Details for: ZNF460

Gene ID: 10794

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: ZNF460

Ensembl ID: ENSG00000197714

Description: zinc finger protein 460

Cell Significance Landscape

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • pro-B cell CL0000826
    CSI 2.98
    rCSI 2.47%
    PRS 94.92
  • B cell CL0000236
    CSI 2.81
    rCSI 3.75%
    PRS 93.07
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 2.73
    rCSI 2.78%
    PRS 97.28
  • group 3 innate lymphoid cell CL0001071
    CSI 2.66
    rCSI 2%
    PRS 96.02
  • alpha-beta T cell CL0000789
    CSI 2.65
    rCSI 3.1%
    PRS 98.3
  • activated CD8-positive, alpha-beta T cell, human CL0001049
    CSI 2.03
    rCSI 3.48%
    PRS 97.62
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 1.97
    rCSI 2.45%
    PRS 82.92
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.85
    rCSI 3.26%
    PRS 84.5
  • vascular associated smooth muscle cell CL0000359
    CSI 1.68
    rCSI 5.45%
    PRS 92.91
  • stromal cell CL0000499
    CSI 1.67
    rCSI 4.71%
    PRS 91.22
  • basal cell CL0000646
    CSI 1.42
    rCSI 1.9%
    PRS 91.77
  • basal cell of epidermis CL0002187
    CSI 1.19
    rCSI 2.12%
    PRS 69.38

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

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  • Node Color (Target Cell CSI, relative to current network):
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    • High
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    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [ZNF460](/details-gene/10794) is a protein-coding gene located on chromosome 19q13.43 that encodes Zinc Finger Protein 460. This protein is characterized as a KRAB-domain-containing zinc finger protein, a family of proteins typically involved in transcriptional regulation ([Link](https://doi.org/10.1159/000076292)). Functional annotations confirm its role as a DNA-binding transcription factor that operates within the [nucleus](/details-cell/GO:0005634) to regulate gene expression via RNA polymerase II. **Overall**, expression data reveals that [ZNF460](/details-gene/10794) is a significant gene in various lymphoid cell populations, including early B cell and T cell progenitors, suggesting it plays a critical role in lymphocyte development and function. ## Cellular Roles and Expression Landscape The expression profile of [ZNF460](/details-gene/10794) highlights its prominent role within the hematopoietic system, particularly in the lymphoid lineage. It shows the highest significance in progenitor and mature lymphocyte populations, including [pro-B cells](/details-cell/CL0000826) (CSI: 2.98), [B cells](/details-cell/CL0000236) (CSI: 2.81), and [double-positive, alpha-beta thymocytes](/details-cell/CL0000809) (CSI: 2.73). Its significance extends to mature and specialized immune cells such as [group 3 innate lymphoid cells](/details-cell/CL0001071) (CSI: 2.66), [alpha-beta T cells](/details-cell/CL0000789) (CSI: 2.65), and [activated CD8-positive, alpha-beta T cells](/details-cell/CL0001049) (CSI: 2.03). This pattern suggests that [ZNF460](/details-gene/10794) is likely involved in establishing or maintaining the transcriptional programs essential for both early lymphocyte commitment and the function of differentiated immune effectors. Interestingly, [ZNF460](/details-gene/10794) also shows notable significance in several non-immune cell types. These include specific neuronal subtypes, such as [pvalb GABAergic cortical interneurons](/details-cell/CL4023018) (CSI: 1.97), and mesenchymal cells like [vascular associated smooth muscle cells](/details-cell/CL0000359) (CSI: 1.68) and [stromal cells](/details-cell/CL0000499) (CSI: 1.67). This broader expression pattern indicates that its function may not be exclusively restricted to the immune system. ## Pathways and Molecular Function Functionally, [ZNF460](/details-gene/10794) is annotated as a sequence-specific, DNA-binding transcription factor ([GO:0000981](https://www.ebi.ac.uk/QuickGO/term/GO:0000981), [GO:1990837](https://www.ebi.ac.uk/QuickGO/term/GO:1990837)) that participates in the regulation of transcription ([GO:0006355](https://www.ebi.ac.uk/QuickGO/term/GO:0006355)). Its involvement in fundamental transcriptional processes is further supported by its association with Reactome pathways such as 'Gene expression (transcription)' ([R-HSA-74160](https://reactome.org/content/detail/R-HSA-74160)) and 'RNA polymerase II transcription' ([R-HSA-73857](https://reactome.org/content/detail/R-HSA-73857)). These molecular functions are consistent with its high expression in developing lymphocytes, where precise control of gene expression is paramount for lineage specification and maturation. Furthermore, large-scale proteomics studies have identified [ZNF460](/details-gene/10794) as a target of post-translational modifications, including phosphorylation ([Link](https://doi.org/10.1073/pnas.0805139105)) and SUMOylation ([Link](https://doi.org/10.1038/nsmb.2890), [Link](https://doi.org/10.1038/nsmb.3366)), suggesting its activity as a transcription factor may be dynamically regulated by cellular signaling pathways. ## Research Directions The specific role of [ZNF460](/details-gene/10794) in cellular biology, particularly in lymphocyte development, remains largely uncharacterized. The available expression data supports the generation of several testable hypotheses: 1. Given its high significance in [pro-B cells](/details-cell/CL0000826) and [double-positive, alpha-beta thymocytes](/details-cell/CL0000809), [ZNF460](/details-gene/10794) may function as a critical regulator of gene expression programs that govern the commitment and differentiation of B and T lymphocyte lineages from common lymphoid progenitors. 2. The significant expression of [ZNF460](/details-gene/10794) in both lymphoid cells and distinct neuronal populations suggests it may regulate a core set of genes involved in shared biological processes, such as cell survival, migration, or metabolic programming, in these otherwise disparate cell types. To investigate the first hypothesis, a key experiment would be to generate a conditional knockout of the *ZNF460* gene in the hematopoietic stem cell compartment of a mouse model. Subsequent analysis using flow cytometry could then determine if the loss of [ZNF460](/details-gene/10794) leads to blocks or skewing in B and T cell development in the bone marrow and thymus. This could be complemented with single-cell RNA sequencing of lymphoid progenitor populations to identify the specific downstream transcriptional targets regulated by [ZNF460](/details-gene/10794). From a therapeutic standpoint, as an intracellular transcription factor, [ZNF460](/details-gene/10794) represents a challenging direct drug target. However, if its dysregulation is implicated in lymphoid malignancies, it could serve as a valuable biomarker. Furthermore, understanding its downstream target genes could reveal novel, more druggable nodes in pathways relevant to these diseases, making inhibition of its downstream effectors a more viable therapeutic strategy.

Genular Protein ID: 1973663821

Symbol: ZN460_HUMAN

Name: Zinc finger protein 460

UniProtKB Accession Codes:

Q14592 A4FU64 B4DNX9 Q2VPC7 Q6VSF8

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CDD 1 CTD 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 7 Ensembl 2 ExpressionAtlas 1 GO 6 Gene3D 2 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 5 KEGG 1 MANE-Select 1 MIM 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PIR 1 PRO 1 PROSITE 3 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 2 Pumba 1 RNAct 1 Reactome 1 RefSeq 2 SMART 2 SMR 1 STRING 1 SUPFAM 2 SignaLink 1 SwissPalm 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 15004467

Title: Characterization of two novel KRAB-domain-containing zinc finger genes, ZNF460 and ZNF461, on human chromosome 19q13.1-q13.4.

PubMed ID: 15004467

DOI: 10.1159/000076292

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15057824

Title: The DNA sequence and biology of human chromosome 19.

PubMed ID: 15057824

DOI: 10.1038/nature02399

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 7865130

Title: Isolation of cDNA clones for 42 different Kruppel-related zinc finger proteins expressed in the human monoblast cell line U-937.

PubMed ID: 7865130

DOI: 10.1089/dna.1995.14.125

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 25218447

Title: Uncovering global SUMOylation signaling networks in a site-specific manner.

PubMed ID: 25218447

DOI: 10.1038/nsmb.2890

PubMed ID: 25772364

Title: SUMO-2 orchestrates chromatin modifiers in response to DNA damage.

PubMed ID: 25772364

DOI: 10.1016/j.celrep.2015.02.033

PubMed ID: 25755297

Title: System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel small ubiquitin-like modified target proteins and acceptor lysines relevant for genome stability.

PubMed ID: 25755297

DOI: 10.1074/mcp.o114.044792

PubMed ID: 28112733

Title: Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation.

PubMed ID: 28112733

DOI: 10.1038/nsmb.3366

Sequence Information:

  • Length: 562
  • Mass: 63665
  • Checksum: D74C8AA7DC4ECC79
  • Sequence:
    • MAAAWMAPAQ ESVTFEDVAV TFTQEEWGQL DVTQRALYVE VMLETCGLLV ALGDSTKPET 
VEPIPSHLAL PEEVSLQEQL AQGVPRYSYL GQAMDQDGPS EMQEYFLRPG TDPQSEKLHG 
KMSLEHEGLA TADGICSMMI QNQVSPEDAL YGFDSYGPVT DSLIHEGENS YKFEEMFNEN 
CFLVQHEQIL PRVKPYDCPE CGKAFGKSKH LLQHHIIHTG EKPYKCLECG KDFNRRSHLT 
RHQRTHNGDK PFVCSECGRT FNRGSHLTRH QRVHSGEKPF VCNECGKAFT YRSNFVLHNK 
SHNEKKPFAC SECGKGFYES TALIQHFIIH TGERPFKCLE CGKAFNCRSH LKQHERIHTG 
EKPFVCSQCG KAFTHYSTYV LHERAHTGEK PFECKECGKA FSIRKDLIRH FNIHTGEKPY 
ECLQCGKAFT RMSGLTRHQW IHTGEKPYVC IQCGKAFCRT TNLIRHFSIH TGEKPYECVE 
CGKAFNRRSP LTRHQRIHTA EKSHEPIQSG NVSCESTDLI QHSIIHTESS PVSAVNMETP 
SIAAHSSSLD INGFIVEETL PL