ZC3H13 Gene

HGNC Family	Zinc fingers
Name	zinc finger CCCH-type containing 13
Description	Enables RNA binding activity. Involved in mRNA processing. Located in nuclear speck. Part of RNA N6-methyladenosine methyltransferase complex. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nZC3H13 has been implicated as a tumor suppressor in colorectal cancer, where it inactivates the Ras-ERK signaling pathway to downregulate oncogenic factors (Snail, Cyclin D1, and Cyclin E1) while upregulating tight junction proteins such as Occludin and Zo-1. Its reduction is associated with advanced disease stage and lymph node metastasis, underscoring its importance in suppressing cancer cell invasion and proliferation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its role in solid tumors, genetic and transcriptomic studies in schizophrenia have identified ZC3H13 as a gene contributing to differential exon expression and splicing regulation, suggesting that m6A‐dependent mechanisms involving this zinc finger protein may influence disease susceptibility."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn other malignancies, ZC3H13 functions through N6-methyladenosine (m6A) RNA modification to exert diverse regulatory roles. In pancreatic ductal adenocarcinoma, fisetin-induced DNA double-strand breaks are accompanied by a decrease in m6A methylation of PHF10 mRNA following ZC3H13 knockdown, thereby impairing homologous recombination repair and influencing chemo-sensitivity. In hepatocellular carcinoma, studies demonstrate that low ZC3H13 expression—regulated by upstream miRNAs such as miR-362-3p/miR-425-5p—is correlated with poor patient outcome, increased tumor cell migration and invasion, and alterations in pathways including transcriptional dysregulation and JAK-STAT signaling. In laryngeal squamous cell carcinoma, ZC3H13 modulates ferroptosis through an m6A-dependent mechanism on the DUOX1 gene, affecting cellular reactive oxygen species and iron homeostasis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "3", "end_ref": "6"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nFurthermore, in keloid formation, ZC3H13 promotes pathogenic fibroblast behavior by mediating m6A modification of HIPK2 mRNA. Its overexpression increases HIPK2 mRNA stability, which enhances fibroblast proliferation and migration while reducing apoptosis, thereby contributing to aberrant wound-healing and keloid development."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Dehua Zhu, Jianping Zhou, Jinbo Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ZC3H13 suppresses colorectal cancer proliferation and invasion via inactivating Ras-ERK signaling."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Physiol (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcp.27551"}], "href": "https://doi.org/10.1002/jcp.27551"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30311220"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30311220"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Christopher Oldmeadow, David Mossman, Tiffany-Jane Evans, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Combined analysis of exon splicing and genome wide polymorphism data predict schizophrenia risk loci."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Psychiatr Res (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jpsychires.2014.01.011"}], "href": "https://doi.org/10.1016/j.jpsychires.2014.01.011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24507884"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24507884"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Chaojie Huang, Senhao Zhou, Chaolei Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ZC3H13-mediated N6-methyladenosine modification of PHF10 is impaired by fisetin which inhibits the DNA damage response in pancreatic cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Lett (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.canlet.2022.01.013"}], "href": "https://doi.org/10.1016/j.canlet.2022.01.013"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35033590"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35033590"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Shuang Wu, Shihai Liu, Yongxian Cao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Downregulation of ZC3H13 by miR-362-3p/miR-425-5p is associated with a poor prognosis and adverse outcomes in hepatocellular carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Aging (Albany NY) (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.18632/aging.203939"}], "href": "https://doi.org/10.18632/aging.203939"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35278064"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35278064"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Shuang Wu, Guifang He, Shihai Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Identification and validation of the N6-methyladenosine RNA methylation regulator ZC3H13 as a novel prognostic marker and potential target for hepatocellular carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Med Sci (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.7150/ijms.69645"}], "href": "https://doi.org/10.7150/ijms.69645"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35582419"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35582419"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Lili Huang, Guangli Chen, Jing He, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ZC3H13 reduced DUOX1-mediated ferroptosis in laryngeal squamous cell carcinoma cells through m6A-dependent modification."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Tissue Cell (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.tice.2023.102187"}], "href": "https://doi.org/10.1016/j.tice.2023.102187"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37536262"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37536262"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Manni Fu, Yongjun Chen, Xian Shi "}, {"type": "b", "children": [{"type": "t", "text": "ZC3H13 Accelerates Keloid Formation by Mediating N"}, {"type": "a", "children": [{"type": "t", "text": "sup"}], "href": "sup"}, {"type": "t", "text": "6"}, {"type": "a", "children": [{"type": "t", "text": "/sup"}], "href": "/sup"}, {"type": "t", "text": "-methyladenosine Modification of HIPK2."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Genet (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s10528-023-10514-6"}], "href": "https://doi.org/10.1007/s10528-023-10514-6"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37752292"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37752292"}]}]}]}
Synonyms	Xio, KIAA0853
Proteins	ZC3HD_HUMAN
NCBI Gene ID	23091
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

ZC3H13 has 6,633 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 110 datasets.

Click the + buttons to view associations for ZC3H13 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

ZC3H13 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by ZC3H13 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of ZC3H13 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of ZC3H13 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of ZC3H13 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of ZC3H13 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of ZC3H13 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of ZC3H13 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of ZC3H13 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of ZC3H13 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of ZC3H13 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of ZC3H13 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with ZC3H13 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with ZC3H13 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of ZC3H13 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of ZC3H13 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of ZC3H13 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of ZC3H13 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing ZC3H13 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with ZC3H13 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with ZC3H13 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing ZC3H13 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of ZC3H13 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with ZC3H13 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with ZC3H13 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of ZC3H13 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with ZC3H13 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with ZC3H13 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with ZC3H13 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with ZC3H13 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at ZC3H13 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of ZC3H13 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of ZC3H13 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing ZC3H13 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of ZC3H13 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with ZC3H13 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing ZC3H13 from the GeneSigDB Published Gene Signatures dataset.
	GEO Signatures of Differentially Expressed Genes for Diseases	disease perturbations changing expression of ZC3H13 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.
	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	gene perturbations changing expression of ZC3H13 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
	GEO Signatures of Differentially Expressed Genes for Kinase Perturbations	kinase perturbations changing expression of ZC3H13 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset.
	GEO Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of ZC3H13 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.