PAOX

polyamine oxidase

Basic information

Region (hg38): 10:133379261-133391694

Links

ENSG00000148832 ∙ NCBI:196743 ∙ OMIM:615853 ∙ HGNC:20837 ∙ Uniprot:Q6QHF9 ∙ 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 PAOX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAOX 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			40	8		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	9	0

Variants in PAOX

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

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

Position	Type	Phenotype	Significance	ClinVar
10-133379341-G-A		not specified	Likely benign (Jan 24, 2025)
10-133379390-G-T		not specified	Uncertain significance (Jun 07, 2023)
10-133379416-G-T		not specified	Uncertain significance (Apr 07, 2023)
10-133379420-A-G		not specified	Uncertain significance (Feb 05, 2025)
10-133379444-T-C		not specified	Uncertain significance (Dec 06, 2022)
10-133379473-C-T		not specified	Uncertain significance (Jul 10, 2024)
10-133379479-C-T		not specified	Uncertain significance (Apr 07, 2023)
10-133379480-G-A		not specified	Uncertain significance (Dec 24, 2024)
10-133380004-G-A		not specified	Uncertain significance (Dec 22, 2023)
10-133380044-G-T		not specified	Uncertain significance (Jan 29, 2024)
10-133380099-G-A			Likely benign (Jul 01, 2022)
10-133380149-C-T		not specified	Uncertain significance (Dec 23, 2024)
10-133380154-G-A		not specified	Uncertain significance (May 01, 2024)
10-133380163-G-T		not specified	Uncertain significance (Dec 22, 2023)
10-133380200-C-T		not specified	Uncertain significance (Feb 28, 2023)
10-133380209-C-G		not specified	Uncertain significance (May 23, 2023)
10-133380223-G-A		not specified	Uncertain significance (Mar 16, 2022)
10-133380264-G-T		not specified	Uncertain significance (Mar 18, 2024)
10-133380284-G-A		not specified	Uncertain significance (Feb 26, 2025)
10-133380299-A-G		not specified	Uncertain significance (Feb 12, 2025)
10-133380344-C-T		not specified	Uncertain significance (Feb 08, 2025)
10-133380374-C-T		not specified	Uncertain significance (Mar 06, 2025)
10-133380403-G-A		not specified	Uncertain significance (Aug 20, 2024)
10-133380460-C-T		not specified	Uncertain significance (Aug 05, 2024)
10-133381461-G-A		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAOX	protein_coding	protein_coding	ENST00000278060	7	12504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.86e-9	0.218	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.211	281	291	0.965	0.0000191	3265
Missense in Polyphen		95	108.09	0.87891		1189
Synonymous	0.340	138	143	0.964	0.0000113	1112
Loss of Function	0.499	14	16.2	0.866	7.92e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000636	0.000572
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000277	0.000273
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Flavoenzyme which catalyzes the oxidation of N(1)- acetylspermine to spermidine and is thus involved in the polyamine back-conversion. Can also oxidize N(1)-acetylspermidine to putrescine. Substrate specificity: N(1)-acetylspermine = N(1)- acetylspermidine > N(1),N(12)-diacylspermine >> spermine. Does not oxidize spermidine. Plays an important role in the regulation of polyamine intracellular concentration and has the potential to act as a determinant of cellular sensitivity to the antitumor polyamine analogs.
• Pathway: Peroxisome - Homo sapiens (human);PAOs oxidise polyamines to amines;Amine Oxidase reactions;Phase I - Functionalization of compounds;Metabolism of proteins;Interconversion of polyamines;Metabolism of polyamines;Metabolism of amino acids and derivatives;Biological oxidations;Metabolism;Peroxisomal protein import;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;spermine and spermidine degradation I;Alpha9 beta1 integrin signaling events (Consensus)

Recessive Scores

• pRec: 0.185

Intolerance Scores

• loftool: 0.103
• rvis_EVS: 0.53
• rvis_percentile_EVS: 81.01

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.197
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.300

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Paox

Gene ontology

• Biological process: polyamine biosynthetic process;protein targeting to peroxisome;putrescine biosynthetic process;putrescine catabolic process;spermidine catabolic process;spermine catabolic process;oxidation-reduction process;positive regulation of spermidine biosynthetic process
• Cellular component: peroxisomal matrix;cytosol
• Molecular function: signaling receptor binding;oxidoreductase activity;polyamine oxidase activity;N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity;spermine:oxygen oxidoreductase (spermidine-forming) activity;spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity;N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity;N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity