PAXX
protein-codingPAXX non-homologous end joining factor
Gene summary
The protein encoded by this gene plays a role in the nonhomologous end joining (NHEJ) pathway of DNA double-strand break repair. The encoded protein may function to stabilize the Ku70/Ku80 heterodimer to facilitate the assembly and maintain the stability of the NHEJ complex. [provided by RefSeq, Jul 2016]
- C9orf142
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.6 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 PAXX variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_183241.3. 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 | 0 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 7 | 0 | 0 | 7 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_899064.1 | 7 | MANE Select | |
| Ensembl | ENSP00000360682.3 | 7 | MANE Select | |
| RefSeq | NP_001316607.1 | 7 | Standard | |
| Ensembl | ENSP00000525150.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- double-strand break repair via nonhomologous end joining
- cellular response to DNA damage stimulus
- DNA ligation involved in DNA repair
Molecular Function
- protein binding
- protein-containing complex scaffold activity
- protein homodimerization activity
Cellular Component
- nucleus
- site of double-strand break
- Ku70:Ku80 complex
- nonhomologous end joining complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371620
- Coding exons
- 7
- Length
- 1567
- Individuals with no LoFs
- 125019
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 37
- Defined
- 125056
- p
- 0.000148
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.410 | 99 | 111 | 0.891 | 0.00000641 | 1257 |
| Missense (PolyPhen) | 30 | 36.802 | 0.81516 | 403 | ||
| Synonymous | 0.139 | 48 | 49.2 | 0.975 | 0.00000286 | 446 |
| Loss of Function | 1.45 | 5 | 9.92 | 0.504 | 5.11e-7 | 111 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00030 | 0.00029 | rare |
| South Asian | 0.000068 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in non-homologous end joining (NHEJ), a major pathway to repair double-strand breaks in DNA. May act as a scaffold required to stabilize the Ku heterodimer, composed of XRCC5/Ku80 and XRCC6/Ku70, at double-strand break sites and promote the assembly and/or stability of the NHEJ machinery. {ECO:0000269|PubMed:25574025, ECO:0000269|PubMed:25670504, ECO:0000269|PubMed:25941166}.;
Intolerance Scores
- RVIS EVS
- 0.06
- RVIS percentile EVS
- 58.26
Essentials
- Essential (gene trap)
- N