PAXX

PAXX non-homologous end joining factor

Basic information

Region (hg38): 9:136992422-136993984

Previous symbols: [ "C9orf142" ]

Links

ENSG00000148362

∙ NCBI:286257 ∙ OMIM:616315 ∙ HGNC:27849 ∙ Uniprot:Q9BUH6 ∙ 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 PAXX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAXX 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						0
missense						0
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	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAXX	protein_coding	protein_coding	ENST00000371620	7	1567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00542	0.904	125019	0	37	125056	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.410	99	111	0.891	0.00000641	1257
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000910	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000297	0.000293
Middle Eastern	0.00	0.00
South Asian	0.0000682	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

loftool
rvis_EVS: 0.06
rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

pHI: 0.106
hipred: N
hipred_score: 0.145
ghis: 0.501

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Paxx
Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype;

Gene ontology

Biological process: double-strand break repair via nonhomologous end joining;cellular response to DNA damage stimulus;DNA ligation involved in DNA repair
Cellular component: nucleus;site of double-strand break;Ku70:Ku80 complex;nonhomologous end joining complex
Molecular function: protein binding;protein-containing complex scaffold activity;protein homodimerization activity