi:“MI:0915”(physical association)0.710
NKRFZNF346psi-mi:“MI:0915”(physical association)0.670
STRBPZNF346psi-mi:“MI:0915”(physical association)0.560
RNF8ZNF346psi-mi:“MI:0915”(physical association)0.560
ADARB1ZNF346psi-mi:“MI:0915”(physical association)0.560
LNX1ZNF346psi-mi:“MI:0915”(physical association)0.560
ZNF346YWHAGpsi-mi:“MI:0915”(physical association)0.560
BAG6ZNF346psi-mi:“MI:0915”(physical association)0.560
KLF11ZNF346psi-mi:“MI:0915”(physical association)0.560
ZNF346SETDB1psi-mi:“MI:0915”(physical association)0.560
ZNF346KAT5psi-mi:“MI:0915”(physical association)0.560
LMO3ZNF346psi-mi:“MI:0915”(physical association)0.560
HNRNPDHNRNPDLpsi-mi:“MI:0914”(association)0.560
NNOP56psi-mi:“MI:0914”(association)0.530

BioGRID (444): ZNF346 (Two-hybrid), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS), ZNF346 (Affinity Capture-MS)

ESM2 similar proteins: A2RV29, A4QP16, B0JZ85, F4I7L1, O23463, O48772, O64571, P43243, P43244, Q0VD35, Q10KL8, Q28EG9, Q32NW2, Q3KQ71, Q569K4, Q5R4W8, Q5ZDJ6, Q66IH2, Q6AXX3, Q6NPP4, Q6PBT9, Q7XHR2, Q8BXJ8, Q8GSA7, Q8K310, Q8LMR2, Q8S9H7, Q90Y35, Q94AD9, Q9C682, Q9D8C3, Q9ERV1, Q9FFH1, Q9FH37, Q9FYG2, Q9H000, Q9H6B1, Q9H898, Q9LES2, Q9LES3

Diamond homologs: A2RV29, B0JZ85, O08781, O54836, Q0IIC4, Q0VD35, Q28EG9, Q5H9K5, Q5R4W8, Q8AVN9, Q8BZ94, Q9H898, Q9HA38, Q9R0B7, Q9UL40, O88532, Q5REX3, Q5U231, Q6GPM1, Q96KR1, Q17QQ9, Q5PPL1, Q5R6I3, Q99JT5, Q9NPI7, Q3V0C1, A0A096LPI5, A6NJG6, F2Z398, Q09FC8, Q68CZ1, Q8IV13, Q8N9N2, Q8TDM0, Q92918, Q96J02, Q96MD7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 127 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:

PathwayPartnersFoldFDR
Eukaryotic Translation Initiation830.5×5e-09
Cap-dependent Translation Initiation830.5×5e-09
SARS-CoV-1 modulates host translation machinery830.5×5e-09
Eukaryotic Translation Elongation827.5×1e-08
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S826.9×1e-08
Nonsense-Mediated Decay (NMD)823.0×3e-08
SARS-CoV-2 modulates host translation machinery822.1×4e-08
Influenza Viral RNA Transcription and Replication821.3×6e-08

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1220.8×3e-10
ribosomal small subunit biogenesis919.1×2e-07
RNA processing612.3×1e-03
translation1211.5×2e-07
rRNA processing79.3×1e-03
negative regulation of translation59.2×9e-03
mRNA splicing, via spliceosome76.0×8e-03
RNA splicing75.8×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance35
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1526 predictions. Top by Δscore:

VariantEffectΔscore
5:177041121:TATA:Tacceptor_loss1.0000
5:177041122:ATAGT:Aacceptor_gain1.0000
5:177041123:T:Gacceptor_gain1.0000
5:177041124:A:ACacceptor_loss1.0000
5:177041124:A:AGacceptor_gain1.0000
5:177041124:AGT:Aacceptor_gain1.0000
5:177041124:AGTG:Aacceptor_gain1.0000
5:177041125:G:Aacceptor_loss1.0000
5:177041125:G:GTacceptor_gain1.0000
5:177041125:GT:Gacceptor_gain1.0000
5:177041125:GTG:Gacceptor_gain1.0000
5:177041125:GTGG:Gacceptor_gain1.0000
5:177041125:GTGGA:Gacceptor_gain1.0000
5:177041226:CCAG:Cdonor_loss1.0000
5:177041227:CAG:Cdonor_loss1.0000
5:177041229:GGTAT:Gdonor_loss1.0000
5:177041230:G:Adonor_loss1.0000
5:177041231:T:Adonor_loss1.0000
5:177041766:G:Aacceptor_gain1.0000
5:177041777:GAGC:Gacceptor_gain1.0000
5:177044383:A:AGacceptor_gain1.0000
5:177044384:A:Gacceptor_gain1.0000
5:177044388:GA:Gacceptor_gain1.0000
5:177064400:A:Tdonor_gain1.0000
5:177041122:A:AGacceptor_gain0.9900
5:177041172:GT:Gdonor_gain0.9900
5:177041765:T:TAacceptor_gain0.9900
5:177041772:TTGCA:Tacceptor_loss0.9900
5:177041773:TGCA:Tacceptor_loss0.9900
5:177041774:GCA:Gacceptor_loss0.9900

AlphaMissense

1947 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:177041159:T:CF70S1.000
5:177041173:T:AC75S1.000
5:177041173:T:CC75R1.000
5:177041174:G:CC75S1.000
5:177041175:T:GC75W1.000
5:177041182:T:CC78R1.000
5:177041183:G:AC78Y1.000
5:177041184:C:GC78W1.000
5:177041221:C:AH91N1.000
5:177041221:C:GH91D1.000
5:177041223:T:AH91Q1.000
5:177041223:T:GH91Q1.000
5:177041224:T:GY92D1.000
5:177041789:T:AH97Q1.000
5:177041789:T:GH97Q1.000
5:177044431:T:CC139R1.000
5:177044470:C:GH152D1.000
5:177044472:C:AH152Q1.000
5:177044472:C:GH152Q1.000
5:177044480:G:AG155E1.000
5:177050792:T:CC187R1.000
5:177062114:T:GY254D1.000
5:177041158:T:CF70L0.999
5:177041160:C:AF70L0.999
5:177041160:C:GF70L0.999
5:177041174:G:AC75Y0.999
5:177041174:G:TC75F0.999
5:177041180:T:AV77D0.999
5:177041182:T:AC78S0.999
5:177041183:G:CC78S0.999

dbSNP variants (sampled 300 via entrez): RS1000081300 (5:177067063 CAAAAT>C), RS1000097001 (5:177058909 T>G), RS1000129732 (5:177058586 T>C,G), RS1000153445 (5:177037423 C>CTA), RS1000185971 (5:177042109 A>G), RS1000211613 (5:177061047 G>C,T), RS1000240271 (5:177023456 A>G), RS1000321140 (5:177035572 T>C), RS1000324859 (5:177078237 G>A), RS1000347644 (5:177078866 G>A), RS1000358683 (5:177049233 C>T), RS1000369643 (5:177064885 C>T), RS1000371845 (5:177035806 C>T), RS1000409765 (5:177053009 A>T), RS1000576018 (5:177054201 T>G)

Disease associations

OMIM: gene MIM:605308 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST005956_15Waist-to-hip ratio adjusted for BMI1.000000e-07
GCST005957_13Waist-to-hip ratio adjusted for BMI (age <50)3.000000e-07
GCST005962_42Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)1.000000e-08
GCST006462_28Uterine fibroids2.000000e-09
GCST007847_86Type 2 diabetes4.000000e-10
GCST008163_436Height3.000000e-06
GCST008163_499Height1.000000e-06
GCST008839_14Height1.000000e-11
GCST009158_5Uterine fibroids1.000000e-11

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression4
bisphenol Aaffects cotreatment, increases methylation, decreases expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Arsenicaffects methylation1
Atrazinedecreases expression1
Cannabidioldecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ivermectindecreases expression1
Ribonucleotidesaffects binding1
Rotenonedecreases expression1
T-2 Toxinincreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Antirheumatic Agentsincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_XW35HEK293 eGFP-ZNF346Transformed cell lineFemale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): uterine corpus leiomyoma