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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
  • EC 3.4.24 58

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

Regulatory Elements for ATP23 Gene

Enhancers for ATP23 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H057939 1.4 ENCODE dbSUPER 102.6 -0.3 -295 2.5 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ATP23 NEMP1 DTX3 ENSG00000270039 NAB2 OS9 MBD6 ARHGAP9 LOC100506844
GH12H057933 1.3 ENCODE dbSUPER 102.3 -6.2 -6183 3.3 HDGF PKNOX1 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF766 ZNF207 ZNF143 ATP23 NEMP1 OS9 MBD6 NXPH4 PIR37489 PIR56855
GH12H057886 1.9 FANTOM5 Ensembl ENCODE dbSUPER 42.4 -48.2 -48246 13.7 HDGF PKNOX1 ZNF2 TCF12 ZNF121 GLIS2 ZNF143 FOS ATF7 RUNX3 ATP23 EEF1AKMT3 CTDSP2 TSFM MIR26A2 AVIL RNU6-1083P ENSG00000224713 MARCH9 LOC283387
GH12H057905 1.6 Ensembl ENCODE dbSUPER 33.5 -35.9 -35912 0.9 ARID4B SIN3A ZNF2 YY1 ZNF143 DEK MXD4 ZC3H11A REST ZNF592 ATP23 MIR26A2 RNU6-1083P CTDSP2 AVIL TSFM CYP27B1 EEF1AKMT3 METTL1 CDK4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ATP23 on UCSC Golden Path with GeneCards custom track

Promoters for ATP23 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Locations for ATP23 Gene

Genomic Locations for ATP23 Gene
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

Selected DME Specific Peptides for ATP23 Gene


Post-translational modifications for ATP23 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References 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

Inhibitory RNA Products

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:0005886 plasma membrane IDA --
GO:0005958 DNA-dependent protein kinase-DNA ligase 4 complex NAS 10219089
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

Inhibitory RNA Products

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

Primer Products

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 33 34
  • 99.19 (n)
(Canis familiaris)
Mammalia XRCC6BP1 33 34
  • 90.62 (n)
(Bos Taurus)
Mammalia XRCC6BP1 33 34
  • 89.16 (n)
(Mus musculus)
Mammalia Xrcc6bp1 33 34
  • 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 33 34
  • 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 33 34
  • 64.57 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5131 33 34
  • 52.64 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009567 33
  • 51.3 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATP23 34 36
  • 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)

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 Sequence Context AA Info Type
rs1000233457 -- 57,941,958(+) GGGCC(C/T)GGGCA intron-variant
rs1000240419 -- 57,956,051(+) GTATT(A/G)AGAAA intron-variant
rs1000460596 -- 57,957,262(+) AAATG(G/T)GTACT downstream-variant-500B, utr-variant-3-prime
rs1000500735 -- 57,941,571(+) CAGCC(A/C/T)AGCCA upstream-variant-2KB, utr-variant-5-prime
rs1000748061 -- 57,956,849(+) CTCAC(A/G)GAGAC reference, missense

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)

Relevant External Links for ATP23 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for ATP23 Gene

Relevant External Links for ATP23

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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 60
  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 60
  3. KUB3 amplification and overexpression in human gliomas. (PMID: 11571779) Fischer U … Meese E (Glia 2001) 3 22 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 60

Products for ATP23 Gene

Sources for ATP23 Gene

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