ATP23

ATP23 metallopeptidase and ATP synthase assembly factor homolog, the group of M76 metallopeptidase family

Basic information

Region (hg38): 12:57906039-57959148

Previous symbols: [ "XRCC6BP1" ]

Links

ENSG00000166896 ∙ NCBI:91419 ∙ OMIM:619760 ∙ HGNC:29452 ∙ Uniprot:Q9Y6H3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP23 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	2	0

Variants in ATP23

This is a list of pathogenic ClinVar variants found in the ATP23 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-57941815-G-A			Likely benign (Mar 01, 2022)
12-57956835-C-T			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP23	protein_coding	protein_coding	ENST00000300145	6	15729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000161	0.678	124753	0	41	124794	0.000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.719	111	134	0.825	0.00000674	1636
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000370	0.000369
Ashkenazi Jewish	0.000101	0.0000993
East Asian	0.000122	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000168
Middle Eastern	0.000122	0.0000556
South Asian	0.000360	0.000360
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.128
• hipred: Y
• hipred_score: 0.626
• ghis: 0.488

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Atp23

Gene ontology

• Biological process: double-strand break repair via nonhomologous end joining;protein phosphorylation;proteolysis;mitochondrial proton-transporting ATP synthase complex assembly;mitochondrial protein processing
• Cellular component: cytosol;plasma membrane;DNA-dependent protein kinase-DNA ligase 4 complex;cell junction;extrinsic component of mitochondrial inner membrane;intracellular membrane-bounded organelle
• Molecular function: metalloendopeptidase activity;DNA-dependent protein kinase activity;metal ion binding