NOXO1

NADPH oxidase organizer 1

Basic information

Region (hg38): 16:1978917-1984192

Links

ENSG00000196408 ∙ ∙ OMIM:611256 ∙ HGNC:19404 ∙ Uniprot:Q8NFA2 ∙ 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 NOXO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOXO1 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			38	4		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	4	0

Variants in NOXO1

This is a list of pathogenic ClinVar variants found in the NOXO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1979090-A-C		not specified	Uncertain significance (Oct 05, 2021)
16-1979104-C-T		not specified	Uncertain significance (Feb 27, 2023)
16-1979110-C-T		not specified	Uncertain significance (Apr 25, 2022)
16-1979122-C-T		not specified	Likely benign (Sep 03, 2024)
16-1979128-A-C		not specified	Uncertain significance (Apr 10, 2023)
16-1979144-C-T		not specified	Likely benign (Feb 16, 2023)
16-1979164-A-G		not specified	Uncertain significance (Jan 30, 2024)
16-1979179-G-T		not specified	Uncertain significance (Aug 02, 2022)
16-1979197-G-A		not specified	Uncertain significance (Dec 09, 2023)
16-1979197-G-C		not specified	Uncertain significance (Jun 29, 2022)
16-1979248-G-A		not specified	Uncertain significance (Dec 17, 2023)
16-1979255-C-T		not specified	Likely benign (Feb 23, 2023)
16-1979291-C-T		not specified	Uncertain significance (Nov 21, 2022)
16-1979333-C-T		not specified	Uncertain significance (Nov 10, 2024)
16-1979457-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
16-1979462-C-G		not specified	Uncertain significance (Dec 02, 2022)
16-1979470-C-T		not specified	Uncertain significance (Jan 31, 2024)
16-1979474-C-T		not specified	Uncertain significance (May 17, 2023)
16-1979497-T-A		not specified	Uncertain significance (Dec 21, 2023)
16-1979501-C-T		not specified	Uncertain significance (Dec 04, 2024)
16-1979519-C-T		not specified	Uncertain significance (Mar 31, 2024)
16-1979521-C-T		not specified	Uncertain significance (Sep 23, 2023)
16-1979531-A-T		not specified	Uncertain significance (Feb 26, 2024)
16-1979819-C-A		not specified	Uncertain significance (Oct 08, 2024)
16-1979837-G-T		not specified	Uncertain significance (Sep 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOXO1	protein_coding	protein_coding	ENST00000397280	8	5276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.34e-11	0.0417	123047	20	2550	125617	0.0103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.811	252	218	1.15	0.0000127	2257
Missense in Polyphen		84	67.332	1.2476		765
Synonymous	-1.31	115	98.4	1.17	0.00000568	842
Loss of Function	-0.213	15	14.1	1.06	6.90e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0116	0.0110
Ashkenazi Jewish	0.0200	0.0191
East Asian	0.00475	0.00474
Finnish	0.00832	0.00719
European (Non-Finnish)	0.0166	0.0149
Middle Eastern	0.00475	0.00474
South Asian	0.00226	0.00209
Other	0.0164	0.0146

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Constitutively potentiates the superoxide-generating activity of NOX1 and NOX3 and is required for the biogenesis of otoconia/otolith, which are crystalline structures of the inner ear involved in the perception of gravity. Isoform 3 is more potent than isoform 1 in activating NOX3. Together with NOXA1, may also substitute to NCF1/p47phox and NCF2/p67phox in supporting the phagocyte NOX2/gp91phox superoxide-generating activity. {ECO:0000269|PubMed:12657628, ECO:0000269|PubMed:14617635, ECO:0000269|PubMed:15326186, ECO:0000269|PubMed:15824103, ECO:0000269|PubMed:15949904, ECO:0000269|PubMed:16329988, ECO:0000269|PubMed:17126813, ECO:0000269|PubMed:19755710}.
• Pathway: TNF alpha Signaling Pathway;Signal Transduction;RHO GTPases Activate NADPH Oxidases;RHO GTPase Effectors;Signaling by Rho GTPases;RAC1 signaling pathway (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.961
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.0626
• hipred: N
• hipred_score: 0.180
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.402

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Noxo1
• Phenotype: hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: superoxide metabolic process;regulation of hydrogen peroxide metabolic process;extracellular matrix disassembly;positive regulation of catalytic activity;regulation of respiratory burst
• Cellular component: plasma membrane;NADPH oxidase complex
• Molecular function: protein binding;phospholipid binding;superoxide-generating NADPH oxidase activator activity;enzyme binding;phosphatidylinositol binding