ATP23 Gene (Protein Coding)

ATP23 Metallopeptidase And ATP Synthase Assembly Factor Homolog

GC12P057942
GIFtS:
27
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 metalloprotea... See more...

Aliases for ATP23 Gene

Aliases for ATP23 Gene

  • ATP23 Metallopeptidase And ATP Synthase Assembly Factor Homolog 2 3 5
  • KUB3 2 3 4
  • Mitochondrial Inner Membrane Protease ATP23 Homolog 3 4
  • XRCC6-Binding Protein 1 3 4
  • Ku70-Binding Protein 3 3 4
  • XRCC6BP1 3 4
  • ATP23 Metallopeptidase And ATP Synthase Assembly Factor Homolog (S. Cerevisiae) 2
  • XRCC6 Binding Protein 1 2
  • Ku70 Binding Protein 3 2
  • EC 3.4.24.- 4
  • EC 3.4.24 51
  • ATP23 5

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 Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATP23 Gene

Genomics for ATP23 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ATP23 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATP23

Genomic Locations for ATP23 Gene

Genomic Locations for ATP23 Gene
chr12:57,906,039-57,959,148
(GRCh38/hg38)
Size:
53,110 bases
Orientation:
Plus strand
chr12:58,335,324-58,351,052
(GRCh37/hg19)
Size:
15,729 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for ATP23 Gene

Proteins for ATP23 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    Q9Y6H3-ATP23_HUMAN
    Recommended name:
    Mitochondrial inner membrane protease ATP23 homolog
    Protein Accession:
    Q9Y6H3
    Secondary Accessions:
    • Q1RLM4
    • Q96E81

    Protein attributes for ATP23 Gene

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

neXtProt entry for ATP23 Gene

Selected DME Specific Peptides for ATP23 Gene

Q9Y6H3:
  • RHLACSE
  • RAANLSGDC
  • HAFDHCR

Post-translational modifications for ATP23 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATP23 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for ATP23 Gene

Gene Families for ATP23 Gene

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

Protein Domains for ATP23 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ATP23 Gene

GenScript: Design optimal peptide antigens:
  • XRCC6-binding protein 1 (ATP23_HUMAN)
  • XRCC6BP1 protein (Q8N4L5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y6H3

UniProtKB/Swiss-Prot:

ATP23_HUMAN :
  • Belongs to the peptidase M76 family.
Family:
  • Belongs to the peptidase M76 family.
genes like me logo Genes that share domains with ATP23: view

Function for ATP23 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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

COMPARTMENTS
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
nucleus 5
cytosol 5
plasma membrane 4
mitochondrion 4
extracellular 2
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 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:0031314 extrinsic component of mitochondrial inner membrane IBA 21873635
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

PathCards logo

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 --
GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly IBA 21873635
GO:0034982 mitochondrial protein processing IBA 21873635
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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for ATP23 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for ATP23 Gene

4 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

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
ATP23

Expression for ATP23 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATP23

Evidence on tissue expression from TISSUES for ATP23 Gene

  • Lung(4.2)
  • Liver(4.2)
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
Chimpanzee
(Pan troglodytes)
 Mammalia XRCC6BP1 30 31
  • 99.19 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia XRCC6BP1 30 31
  • 90.62 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia XRCC6BP1 30 31
  • 89.16 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Xrcc6bp1 30 31
  • 79.95 (n)
 OneToOne
Atp23 17
Rat
(Rattus norvegicus)
 Mammalia Xrcc6bp1 30
  • 79.27 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia XRCC6BP1 31
  • 79 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia XRCC6BP1 31
  • 63 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves XRCC6BP1 30 31
  • 70.96 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia XRCC6BP1 31
  • 64 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia xrcc6bp1 30
  • 72.15 (n)
Str.16237 30
African clawed frog
(Xenopus laevis)
 Amphibia kub3-prov 30
Zebrafish
(Danio rerio)
 Actinopterygii xrcc6bp1 30 31
  • 64.57 (n)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta CG5131 30 31
  • 52.64 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP009567 30
  • 51.3 (n)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes ATP23 31 33
  • 26 (a)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT3G03420 30
  • 52.52 (n)
Rice
(Oryza sativa)
 Liliopsida Os12g0288900 30
  • 47.22 (n)
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes atp23 30
  • 50.67 (n)
Species where no ortholog for ATP23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

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

Paralogs for ATP23 Gene

No data available for Paralogs for ATP23 Gene

Variants for ATP23 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATP23 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs3751325 - p.Ser48Cys

Additional dbSNP identifiers (rs#s) for ATP23 Gene

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)
ATP23
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATP23

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

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

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
  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
  3. KUB3 amplification and overexpression in human gliomas. (PMID: 11571779) Fischer U … Meese E (Glia 2001) 3 23
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. (PMID: 31091453) Shami Shah A … Baskin JM (Cell reports 2019) 3

ExternalLinks

View latest publications for ATP23 gene in Mastermind

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