ZKSCAN3
Zinc finger protein with KRAB and SCAN domains 3
Also known as: ZF47, Zfp47, ZKSC3_HUMAN, ZNF306, ZNF309, ZSCAN35
Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene
Protein identityUniProt · HPA
- UniProt accession
- Q9BRR0
- Gene
- ZKSCAN3
- Ensembl
- ENSG00000189298
- Chromosome
- 6
- Canonical length
- 538 aa
- Protein class
- Predicted intracellular proteins, Transcription factors
- Subcellular location
- Nucleoplasm
OverviewNCBI Gene
Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of DNA-templated transcription. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
Canonical amino-acid sequenceUniProt
538 residues, UniProt reviewed canonical sequence.
>Q9BRR0|ZKSCAN3
1 MARELSESTA LDAQSTEDQM ELLVIKVEEE EAGFPSSPDL GSEGSRERFR GFRYPEAAGP
61 REALSRLREL CRQWLQPEMH SKEQILELLV LEQFLTILPG NLQSWVREQH PESGEEVVVL
121 LEYLERQLDE PAPQVSGVDQ GQELLCCKMA LLTPAPGSQS SQFQLMKALL KHESVGSQPL
181 QDRVLQVPVL AHGGCCREDK VVASRLTPES QGLLKVEDVA LTLTPEWTQQ DSSQGNLCRD
241 EKQENHGSLV SLGDEKQTKS RDLPPAEELP EKEHGKISCH LREDIAQIPT CAEAGEQEGR
301 LQRKQKNATG GRRHICHECG KSFAQSSGLS KHRRIHTGEK PYECEECGKA FIGSSALVIH
361 QRVHTGEKPY ECEECGKAFS HSSDLIKHQR THTGEKPYEC DDCGKTFSQS CSLLEHHRIH
421 TGEKPYQCSM CGKAFRRSSH LLRHQRIHTG DKNVQEPEQG EAWKSRMESQ LENVETPMSY
481 KCNECERSFT QNTGLIEHQK IHTGEKPYQC NACGKGFTRI SYLVQHQRSH VGKNILSQLocalizationUniProt · AlphaFold · HPA
Whether an antibody against ZKSCAN3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.
- Antibody reachability
- Intracellular
- Secreted
- No
- Transmembrane segments
- 0
- Mean surface accessibility (rSASA)
- 0.5
- Highest tissue expression
- 4.9 nTPM
Expression across tissuesHPA
Tissue
- ovary: 4.9 nTPM
- parathyroid gland: 4.4 nTPM
- smooth muscle: 4.4 nTPM
- epididymis: 4.3 nTPM
- seminal vesicle: 4.1 nTPM
- thyroid gland: 4.1 nTPM
Single-cell type
- epicardial cells: 36 nCPM
- tuft cells: 35 nCPM
- parietal cells: 16 nCPM
- medullary thymic epithelial cells: 12 nCPM
- retinal ganglion cells: 12 nCPM
- choroid plexus epithelial cells: 11 nCPM
Immune cell
- eosinophil: 5.2 nTPM
- MAIT T-cell: 2.3 nTPM
- naive CD8 T-cell: 2.3 nTPM
- gdT-cell: 2.2 nTPM
- memory B-cell: 2.2 nTPM
- T-reg: 2.2 nTPM
Brain region
- cerebellum: 13 nTPM
- choroid plexus: 12 nTPM
- white matter: 12 nTPM
- cerebral cortex: 11 nTPM
- thalamus: 11 nTPM
- pons: 11 nTPM
Genetic constraint and essentialitygnomAD · DepMap
Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.
- gnomAD LOEUF (loss-of-function intolerance)
- 1.19
- gnomAD pLI
- 0
- gnomAD missense Z
- 1.64
- DepMap mean gene effect
- -0.05
- DepMap dependency class
- selective
Cancer expressionTCGA
Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).
OntologyGO
Biological processes
- autophagy
- lysosome organization
- negative regulation of autophagy
- negative regulation of cellular senescence
- negative regulation of DNA-templated transcription
- negative regulation of transcription by RNA polymerase II
- positive regulation of DNA-templated transcription
- regulation of transcription by RNA polymerase II
Molecular functions
- chromatin binding
- DNA binding
- DNA-binding transcription factor activity
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription repressor activity, RNA polymerase II-specific
- RNA polymerase II cis-regulatory region sequence-specific DNA binding
- sequence-specific DNA binding
- zinc ion binding
Cellular components
Protein domainsUniProt · Pfam · InterPro
KeywordsUniProt
Antibody and autoantibody relevanceSeroatlas analysis
Seroatlas reads ZKSCAN3 as an antibody target. Whether an autoantibody or antibody against ZKSCAN3 could matter depends on whether native ZKSCAN3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.
ZKSCAN3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.
Annotation status
The present source text does not explicitly label ZKSCAN3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.
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