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Aliases for ATP23 Gene

Aliases for ATP23 Gene

  • ATP23 Metallopeptidase And ATP Synthase Assembly Factor Homolog 2 3 5
  • XRCC6-Binding Protein 1 3 4
  • Ku70-Binding Protein 3 3 4
  • XRCC6BP1 3 4
  • KUB3 3 4
  • ATP23 Metallopeptidase And ATP Synthase Assembly Factor Homolog (S. Cerevisiae) 2
  • Mitochondrial Inner Membrane Protease ATP23 Homolog 3
  • XRCC6 Binding Protein 1 2
  • Ku70 Binding Protein 3 2
  • EC 3.4.24.- 4

External Ids for ATP23 Gene

Previous HGNC Symbols for ATP23 Gene

  • XRCC6BP1

Summaries for ATP23 Gene

Entrez Gene Summary for ATP23 Gene

  • The protein encoded by this gene is amplified in glioblastomas and interacts with the DNA binding subunit of DNA-dependent protein kinase. This kinase is involved in double-strand break repair (DSB), and higher expression of the encoded protein increases the efficiency of DSB. In addition, comparison to orthologous proteins strongly suggests that this protein is a metalloprotease important in the biosynthesis of mitochondrial ATPase. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

GeneCards Summary for ATP23 Gene

ATP23 (ATP23 Metallopeptidase And ATP Synthase Assembly Factor Homolog) is a Protein Coding gene.

Additional gene information for ATP23 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATP23 Gene

Genomics for ATP23 Gene

GeneHancer (GH) Regulatory Elements for ATP23 Gene

Promoters and enhancers for ATP23 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J057939 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 752.6 -0.3 -294 2.5 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ATP23 MBD6 NEMP1 CTDSP2 DTX3 ENSG00000270039 CDK4 NAB2 OS9 ARHGAP9
GH12J057933 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 102.3 -6.2 -6183 3.3 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 IRF4 YY1 SLC30A9 POLR2B LOC100506844 PIR56855 PIR34372 PIR53894 PIR62650 ATP23 NEMP1 OS9 MBD6 NXPH4
GH12J057886 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 42.4 -48.2 -48246 13.7 HDGF PKNOX1 SMAD1 SIN3A ZNF2 IRF4 YY1 ZNF143 FOS SP3 LOC101927608 ATP23 EEF1AKMT3 CTDSP2 NEMP1 LOC283387 CDK4 TSFM MIR26A2 AVIL
GH12J057830 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29.5 -102.1 -102061 17 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 ZNF263 SP3 CTDSP2 EEF1AKMT3 TSFM ATP23 NEMP1 NAB2 MBD6 METTL1 TSPAN31 CDK4
GH12J057905 Enhancer 1.4 Ensembl ENCODE dbSUPER 33.5 -35.9 -35912 0.9 CLOCK ARNT ARID4B SIN3A ZNF2 IRF4 YY1 ZNF213 E2F8 ZNF143 ATP23 MIR26A2 RNU6-1083P CTDSP2 AVIL TSFM CYP27B1 METTL1 EEF1AKMT3 CDK4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP23 on UCSC Golden Path with GeneCards custom track

Genomic Locations for ATP23 Gene

Genomic Locations for ATP23 Gene
15,729 bases
Plus strand
15,729 bases
Plus strand

Genomic View for ATP23 Gene

Genes around ATP23 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP23 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP23 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP23 Gene

Proteins for ATP23 Gene

  • Protein details for ATP23 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Mitochondrial inner membrane protease ATP23 homolog
    Protein Accession:
    Secondary Accessions:
    • Q1RLM4
    • Q96E81

    Protein attributes for ATP23 Gene

    246 amino acids
    Molecular mass:
    28081 Da
    Quaternary structure:
    • Interacts with XRCC6.
    • Sequence=AAD31085.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for ATP23 Gene

Post-translational modifications for ATP23 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATP23 Gene

No data available for DME Specific Peptides for ATP23 Gene

Domains & Families for ATP23 Gene

Gene Families for ATP23 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for ATP23 Gene


Suggested Antigen Peptide Sequences for ATP23 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase M76 family.
  • Belongs to the peptidase M76 family.
genes like me logo Genes that share domains with ATP23: view

Function for ATP23 Gene

Enzyme Numbers (IUBMB) for ATP23 Gene

Phenotypes From GWAS Catalog for ATP23 Gene

Gene Ontology (GO) - Molecular Function for ATP23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004222 metalloendopeptidase activity IEA --
GO:0004677 DNA-dependent protein kinase activity TAS 10219089
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with ATP23: view
genes like me logo Genes that share phenotypes with ATP23: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP23

No data available for Molecular function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for ATP23 Gene

Localization for ATP23 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATP23 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 3
extracellular 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (4)
  • Vesicles (4)
  • Cell Junctions (3)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATP23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA --
GO:0005958 DNA-dependent protein kinase-DNA ligase 4 complex NAS 10219089
GO:0030054 cell junction IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with ATP23: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for ATP23 Gene

Pathways & Interactions for ATP23 Gene

SuperPathways for ATP23 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ATP23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006303 double-strand break repair via nonhomologous end joining TAS 10219089
GO:0006468 protein phosphorylation IEA --
GO:0006508 proteolysis IEA --
genes like me logo Genes that share ontologies with ATP23: view

No data available for Pathways by source and SIGNOR curated interactions for ATP23 Gene

Drugs & Compounds for ATP23 Gene

No Compound Related Data Available

Transcripts for ATP23 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP23

Alternative Splicing Database (ASD) splice patterns (SP) for ATP23 Gene

No ASD Table

Relevant External Links for ATP23 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ATP23 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of ATP23 Gene:


Evidence on tissue expression from TISSUES for ATP23 Gene

  • Liver(4.1)
  • Lung(4.1)
genes like me logo Genes that share expression patterns with ATP23: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP23 Gene

Orthologs for ATP23 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATP23 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia XRCC6BP1 34 33
  • 99.19 (n)
(Canis familiaris)
Mammalia XRCC6BP1 34 33
  • 90.62 (n)
(Bos Taurus)
Mammalia XRCC6BP1 34 33
  • 89.16 (n)
(Mus musculus)
Mammalia Xrcc6bp1 34 33
  • 79.95 (n)
Atp23 16
(Rattus norvegicus)
Mammalia Xrcc6bp1 33
  • 79.27 (n)
(Ornithorhynchus anatinus)
Mammalia XRCC6BP1 34
  • 79 (a)
(Monodelphis domestica)
Mammalia XRCC6BP1 34
  • 63 (a)
(Gallus gallus)
Aves XRCC6BP1 34 33
  • 70.96 (n)
(Anolis carolinensis)
Reptilia XRCC6BP1 34
  • 64 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia xrcc6bp1 33
  • 72.15 (n)
Str.16237 33
African clawed frog
(Xenopus laevis)
Amphibia kub3-prov 33
(Danio rerio)
Actinopterygii xrcc6bp1 34 33
  • 64.57 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5131 34 33
  • 52.64 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009567 33
  • 51.3 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATP23 36 34
  • 26 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G03420 33
  • 52.52 (n)
(Oryza sativa)
Liliopsida Os12g0288900 33
  • 47.22 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes atp23 33
  • 50.67 (n)
Species where no ortholog for ATP23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ATP23 Gene

Gene Tree for ATP23 (if available)
Gene Tree for ATP23 (if available)
Evolutionary constrained regions (ECRs) for ATP23: view image

Paralogs for ATP23 Gene

No data available for Paralogs for ATP23 Gene

Variants for ATP23 Gene

Sequence variations from dbSNP and Humsavar for ATP23 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000233457 -- 57,941,958(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000240419 -- 57,956,051(+) G/A intron_variant
rs1000460596 -- 57,957,262(+) T/G 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant
rs1000500735 -- 57,941,571(+) C/A/T 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000748061 -- 57,956,849(+) A/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for ATP23 Gene

Variant ID Type Subtype PubMed ID
nsv523853 CNV gain 19592680
nsv559046 CNV gain 21841781
nsv975500 CNV duplication 23825009

Variation tolerance for ATP23 Gene

Residual Variation Intolerance Score: 66.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.82; 73.79% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP23 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATP23 Gene

Disorders for ATP23 Gene

Additional Disease Information for ATP23

No disorders were found for ATP23 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ATP23 Gene

Publications for ATP23 Gene

  1. Isolation of Ku70-binding proteins (KUBs). (PMID: 10219089) Yang CR … Boothman DA (Nucleic acids research 1999) 2 3 4 58
  2. The metalloprotease encoded by ATP23 has a dual function in processing and assembly of subunit 6 of mitochondrial ATPase. (PMID: 17135290) Zeng X … Tzagoloff A (Molecular biology of the cell 2007) 2 3 58
  3. KUB3 amplification and overexpression in human gliomas. (PMID: 11571779) Fischer U … Meese E (Glia 2001) 3 22 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for ATP23 Gene

Sources for ATP23 Gene

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