ATP23
protein-codingATP23 metallopeptidase and ATP synthase assembly factor homolog, the group of M76 metallopeptidase family
Gene 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]
- XRCC6BP1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~53.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ATP23 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033276.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 1 | 1 | 2 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 3 | 2 | 0 | 5 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_150592.1 | 6 | MANE Select | |
| Ensembl | ENSP00000300145.3 | 6 | MANE Select | |
| RefSeq | NP_001307337.1 | 6 | Standard | |
| RefSeq | NP_001307338.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- double-strand break repair via nonhomologous end joining
- protein phosphorylation
- proteolysis
- mitochondrial proton-transporting ATP synthase complex assembly
- mitochondrial protein processing
Molecular Function
- metalloendopeptidase activity
- DNA-dependent protein kinase activity
- metal ion binding
Cellular Component
- cytosol
- plasma membrane
- DNA-dependent protein kinase-DNA ligase 4 complex
- cell junction
- extrinsic component of mitochondrial inner membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000300145
- Coding exons
- 6
- Length
- 15729
- Individuals with no LoFs
- 124753
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 41
- Defined
- 124794
- p
- 0.000164
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.719 | 111 | 134 | 0.825 | 0.00000674 | 1636 |
| Missense (PolyPhen) | 33 | 54.649 | 0.60385 | 622 | ||
| Synonymous | 0.760 | 42 | 48.8 | 0.861 | 0.00000250 | 442 |
| Loss of Function | 0.976 | 9 | 12.8 | 0.705 | 6.92e-7 | 140 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00012 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- RVIS EVS
- 0.31
- RVIS percentile EVS
- 72.23
Essentials
- Essential (gene trap)
- N