ZNF354A

gene
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Also known as KID-1EZNFHKL1KID1

Summary

ZNF354A (zinc finger protein 354A, HGNC:11628) is a protein-coding gene on chromosome 5q35.3, encoding Zinc finger protein 354A (O60765).

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. Located in cytosol; nucleolus; and nucleoplasm. Biomarker of in situ carcinoma and seminoma.

Source: NCBI Gene 6940 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 79 total
  • MANE Select transcript: NM_005649

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11628
Approved symbolZNF354A
Namezinc finger protein 354A
Location5q35.3
Locus typegene with protein product
StatusApproved
AliasesKID-1, EZNF, HKL1, KID1
Ensembl geneENSG00000169131
Ensembl biotypeprotein_coding
OMIM602444
Entrez6940

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 nonsense_mediated_decay

ENST00000335815, ENST00000518048, ENST00000520331, ENST00000865234, ENST00000865235, ENST00000865236, ENST00000916334, ENST00000916335, ENST00000916336

RefSeq mRNA: 2 — MANE Select: NM_005649 NM_001324339, NM_005649

CCDS: CCDS4438

Canonical transcript exons

ENST00000335815 — 5 exons

ExonStartEnd
ENSE00001194604178711512178713621
ENSE00002108682178730556178730659
ENSE00002499429178728990178729073
ENSE00003832941178726999178727125
ENSE00003837177178725376178725471

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 87.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.9389 / max 208.2473, expressed in 1621 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
651813.31461416
651801.63581063
651820.9885638

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065587.57gold quality
oocyteCL:000002387.25gold quality
cortical plateUBERON:000534387.17gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.47gold quality
ganglionic eminenceUBERON:000402385.31gold quality
monocyteCL:000057684.90gold quality
mononuclear cellCL:000084284.54gold quality
leukocyteCL:000073884.37gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.89gold quality
muscle layer of sigmoid colonUBERON:003580582.92gold quality
lower esophagus muscularis layerUBERON:003583382.71gold quality
lower esophagusUBERON:001347382.69gold quality
metanephros cortexUBERON:001053382.62gold quality
granulocyteCL:000009482.44gold quality
body of pancreasUBERON:000115082.39gold quality
esophagogastric junction muscularis propriaUBERON:003584181.75gold quality
embryoUBERON:000092281.64gold quality
ventricular zoneUBERON:000305381.25gold quality
left lobe of thyroid glandUBERON:000112080.93gold quality
mucosa of stomachUBERON:000119980.81gold quality
left uterine tubeUBERON:000130380.57gold quality
sigmoid colonUBERON:000115980.56gold quality
apex of heartUBERON:000209880.49gold quality
pancreasUBERON:000126480.45gold quality
spleenUBERON:000210680.34gold quality
right lobe of thyroid glandUBERON:000111980.24gold quality
bone marrowUBERON:000237180.13gold quality
thyroid glandUBERON:000204680.12gold quality
body of uterusUBERON:000985380.04gold quality
lower esophagus mucosaUBERON:003583479.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.69

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA1978.1ZNF354AMore than 3 adjacent zinc fingers
MA1978.2ZNF354AMore than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:27852650

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

39 targeting ZNF354A, 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-7110-3P100.0073.182486
HSA-MIR-9-5P100.0072.282361
HSA-MIR-569699.9872.364487
HSA-MIR-539-5P99.9370.302855
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-153-5P99.8973.866317
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-489-3P99.8066.46839
HSA-MIR-6817-3P99.7968.352126
HSA-MIR-7856-5P99.7569.992901
HSA-MIR-556-3P99.7468.751203
HSA-MIR-3913-3P99.7466.53938
HSA-MIR-449999.6267.291470
HSA-MIR-885-5P99.5968.59879
HSA-MIR-432899.5771.064094
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-6740-3P99.4868.491392
HSA-MIR-582-5P99.4770.792635
HSA-MIR-7151-5P99.3767.82613
HSA-MIR-377-3P99.3770.181905
HSA-MIR-520F-5P99.3470.401632
HSA-MIR-133A-3P99.2771.531270
HSA-MIR-133B99.2771.531270
HSA-MIR-472199.2666.05818
HSA-MIR-806599.1970.381289
HSA-MIR-10399-5P99.1769.872610
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-670-3P99.0368.882404
HSA-MIR-323A-5P98.5965.13651

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp354aENSMUSG00000020364
rattus_norvegicusZfp354aENSRNOG00000003634

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 354AO60765 (reviewed: O60765)

Alternative names: Transcription factor 17, Zinc finger protein eZNF

All UniProt accessions (4): O60765, E5RGC2, E5RHT5, V9HWI2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Expressed in kidney and inner ear.

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

RefSeq proteins (2): NP_001311268, NP_005640* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096, PF01352

UniProt features (23 total): zinc finger region 13, cross-link 5, chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O60765-F168.730.22

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 (5): 110, 121, 139, 171, 268

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway
R-HSA-9843940Regulation of endogenous retroelements by KRAB-ZFP proteins

MSigDB gene sets: 82 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, NKX25_02, WOO_LIVER_CANCER_RECURRENCE_UP, GOBP_SENSORY_PERCEPTION, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, GOCC_NUCLEOLUS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN, PGF_UP.V1_UP, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), sensory perception of sound (GO:0007605), 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 (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
RNA Polymerase II Transcription1
Regulation of endogenous retroelements1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
nuclear lumen2
cellular anatomical structure2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
sensory perception of mechanical stimulus1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
cation binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
cytoplasm1

Protein interactions and networks

STRING

674 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF354AUSP50Q70EL3701
ZNF354AFRG2CA6NGY1700
ZNF354ALIN54Q6MZP7581
ZNF354AEML3Q32P44509
ZNF354ASPICE1Q8N0Z3478
ZNF354AZMYM6O95789474
ZNF354ACACHD1Q5VU97461
ZNF354ADCTPP1Q9H773454
ZNF354ASRYQ05066451
ZNF354AUBAC2Q8NBM4438
ZNF354ASNRPFP62306435
ZNF354ACMTM3Q96MX0433
ZNF354AGTF2H1P32780430
ZNF354ARAB30Q15771424
ZNF354AARPP19P56211418

IntAct

48 interactions, top by confidence:

ABTypeScore
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
H1-4IGF2BP3psi-mi:“MI:0914”(association)0.530
ZNF331USP9Ypsi-mi:“MI:0914”(association)0.530
ZNF71NVLpsi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
TRIM28ZNF316psi-mi:“MI:0914”(association)0.530
TRIM28ZNF320psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
ZC3HAV1KHNYNpsi-mi:“MI:0914”(association)0.530
PPANPPM1Gpsi-mi:“MI:0914”(association)0.530
H1-4RRP8psi-mi:“MI:0914”(association)0.530
RPL8ZBTB24psi-mi:“MI:0914”(association)0.530
ZNF354AECE1psi-mi:“MI:0915”(physical association)0.370
TRIM28ZNF320psi-mi:“MI:0914”(association)0.350
PPANIGF2BP3psi-mi:“MI:0914”(association)0.350
RPL28SDCBPpsi-mi:“MI:0914”(association)0.350
ZC3HAV1MPHOSPH10psi-mi:“MI:0914”(association)0.350
GPATCH4NOP56psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
rl3_rl3l_humanMPHOSPH10psi-mi:“MI:0914”(association)0.350
RPS19ZNF320psi-mi:“MI:0914”(association)0.350
ZNF467ZNF320psi-mi:“MI:0914”(association)0.350
RPL36GTPBP10psi-mi:“MI:0914”(association)0.350
RPL28GTPBP10psi-mi:“MI:0914”(association)0.350
ADARB1GTPBP10psi-mi:“MI:0914”(association)0.350
OASLZNF316psi-mi:“MI:0914”(association)0.350

BioGRID (52): ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), HDAC4 (Reconstituted Complex), ZNF354A (Proximity Label-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS), ZNF354A (Affinity Capture-MS)

ESM2 similar proteins: A1YEP8, A1YFW2, A2RRD8, A2T6E3, A2T6V8, A2T7D2, A2T7F4, A2T812, A6NHJ4, O14709, O43309, O60765, P17036, P17097, P51814, P52738, Q02975, Q08ER8, Q0VGE8, Q12901, Q2M218, Q2M3X9, Q3KNS6, Q4V8A8, Q5RBX0, Q5RCD9, Q5VIY5, Q61751, Q6GQR8, Q6ZMS4, Q7TSH9, Q86Y25, Q8BQC8, Q8IYX0, Q8IZ26, Q8N9F8, Q8NF99, Q8TF39, Q8TF47, Q96N58

Diamond homologs: A2A761, A2VDP4, A3KN32, A6QLU5, A6QPT6, A7MBI1, A8MT65, B4DU55, E9PYI1, O60765, O95780, P15622, P17014, P17032, P17098, P21506, P51508, P51814, P52736, P52738, P52742, Q02975, Q06730, Q06732, Q0VCB0, Q14587, Q16587, Q2KI58, Q2M3W8, Q3V080, Q49AA0, Q4R6C2, Q4V8A8, Q571J5, Q5HYK9, Q5JUW0, Q5JVG2, Q5MCW4, Q5MYW4, Q5R4K8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 52 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
Peptide chain elongation1040.9×8e-13
Viral mRNA Translation1040.9×8e-13
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1040.5×8e-13
Selenocysteine synthesis1038.8×8e-13
Eukaryotic Translation Termination1038.8×8e-13
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1038.0×8e-13
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1038.0×8e-13
Formation of a pool of free 40S subunits1036.1×1e-12

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1040.3×1e-11
translation1124.6×7e-11
rRNA processing721.6×3e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance69
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

717 predictions. Top by Δscore:

VariantEffectΔscore
5:178725371:CTTA:Cdonor_loss1.0000
5:178725372:TTAC:Tdonor_loss1.0000
5:178725373:TA:Tdonor_loss1.0000
5:178726993:CCTTA:Cdonor_loss1.0000
5:178726994:CTTA:Cdonor_loss1.0000
5:178726995:TTACC:Tdonor_loss1.0000
5:178726996:TACCC:Tdonor_loss1.0000
5:178726997:A:ACdonor_gain1.0000
5:178726997:A:ATdonor_loss1.0000
5:178726997:AC:Adonor_gain1.0000
5:178726997:ACC:Adonor_gain1.0000
5:178726998:C:CCdonor_gain1.0000
5:178726998:CC:Cdonor_gain1.0000
5:178726998:CCC:Cdonor_gain1.0000
5:178726998:CCCA:Cdonor_gain1.0000
5:178727123:CAC:Cacceptor_gain1.0000
5:178727123:CACCT:Cacceptor_loss1.0000
5:178727125:CCTG:Cacceptor_loss1.0000
5:178727126:C:CCacceptor_gain1.0000
5:178727126:CTGTA:Cacceptor_loss1.0000
5:178727127:T:Gacceptor_loss1.0000
5:178727217:T:TAdonor_gain1.0000
5:178727218:C:Adonor_gain1.0000
5:178728984:GCTCA:Gdonor_loss1.0000
5:178728985:CTCA:Cdonor_loss1.0000
5:178728986:TCA:Tdonor_loss1.0000
5:178728987:CA:Cdonor_loss1.0000
5:178728988:A:AGdonor_loss1.0000
5:178728989:CCT:Cdonor_loss1.0000
5:178730558:C:Adonor_gain1.0000

AlphaMissense

3986 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:178712621:A:CF419L0.999
5:178712621:A:TF419L0.999
5:178712623:A:GF419L0.999
5:178712705:G:CF391L0.998
5:178712705:G:TF391L0.998
5:178712707:A:GF391L0.998
5:178712342:G:CH512Q0.997
5:178712342:G:TH512Q0.997
5:178712604:A:GL425P0.997
5:178712617:A:GS421P0.997
5:178712622:A:GF419S0.997
5:178712678:A:CH400Q0.997
5:178712678:A:TH400Q0.997
5:178712680:G:CH400D0.997
5:178712201:A:CF559L0.996
5:178712201:A:TF559L0.996
5:178712203:A:GF559L0.996
5:178712344:G:CH512D0.996
5:178712369:G:CF503L0.996
5:178712369:G:TF503L0.996
5:178712371:A:GF503L0.996
5:178712453:G:CF475L0.996
5:178712453:G:TF475L0.996
5:178712455:A:GF475L0.996
5:178712688:A:GL397P0.996
5:178712285:A:CF531L0.995
5:178712285:A:TF531L0.995
5:178712287:A:GF531L0.995
5:178712426:A:CH484Q0.995
5:178712426:A:TH484Q0.995

dbSNP variants (sampled 300 via entrez): RS1000180053 (5:178716542 T>C), RS1000247933 (5:178727500 T>C), RS1000261226 (5:178721621 A>G), RS1000316196 (5:178716192 G>A), RS1000350002 (5:178716743 A>C), RS1000383336 (5:178722653 T>C,G), RS1000519013 (5:178717851 G>A), RS1000953408 (5:178718220 T>C), RS1001249948 (5:178711343 C>T), RS1001261077 (5:178728868 G>A,T), RS1001318455 (5:178714705 G>A), RS1001669308 (5:178720603 A>C), RS1001722286 (5:178730888 A>G), RS1001822874 (5:178723331 T>C), RS1002427658 (5:178724728 C>A)

Disease associations

OMIM: gene MIM:602444 | 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):

StudyTraitp-value
GCST002337_127Amyotrophic lateral sclerosis (sporadic)3.000000e-07
GCST007676_103-month functional outcome in ischaemic stroke (modified Rankin score)2.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009603stroke outcome severity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression2
Air Pollutantsdecreases expression, increases abundance, increases expression2
Cyclosporineincreases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
geraniolincreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
abrinedecreases expression1
Benzo(a)pyreneincreases methylation, affects methylation1
Coumestrolaffects cotreatment, decreases expression1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, increases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydedecreases expression1
Hydrogen Peroxideaffects cotreatment, decreases expression1
Phenobarbitalaffects expression1
Smokedecreases expression1
Sulindacincreases expression1
Theophyllineaffects cotreatment, decreases expression1
Urethaneincreases expression1
Valproic Acidincreases expression, increases methylation1
Aflatoxin M1decreases expression1
Asbestos, Crocidolitedecreases methylation1
Cadmium Chloridedecreases expression1

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): sporadic amyotrophic lateral sclerosis