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ATP23 ATP23 metallopeptidase and ATP synthase assembly factor homolog [ Homo sapiens (human) ]

Gene ID: 91419, updated on 5-Mar-2024

Summary

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Official Symbol
ATP23provided by HGNC
Official Full Name
ATP23 metallopeptidase and ATP synthase assembly factor homologprovided by HGNC
Primary source
HGNC:HGNC:29452
See related
Ensembl:ENSG00000166896 MIM:619760; AllianceGenome:HGNC:29452
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KUB3; XRCC6BP1
Summary
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]
Expression
Broad expression in testis (RPKM 13.5), bone marrow (RPKM 4.5) and 24 other tissues See more
Orthologs
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Genomic context

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See ATP23 in Genome Data Viewer
Location:
12q14.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57941567..57959148)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57909929..57927510)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (58335350..58352931)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC283387 Neighboring gene uncharacterized LOC101927608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6566 Neighboring gene Sharpr-MPRA regulatory region 14765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:58329372-58329872 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:58329873-58330373 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:58335219-58336028 Neighboring gene GIHCG inhibitor of miR-200b/200a/429 expression Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29909 Neighboring gene zinc finger protein 100 pseudogene Neighboring gene RN7SK pseudogene 65

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Glioma-amplified sequence KUB3 influences double-strand break repair after ionizing radiation. Fischer U, et al. Int J Oncol, 2013 Jul. PMID 23670597, Free PMC Article
  2. KUB3 amplification and overexpression in human gliomas. Fischer U, et al. Glia, 2001 Oct. PMID 11571779
  3. The metalloprotease encoded by ATP23 has a dual function in processing and assembly of subunit 6 of mitochondrial ATPase. Zeng X, et al. Mol Biol Cell, 2007 Feb. PMID 17135290, Free PMC Article
  4. Isolation of Ku70-binding proteins (KUBs). Yang CR, et al. Nucleic Acids Res, 1999 May 15. PMID 10219089, Free PMC Article
  5. MICALL2 as a substrate of ubiquitinase TRIM21 regulates tumorigenesis of colorectal cancer. Wen P, et al. Cell Commun Signal, 2022 Oct 28. PMID 36307841, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC134817, MGC134818

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-dependent protein kinase activity TAS
Traceable Author Statement
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metalloendopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in double-strand break repair via nonhomologous end joining TAS
Traceable Author Statement
more info
 PubMed 
involved_in mitochondrial protein processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial proton-transporting ATP synthase complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of DNA-dependent protein kinase-DNA ligase 4 complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cell junction IDA
Inferred from Direct Assay
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
mitochondrial inner membrane protease ATP23 homolog
Names
Ku70-binding protein 3
XRCC6-binding protein 1
NP_001307337.1
NP_001307338.1
NP_001307339.1
NP_150592.1
XP_011537278.1
XP_016875695.1
XP_054185539.1
XP_054185540.1
XP_054229779.1
XP_054229780.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001320408.2 → NP_001307337.1  mitochondrial inner membrane protease ATP23 homolog isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice junction in the 5' end compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC084033, BC012776, BM544500, BU601924
    UniProtKB/Swiss-Prot
    Q9Y6H3
    Conserved Domains (1) summary
    pfam09768
    Location:3 → 168
    Peptidase_M76; Peptidase M76 family

  2. NM_001320409.2 → NP_001307338.1  mitochondrial inner membrane protease ATP23 homolog isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' end compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
    Source sequence(s)
    AC084033, BC012776, BU601924, DA711361
    UniProtKB/Swiss-Prot
    Q9Y6H3
    Conserved Domains (1) summary
    pfam09768
    Location:1 → 102
    Peptidase_M76; Peptidase M76 family

  3. NM_001320410.2 → NP_001307339.1  mitochondrial inner membrane protease ATP23 homolog isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
    Source sequence(s)
    AC084033, BC012776, BM557436, BU601924
    UniProtKB/Swiss-Prot
    Q9Y6H3
    Conserved Domains (1) summary
    pfam09768
    Location:1 → 102
    Peptidase_M76; Peptidase M76 family

  4. NM_033276.4 → NP_150592.1  mitochondrial inner membrane protease ATP23 homolog isoform a

    See identical proteins and their annotated locations for NP_150592.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC084033, BC012776, BU601924
    Consensus CDS
    CCDS41802.1
    UniProtKB/Swiss-Prot
    Q1RLM4, Q96E81, Q9Y6H3
    Related
    ENSP00000300145.3, ENST00000300145.4
    Conserved Domains (1) summary
    pfam09768
    Location:50 → 220
    Peptidase_M76; Peptidase M76 family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    57941567..57959148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020206.2 → XP_016875695.1  mitochondrial inner membrane protease ATP23 homolog isoform X2

    Related
    ENST00000647763.1
    Conserved Domains (1) summary
    pfam09768
    Location:1 → 148
    Peptidase_M76; Peptidase M76 family

  2. XM_011538976.3 → XP_011537278.1  mitochondrial inner membrane protease ATP23 homolog isoform X1

    See identical proteins and their annotated locations for XP_011537278.1

    Conserved Domains (1) summary
    pfam09768
    Location:29 → 166
    Peptidase_M76; Peptidase M76 family

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315939.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    142767..160348 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329565.1 → XP_054185540.1  mitochondrial inner membrane protease ATP23 homolog isoform X2

  2. XM_054329564.1 → XP_054185539.1  mitochondrial inner membrane protease ATP23 homolog isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57909929..57927510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373805.1 → XP_054229780.1  mitochondrial inner membrane protease ATP23 homolog isoform X2

  2. XM_054373804.1 → XP_054229779.1  mitochondrial inner membrane protease ATP23 homolog isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y6H3.3 GenPept UniProtKB/Swiss-Prot:Q9Y6H3

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