ZC3H8

gene
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Also known as Fliz1

Summary

ZC3H8 (zinc finger CCCH-type containing 8, HGNC:30941) is a protein-coding gene on chromosome 2q14.1, encoding Zinc finger CCCH domain-containing protein 8 (Q8N5P1). Acts as a transcriptional repressor of the GATA3 promoter. It is a common-essential gene (DepMap: required in 90.8% of cancer cell lines).

Enables RNA binding activity. Involved in several processes, including positive regulation of thymocyte apoptotic process; regulation of DNA-templated transcription; and snRNA transcription. Located in Cajal body; euchromatin; and histone locus body. Part of transcription elongation factor complex.

Source: NCBI Gene 84524 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 7 total
  • Cancer dependency (DepMap): dependent in 90.8% of screened cell lines (common-essential)
  • MANE Select transcript: NM_032494

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30941
Approved symbolZC3H8
Namezinc finger CCCH-type containing 8
Location2q14.1
Locus typegene with protein product
StatusApproved
AliasesFliz1
Ensembl geneENSG00000144161
Ensembl biotypeprotein_coding
OMIM621273
Entrez84524

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000409573, ENST00000464305, ENST00000466259, ENST00000474234, ENST00000476902, ENST00000495264, ENST00000866699, ENST00000866700, ENST00000866701, ENST00000924270, ENST00000957654

RefSeq mRNA: 1 — MANE Select: NM_032494 NM_032494

CCDS: CCDS46392

Canonical transcript exons

ENST00000409573 — 9 exons

ExonStartEnd
ENSE00001009521112230903112230950
ENSE00001579262112254908112255042
ENSE00001579413112211529112216468
ENSE00001587459112231838112231947
ENSE00002462855112233260112233371
ENSE00003463321112234120112234236
ENSE00003491463112238315112238528
ENSE00003518863112250191112250272
ENSE00003566309112236562112236695

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 96.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.5166 / max 229.6578, expressed in 1761 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
3014317.51661761

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065596.06gold quality
oocyteCL:000002394.20gold quality
buccal mucosa cellCL:000233692.69gold quality
Brodmann (1909) area 23UBERON:001355491.19gold quality
calcaneal tendonUBERON:000370191.17gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.65gold quality
endothelial cellCL:000011588.54gold quality
tendonUBERON:000004387.95gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.02gold quality
primary visual cortexUBERON:000243686.77gold quality
corpus callosumUBERON:000233686.07gold quality
body of pancreasUBERON:000115086.00gold quality
occipital lobeUBERON:000202185.34gold quality
muscle of legUBERON:000138385.15gold quality
gastrocnemiusUBERON:000138885.06gold quality
pituitary glandUBERON:000000785.02gold quality
colonic epitheliumUBERON:000039785.01gold quality
skeletal muscle organUBERON:001489284.80gold quality
cortical plateUBERON:000534384.62gold quality
middle temporal gyrusUBERON:000277184.48gold quality
sural nerveUBERON:001548884.24gold quality
hindlimb stylopod muscleUBERON:000425284.21gold quality
vastus lateralisUBERON:000137984.12gold quality
esophagus mucosaUBERON:000246984.03gold quality
embryoUBERON:000092284.00gold quality
ganglionic eminenceUBERON:000402384.00gold quality
quadriceps femorisUBERON:000137783.99gold quality
cartilage tissueUBERON:000241883.80gold quality
tibialis anteriorUBERON:000138583.52gold quality
muscle tissueUBERON:000238583.42gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.62

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
GATA3Repression

miRNA regulators (miRDB)

29 targeting ZC3H8, 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-3646100.0073.565283
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-366299.9973.825684
HSA-MIR-493-5P99.9672.472382
HSA-MIR-568099.9169.833421
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-449699.8868.892236
HSA-MIR-426199.5970.303415
HSA-MIR-147B-5P99.4570.622432
HSA-MIR-377-3P99.3770.181905
HSA-MIR-431199.3170.473041
HSA-MIR-4738-3P98.9867.981846
HSA-MIR-224-3P98.9168.421815
HSA-MIR-522-3P98.9168.561817
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-4477A98.8369.752952
HSA-MIR-513B-3P98.7668.121577
HSA-MIR-6512-5P98.7669.291195
HSA-MIR-451898.1266.821030
HSA-MIR-18B-3P98.0565.55595
HSA-MIR-4769-3P97.9568.171002
HSA-MIR-6817-5P97.9567.861026
HSA-MIR-365297.7165.431890
HSA-MIR-1266-5P97.7166.921052
HSA-MIR-6782-3P97.6067.75931
HSA-MIR-443097.4765.611813
HSA-MIR-6500-3P97.4267.20867
HSA-MIR-6826-5P93.8067.42514

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 90.8% of screened cell lines, common-essential.

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusZc3h8ENSMUSG00000027387
rattus_norvegicusZc3h8ENSRNOG00000017647
caenorhabditis_elegansWBGENE00020827

Paralogs (2): ZC3H4 (ENSG00000130749), ZC3H6 (ENSG00000188177)

Protein

Protein identifiers

Zinc finger CCCH domain-containing protein 8Q8N5P1 (reviewed: Q8N5P1)

All UniProt accessions (1): Q8N5P1

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5’-AGGTCTC-3’ sequence within the negative cis-acting element intronic regulatory region (IRR) of the GATA3 gene. Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III. Induces thymocyte apoptosis when overexpressed, which may indicate a role in regulation of thymocyte homeostasis.

Subunit / interactions. Component of the little elongation complex (LEC), at least composed of ELL (ELL, ELL2 or ELL3), ZC3H8, ICE1 and ICE2. Interacts with ICE1 (via C-terminus domain).

Subcellular location. Nucleus.

Domain organisation. The N-terminal region and all three C3H1-type zinc fingers are necessary to induce transcriptional repression.

RefSeq proteins (1): NP_115883* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000571Znf_CCCHDomain
IPR036855Znf_CCCH_sfHomologous_superfamily
IPR045124Su(sable)-likeFamily
IPR054361Znf-CCCH_ZC3H4/6/8Domain

Pfam: PF00642, PF18345, PF22623

UniProt features (20 total): modified residue 6, zinc finger region 3, region of interest 3, compositionally biased region 3, sequence conflict 2, chain 1, cross-link 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N5P1-F167.700.14

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 (7): 22, 32, 59, 63, 77, 83, 43

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6807505RNA polymerase II transcribes snRNA genes

MSigDB gene sets: 182 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_POSITIVE_REGULATION_OF_LYMPHOCYTE_APOPTOTIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, TGCGCANK_UNKNOWN, GOBP_POSITIVE_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOBP_T_CELL_HOMEOSTASIS, GOBP_LYMPHOCYTE_HOMEOSTASIS, GOBP_TRANSCRIPTION_BY_RNA_POLYMERASE_III, GOBP_REGULATION_OF_LYMPHOCYTE_APOPTOTIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CELL_ADHESION, GOBP_CELL_CELL_ADHESION

GO Biological Process (10): apoptotic process (GO:0006915), negative regulation of T cell differentiation in thymus (GO:0033085), snRNA transcription by RNA polymerase II (GO:0042795), snRNA transcription by RNA polymerase III (GO:0042796), T cell homeostasis (GO:0043029), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of transcription by RNA polymerase III (GO:0045945), response to antibiotic (GO:0046677), positive regulation of thymocyte apoptotic process (GO:0070245), negative regulation of transcription by RNA polymerase II (GO:0000122)

GO Molecular Function (6): RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), RNA binding (GO:0003723), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (8): chromatin (GO:0000785), euchromatin (GO:0000791), nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription elongation factor complex (GO:0008023), Cajal body (GO:0015030), nuclear body (GO:0016604), histone locus body (GO:0035363)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transcription by RNA polymerase II2
snRNA transcription2
transcription by RNA polymerase III2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
cellular anatomical structure2
nucleoplasm2
nuclear ribonucleoprotein granule2
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
T cell differentiation in thymus1
regulation of T cell differentiation in thymus1
negative regulation of T cell differentiation1
lymphocyte homeostasis1
DNA-templated transcription1
regulation of DNA-templated transcription1
negative regulation of RNA biosynthetic process1
regulation of transcription by RNA polymerase III1
positive regulation of DNA-templated transcription1
response to chemical1
positive regulation of T cell apoptotic process1
thymocyte apoptotic process1
regulation of thymocyte apoptotic process1
regulation of transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
intronic transcription regulatory region sequence-specific DNA binding1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
nucleic acid binding1
transition metal ion binding1
binding1
cation binding1
chromosome1
chromatin1
intracellular membrane-bounded organelle1
nuclear lumen1
nuclear protein-containing complex1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1378 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZC3H8ICE1Q9Y2F5878
ZC3H8ICE2Q659A1834
ZC3H8ELLP55199781
ZC3H8SMIM12Q96EX1525
ZC3H8SUB1P53999501
ZC3H8DPY19L3Q6ZPD9494
ZC3H8SYNE1Q8NF91483
ZC3H8LRRC40Q9H9A6480
ZC3H8PRPSAP1Q14558477
ZC3H8CMTM4Q8IZR5475
ZC3H8TMEM87BQ96K49470
ZC3H8MNMIP1A4FU49470
ZC3H8LEPROTL1O95214466
ZC3H8PPP1R3GB7ZBB8459
ZC3H8NLRP13Q86W25452

IntAct

90 interactions, top by confidence:

ABTypeScore
LARP7CCNT1psi-mi:“MI:0914”(association)0.850
H1-1RRP8psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
SNRPA1U2SURPpsi-mi:“MI:0914”(association)0.640
ZNF764ZNF316psi-mi:“MI:0914”(association)0.640
H1-6ZNF724psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
E4F1ZBTB24psi-mi:“MI:0914”(association)0.530
ZCRB1DKC1psi-mi:“MI:0914”(association)0.530
RPS3ZNF316psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
ZC3H8RSL1D1psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
H1-1SURF6psi-mi:“MI:0914”(association)0.530
THUMPD1YBX1psi-mi:“MI:0914”(association)0.530
LIN28BELAVL2psi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RSL1D1METAP1psi-mi:“MI:0914”(association)0.530
CSNK2A1ZC3H8psi-mi:“MI:0217”(phosphorylation reaction)0.440
ZC3H8H3-4psi-mi:“MI:0915”(physical association)0.400
ZC3H8psi-mi:“MI:0915”(physical association)0.370
NLRP3PHRF1psi-mi:“MI:0914”(association)0.350
Tyw3PPP6Cpsi-mi:“MI:0914”(association)0.350
KSR1FAM168Bpsi-mi:“MI:0914”(association)0.350
k8RGL2psi-mi:“MI:0914”(association)0.350

BioGRID (109): ZC3H8 (Affinity Capture-MS), ZC3H8 (Affinity Capture-MS), ZC3H8 (Affinity Capture-MS), LARP7 (Affinity Capture-MS), THUMPD1 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), ZCRB1 (Affinity Capture-MS), C8orf33 (Affinity Capture-MS), TUBA8 (Affinity Capture-MS), SF3B2 (Affinity Capture-MS), ZC3H8 (Affinity Capture-MS), ZC3H8 (Affinity Capture-MS), THUMPD1 (Affinity Capture-MS), TUBA8 (Affinity Capture-MS), ZC3H8 (Affinity Capture-MS)

ESM2 similar proteins: A5WW08, D3ZND0, D4A7V9, E1C760, E7EXT2, F7AEX0, O57589, P09926, P51612, Q01831, Q07617, Q07G43, Q08288, Q0VBD2, Q15527, Q28E45, Q28EG9, Q2YDS5, Q3KQ71, Q5D1Z3, Q5EAW4, Q5I0E6, Q5RDL2, Q5RET9, Q5RHY1, Q5U4Z3, Q5ZJF6, Q6AYK5, Q6DE94, Q6DFQ2, Q6IQ49, Q6XV80, Q7L590, Q7T293, Q7ZVP1, Q7ZZ00, Q80Y44, Q80ZX8, Q8BG17, Q8BVE8

Diamond homologs: P61129, Q6ZPZ3, Q8BYK8, Q8N5P1, Q9JJ48, Q9UPT8, Q9LTS7, P22293

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 112 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 Initiation732.7×3e-08
Cap-dependent Translation Initiation732.7×3e-08
SARS-CoV-1 modulates host translation machinery732.7×3e-08
Eukaryotic Translation Elongation729.5×6e-08
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S728.8×6e-08
Nonsense-Mediated Decay (NMD)828.2×7e-09
rRNA processing in the nucleus and cytosol1024.4×2e-10
SARS-CoV-2 modulates host translation machinery723.8×3e-07

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1221.6×2e-10
ribosomal large subunit biogenesis521.5×3e-04
ribosomal small subunit biogenesis817.7×3e-06
negative regulation of translation713.3×9e-05
RNA processing612.8×6e-04
rRNA processing912.4×7e-06
translation1212.0×1e-07
RNA splicing108.6×3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance3
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2213 predictions. Top by Δscore:

VariantEffectΔscore
2:112234107:CA:Cdonor_gain1.0000
2:112234163:C:Adonor_gain1.0000
2:112235857:AGTGG:Adonor_gain1.0000
2:112236566:T:TAdonor_gain1.0000
2:112236693:CAG:Cacceptor_gain1.0000
2:112236696:C:CCacceptor_gain1.0000
2:112238524:CTAAA:Cacceptor_gain1.0000
2:112238529:C:CCacceptor_gain1.0000
2:112250189:A:ACdonor_gain1.0000
2:112250190:C:CCdonor_gain1.0000
2:112231953:CCAAG:Cacceptor_gain0.9900
2:112231954:CAAG:Cacceptor_gain0.9900
2:112233316:CA:Cdonor_gain0.9900
2:112234106:A:ACdonor_gain0.9900
2:112234107:C:CCdonor_gain0.9900
2:112234131:T:Adonor_gain0.9900
2:112234150:A:ACdonor_gain0.9900
2:112234151:C:CCdonor_gain0.9900
2:112234162:T:Adonor_gain0.9900
2:112234236:CCTT:Cacceptor_gain0.9900
2:112236556:CAATA:Cdonor_loss0.9900
2:112236557:AATAC:Adonor_loss0.9900
2:112236558:ATACC:Adonor_loss0.9900
2:112236559:TA:Tdonor_loss0.9900
2:112236561:CC:Cdonor_loss0.9900
2:112236563:T:TAdonor_gain0.9900
2:112236692:GCAG:Gacceptor_gain0.9900
2:112236693:CAGC:Cacceptor_gain0.9900
2:112236695:GCTA:Gacceptor_loss0.9900
2:112236697:T:Cacceptor_loss0.9900

AlphaMissense

1952 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:112233317:A:GC226R1.000
2:112233361:C:GC211S1.000
2:112233362:A:TC211S1.000
2:112231883:A:CF266L0.999
2:112231883:A:TF266L0.999
2:112231885:A:GF266L0.999
2:112231889:G:CC264W0.999
2:112231890:C:GC264S0.999
2:112231890:C:TC264Y0.999
2:112231891:A:GC264R0.999
2:112231891:A:TC264S0.999
2:112231908:C:GC258S0.999
2:112231909:A:GC258R0.999
2:112231909:A:TC258S0.999
2:112231924:G:CH253D0.999
2:112231934:A:CC249W0.999
2:112231935:C:AC249F0.999
2:112231935:C:GC249S0.999
2:112231935:C:TC249Y0.999
2:112231936:A:GC249R0.999
2:112231936:A:TC249S0.999
2:112233275:A:GC240R0.999
2:112233291:A:CC234W0.999
2:112233292:C:GC234S0.999
2:112233292:C:TC234Y0.999
2:112233293:A:GC234R0.999
2:112233293:A:TC234S0.999
2:112233309:A:CF228L0.999
2:112233309:A:TF228L0.999
2:112233311:A:GF228L0.999

dbSNP variants (sampled 300 via entrez): RS1000029067 (2:112214182 A>G), RS1000213601 (2:112230368 T>C), RS1000225168 (2:112243963 T>C), RS1000278159 (2:112251435 A>G), RS1000304748 (2:112237037 G>A), RS1000325434 (2:112246717 G>T), RS1000339991 (2:112216163 A>G), RS1000343936 (2:112223840 T>TAATC), RS1000461246 (2:112245898 C>A,T), RS1000462440 (2:112216636 A>G), RS1000501391 (2:112232489 TTATAA>T), RS1000565640 (2:112230635 T>C), RS1000607336 (2:112225310 G>A), RS1000614092 (2:112252928 G>A), RS1000788182 (2:112218677 CAT>C)

Disease associations

OMIM: gene MIM:621273 | 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

34 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Cyclosporineincreases expression2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
trichostatin Aincreases expression1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression1
aflatoxin B2decreases methylation1
perfluorooctane sulfonic acidincreases expression1
CGP 52608increases reaction, affects binding1
perfluoro-n-nonanoic acidincreases expression1
2-palmitoylglycerolincreases expression1
K 7174increases expression1
MT19c compoundincreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-oldecreases expression1
Resveratrolaffects cotreatment, increases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsincreases abundance, increases expression1
Atrazinedecreases expression1
Cisplatinincreases expression1
Doxorubicinincreases expression1
Ethyl Methanesulfonateincreases expression1
Methyl Methanesulfonateincreases expression1
Nickelincreases expression1
Plant Extractsaffects cotreatment, increases expression1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Sodium Dodecyl Sulfatedecreases expression1
T-2 Toxinincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.