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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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ZFC3H1
zinc finger C3H1-type containing
Chromosome 12 · 12q21.1
NCBI Gene: 196441Ensembl: ENSG00000133858.17HGNC: HGNC:28328UniProt: O60293
82PubMed Papers
20Diseases
0Drugs
2Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
nucleolusprotein bindingnucleusGO:0005615neurodegenerative diseaseShort statureprostate adenocarcinomahepatocellular carcinoma
✦AI Summary

ZFC3H1 (zinc finger C3H1-type containing) is a core component of the poly(A) tail exosome targeting (PAXT) complex, which directs polyadenylated RNAs for nuclear degradation by the RNA exosome 1. ZFC3H1 functions as a central link between the exosome cofactor hMTR4 and nuclear poly(A)-binding protein PABPN1, targeting longer and more extensively polyadenylated transcripts compared to other exosome targeting complexes 1. The protein exhibits dual operational modes: it is co-transcriptionally loaded onto RNA precursors in a 'closed' conformation that blocks exosome recruitment, but can transition to an 'open' state that facilitates degradation of shorter RNAs with fewer exons 2. ZFC3H1 also serves as a nuclear RNA retention factor, forming condensates that prevent RNA trafficking to nuclear speckles where RNAs typically gain export competence 34. Additionally, ZFC3H1 participates in quality control mechanisms by interacting with YTHDC1/YTHDC2 to retain misprocessed mRNAs containing intact splice site motifs through m6A modification-dependent pathways 5. Clinically, ZFC3H1 expression correlates with cancer prognosis across multiple tumor types, with altered expression affecting cell viability and metastatic potential 67.

Sources cited
1
ZFC3H1 is a core PAXT component linking hMTR4 to PABPN1 for targeting polyadenylated transcripts to exosome degradation
PMID: 27871484
2
ZFC3H1 has dual conformational modes - closed for blocking exosome recruitment and open for facilitating degradation based on RNA features
PMID: 39461342
3
ZFC3H1 forms nuclear condensates to prevent RNA trafficking to nuclear speckles upon degradation inhibition
PMID: 34530450
4
ZFC3H1 functions as a nuclear RNA retention factor that competes with nuclear export activity
PMID: 29768216
5
ZFC3H1 interacts with YTHDC1/YTHDC2 in quality control mechanisms for retaining misprocessed mRNAs
PMID: 39626965
6
ZFC3H1 expression correlates with cancer prognosis across multiple tumor types
PMID: 35131366
7
ZFC3H1 knockdown affects cell viability and metastatic potential in prostate cancer
PMID: 34514952
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.53Moderate
Short statureOpen Targets
0.32Weak
prostate adenocarcinomaOpen Targets
0.08Suggestive
hepatocellular carcinomaOpen Targets
0.04Suggestive
diabetes mellitusOpen Targets
0.03Suggestive
type 2 diabetes mellitusOpen Targets
0.03Suggestive
orofacial cleftOpen Targets
0.03Suggestive
response to stimulusOpen Targets
0.03Suggestive
gallbladder diseaseOpen Targets
0.03Suggestive
asthmaOpen Targets
0.02Suggestive
PainOpen Targets
0.02Suggestive
adverse effectOpen Targets
0.02Suggestive
liver diseaseOpen Targets
0.02Suggestive
ovarian dysfunctionOpen Targets
0.02Suggestive
cancerOpen Targets
0.01Suggestive
neoplasmOpen Targets
0.01Suggestive
colorectal cancerOpen Targets
0.01Suggestive
Hepatic fibrosisOpen Targets
0.01Suggestive
psoriasisOpen Targets
0.01Suggestive
adrenal cortex carcinomaOpen Targets
0.00Suggestive
Pathogenic Variants2
NM_144982.5(ZFC3H1):c.5885T>C (p.Leu1962Pro)Likely pathogenic
Short stature
☆☆☆☆2001→ Residue 1962
NM_144982.5(ZFC3H1):c.947G>A (p.Arg316His)Likely pathogenic
Short stature
☆☆☆☆2001→ Residue 316
View on ClinVar ↗
Related Genes
SRRTProtein interaction100%NRDE2Protein interaction100%EXOSC1Protein interaction98%EXOSC9Protein interaction96%EXOSC10Protein interaction96%EXOSC8Protein interaction96%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
92%
Lung
86%
Heart
52%
Liver
42%
Brain
20%
Gene Interaction Network
Click a node to explore
ZFC3H1SRRTNRDE2EXOSC1EXOSC9EXOSC10EXOSC8
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt O60293
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.37Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.30 [0.25–0.37]
RankingsWhere ZFC3H1 stands among ~20K protein-coding genes
  • #5,837of 20,598
    Most Researched82
  • #4,353of 5,498
    Most Pathogenic Variants2
  • #1,684of 17,882
    Most Constrained (LOEUF)0.37 · top 10%
Genes detectedZFC3H1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs.
PMID: 37875486
Nat Commun · 2023
1.00
2
Dual modes of ZFC3H1 confer selectivity in nuclear RNA sorting.
PMID: 39461342
Mol Cell · 2024
0.90
3
PMID: 39626965
Life Sci Alliance · 2025
0.80
4
Zinc finger C3H1-type containing serves as a novel prognostic biomarker in human pan-cancer.
PMID: 35131366
Gene · 2022
0.70
5
ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation.
PMID: 34530450
Nucleic Acids Res · 2021
0.60